@article {pmid39222712, year = {2024}, author = {Liu, H and Ma, W}, title = {DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.}, journal = {Genomics, proteomics & bioinformatics}, volume = {22}, number = {2}, pages = {}, doi = {10.1093/gpbjnl/qzae028}, pmid = {39222712}, issn = {2210-3244}, mesh = {Humans ; Mice ; Animals ; *Chromatin/genetics/metabolism ; *Software ; Genomics/methods ; Chromosome Mapping/methods ; }, abstract = {Recent advances in high-throughput chromosome conformation capture (Hi-C) techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures, thereby shedding light on the principles of genome architecture and functions. However, statistical methods for detecting changes in large-scale chromatin organization such as topologically associating domains (TADs) are still lacking. Here, we proposed a new statistical method, DiffGR, for detecting differentially interacting genomic regions at the TAD level between Hi-C contact maps. We utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD regions. We then developed a nonparametric approach to identify statistically significant changes of genomic interacting regions. Through simulation studies, we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various conditions. Furthermore, we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets, and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection methods. The DiffGR R package is published under the GNU General Public License (GPL) ≥ 2 license and is publicly available at https://github.com/wmalab/DiffGR.}, }
@article {pmid39198689, year = {2024}, author = {Lu, B and Qiu, R and Wei, J and Wang, L and Zhang, Q and Li, M and Zhan, X and Chen, J and Hsieh, IY and Yang, C and Zhang, J and Sun, Z and Zhu, Y and Jiang, T and Zhu, H and Li, J and Zhao, W}, title = {Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer.}, journal = {Nature cancer}, volume = {}, number = {}, pages = {}, pmid = {39198689}, issn = {2662-1347}, support = {81972651//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172698//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82372857//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {How dysregulated liquid-liquid phase separation (LLPS) contributes to the oncogenesis of female triple-negative breast cancer (TNBC) remains unknown. Here we demonstrate that phosphorylated histone deacetylase 6 (phospho-HDAC6) forms LLPS condensates in the nuclei of TNBC cells that are essential for establishing aberrant chromatin architecture. The disordered N-terminal domain and phosphorylated residue of HDAC6 facilitate effective LLPS, whereas nuclear export regions exert a negative dominant effect. Through phase-separation-based screening, we identified Nexturastat A as a specific disruptor of phospho-HDAC6 condensates, which effectively suppresses tumor growth. Mechanistically, importin-β interacts with phospho-HDAC6, promoting its translocation to the nucleus, where 14-3-3θ mediates the condensate formation. Disruption of phospho-HDAC6 LLPS re-established chromatin compartments and topologically associating domain boundaries, leading to disturbed chromatin loops. The phospho-HDAC6-induced aberrant chromatin architecture affects chromatin accessibility, histone acetylation, RNA polymerase II elongation and transcriptional profiles in TNBC. This study demonstrates phospho-HDAC6 LLPS as an emerging mechanism underlying the dysregulation of chromatin architecture in TNBC.}, }
@article {pmid39190242, year = {2024}, author = {Carballo-Pacoret, P and Carracedo, A and Rodriguez-Fontenla, C}, title = {Unraveling the three-dimensional (3D) genome architecture in Neurodevelopmental Disorders (NDDs).}, journal = {Neurogenetics}, volume = {}, number = {}, pages = {}, pmid = {39190242}, issn = {1364-6753}, support = {PI22/00208//Instituto de Salud Carlos III/ ; PI22/00208//Instituto de Salud Carlos III/ ; PI22/00208//Instituto de Salud Carlos III/ ; }, abstract = {The human genome, comprising millions of pairs of bases, serves as the blueprint of life, encoding instructions for cellular processes. However, genomes are not merely linear sequences; rather, the complex of DNA and histones, known as chromatin, exhibits complex organization across various levels, which profoundly influence gene expression and cellular function. Central to understanding genome organization is the emerging field of three-dimensional (3D) genome studies. Utilizing advanced techniques such as Hi-C, researchers have unveiled non-random dispositions of genomic elements, highlighting their importance in transcriptional regulation and disease mechanisms. Topologically Associating Domains (TADs), that demarcate regions of chromatin with preferential internal interactions, play crucial roles in gene regulation and are increasingly implicated in various diseases such as cancer and schizophrenia. However, their role in Neurodevelopmental Disorders (NDDs) remains poorly understood. Here, we focus on TADs and 3D conservation across the evolution and between cell types in NDDs. The investigation into genome organization and its impact on disease has led to significant breakthroughs in understanding NDDs etiology such ASD (Autism Spectrum Disorder). By elucidating the wide spectrum of ASD manifestations, researchers aim to uncover the underlying genetic and epigenetic factors contributing to its heterogeneity. Moreover, studies linking TAD disruption to NDDs underscore the importance of spatial genome organization in maintaining proper brain development and function. In summary, this review highlights the intricate interplay between genome organization, transcriptional control, and disease pathology, shedding light on fundamental biological processes and offering insights into the mechanisms underlying NDDs like ASD.}, }
@article {pmid39179577, year = {2024}, author = {Ealo, T and Sanchez-Gaya, V and Respuela, P and Muñoz-San Martín, M and Martin-Batista, E and Haro, E and Rada-Iglesias, A}, title = {Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7258}, pmid = {39179577}, issn = {2041-1723}, support = {862022//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; H2020-MSCA-ITN-2019-860002//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; MSCA-2021-DN-01-101073334//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; PID2021-123030NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RED2022-134100-T//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; }, mesh = {Animals ; *CCCTC-Binding Factor/metabolism/genetics ; Mice ; *Promoter Regions, Genetic/genetics ; *Enhancer Elements, Genetic/genetics ; *Mouse Embryonic Stem Cells/metabolism ; Gene Expression Regulation, Developmental ; Insulator Elements/genetics ; }, abstract = {The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across regulatory domains, which is at odds with the specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites cooperatively foster the robust insulation of regulatory domains. By genetically dissecting a couple of representative loci in mouse embryonic stem cells, we show that CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), while developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the insulation of regulatory domains, which in turn might help interpreting the pathological consequences of certain structural variants.}, }
@article {pmid39169755, year = {2024}, author = {Huang, H and Wu, Q}, title = {Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2400121}, doi = {10.1002/bies.202400121}, pmid = {39169755}, issn = {1521-1878}, support = {32330016//National Natural Science Foundation of China/ ; 2022YFC3400200//National Key R&D Program of China/ ; }, abstract = {Topologically associating domain (TAD) boundaries are the flanking edges of TADs, also known as insulated neighborhoods, within the 3D structure of genomes. A prominent feature of TAD boundaries in mammalian genomes is the enrichment of clustered CTCF sites often with mixed orientations, which can either block or facilitate enhancer-promoter (E-P) interactions within or across distinct TADs, respectively. We will discuss recent progress in the understanding of fundamental organizing principles of the clustered CTCF insulator codes at TAD boundaries. Specifically, both inward- and outward-oriented CTCF sites function as topological chromatin insulators by asymmetrically blocking improper TAD-boundary-crossing cohesin loop extrusion. In addition, boundary stacking and enhancer clustering facilitate long-distance E-P interactions across multiple TADs. Finally, we provide a unified mechanism for RNA-mediated TAD boundary function via R-loop formation for both insulation and facilitation. This mechanism of TAD boundary formation and insulation has interesting implications not only on how the 3D genome folds in the Euclidean nuclear space but also on how the specificity of E-P interactions is developmentally regulated.}, }
@article {pmid39152239, year = {2024}, author = {Denaud, S and Bardou, M and Papadopoulos, GL and Grob, S and Di Stefano, M and Sabarís, G and Nollmann, M and Schuettengruber, B and Cavalli, G}, title = {A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication.}, journal = {Nature structural & molecular biology}, volume = {}, number = {}, pages = {}, pmid = {39152239}, issn = {1545-9985}, abstract = {Three-dimensional (3D) genome folding has a fundamental role in the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CRE involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TAD) called a Polycomb domain. PREs can establish looping contacts that stabilize the gene repression of key developmental genes during development. However, the mechanism by which PRE loops fine-tune gene expression is unknown. Using clustered regularly interspaced short palindromic repeats and Cas9 genome engineering, we specifically perturbed PRE contacts or enhancer function and used complementary approaches including 4C-seq, Hi-C and Hi-M to analyze how chromatin architecture perturbation affects gene expression. Our results suggest that the PRE loop at the dac gene locus acts as a constitutive 3D chromatin scaffold during Drosophila development that forms independently of gene expression states and has a versatile function; it restricts enhancer-promoter communication and contributes to enhancer specificity.}, }
@article {pmid39152238, year = {2024}, author = {Yao, Q and Zhu, L and Shi, Z and Banerjee, S and Chen, C}, title = {Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.}, journal = {Nature structural & molecular biology}, volume = {}, number = {}, pages = {}, pmid = {39152238}, issn = {1545-9985}, abstract = {DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.}, }
@article {pmid39149372, year = {2024}, author = {Kearly, A and Saelee, P and Bard, J and Sinha, S and Satterthwaite, A and Garrett-Sinha, LA}, title = {Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.08.02.606433}, pmid = {39149372}, issn = {2692-8205}, abstract = {The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1 .}, }
@article {pmid39094522, year = {2024}, author = {Na, J and Tai, C and Wang, Z and Yang, Z and Chen, X and Zhang, J and Zheng, L and Fan, Y}, title = {Stiff extracellular matrix drives the differentiation of mesenchymal stem cells toward osteogenesis by the multiscale 3D genome reorganization.}, journal = {Biomaterials}, volume = {312}, number = {}, pages = {122715}, doi = {10.1016/j.biomaterials.2024.122715}, pmid = {39094522}, issn = {1878-5905}, abstract = {Extracellular matrix (ECM) stiffness is a major driver of stem cell fate. However, the involvement of the three-dimensional (3D) genomic reorganization in response to ECM stiffness remains unclear. Here, we generated comprehensive 3D chromatin landscapes of mesenchymal stem cells (MSCs) exposed to various ECM stiffness. We found that there were more long-range chromatin interactions, but less compartment A in MSCs cultured on stiff ECM than those cultured on soft ECM. However, the switch from compartment B in MSCs cultured on soft ECM to compartment A in MSCs cultured on stiff ECM included genes encoding proteins primarily enriched in cytoskeleton organization. At the topologically associating domains (TADs) level, stiff ECM tends to have merged TADs on soft ECM. These merged TADs on stiff ECM include upregulated genes encoding proteins enriched in osteogenesis, such as SP1, ETS1, and DCHS1, which were validated by quantitative real-time polymerase chain reaction and found to be consistent with the increase of alkaline phosphatase staining. Knockdown of SP1 or ETS1 led to the downregulation of osteogenic marker genes, including COL1A1, RUNX2, ALP, and OCN in MSCs cultured on stiff ECM. Our study provides an important insight into the stiff ECM-mediated promotion of MSC differentiation towards osteogenesis, emphasizing the influence of mechanical cues on the reorganization of 3D genome architecture and stem cell fate.}, }
@article {pmid39093600, year = {2024}, author = {Chang, LH and Noordermeer, D}, title = {Permeable TAD boundaries and their impact on genome-associated functions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2400137}, doi = {10.1002/bies.202400137}, pmid = {39093600}, issn = {1521-1878}, support = {ANR-21-CE12-0034//Agence Nationale de la Recherche/ ; ANR-21-CE12-0034//Agence Nationale de la Recherche/ ; ANR-22-CE12-0016//Agence Nationale de la Recherche/ ; ANR-22-CE14-0021//Agence Nationale de la Recherche/ ; //Blood and Transplant Research Unit in Precision Cellular Therapeutics/ ; }, abstract = {TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.}, }
@article {pmid39083950, year = {2024}, author = {Oji, A and Choubani, L and Miura, H and Hiratani, I}, title = {Structure and dynamics of nuclear A/B compartments and subcompartments.}, journal = {Current opinion in cell biology}, volume = {90}, number = {}, pages = {102406}, doi = {10.1016/j.ceb.2024.102406}, pmid = {39083950}, issn = {1879-0410}, abstract = {Mammalian chromosomes form a hierarchical structure within the cell nucleus, from chromatin loops, megabase (Mb)-sized topologically associating domains (TADs) to larger-scale A/B compartments. The molecular basis of the structures of loops and TADs has been actively studied. However, the A and B compartments, which correspond to early-replicating euchromatin and late-replicating heterochromatin, respectively, are still relatively unexplored. In this review, we focus on the A/B compartments, discuss their close relationship to DNA replication timing (RT), and introduce recent findings on the features of subcompartments revealed by detailed classification of the A/B compartments. In doing so, we speculate on the structure, potential function, and developmental dynamics of A/B compartments and subcompartments in mammalian cells.}, }
@article {pmid39078102, year = {2024}, author = {Dimartino, P and Zadorozhna, M and Yumiceba, V and Basile, A and Cani, I and Melo, US and Henck, J and Breur, M and Tonon, C and Lodi, R and Brusco, A and Pippucci, T and Koufi, FD and Boschetti, E and Ramazzotti, G and Manzoli, L and Ratti, S and Pinto E Vairo, F and Delatycki, MB and Vaula, G and Cortelli, P and Bugiani, M and Spielmann, M and Giorgio, E}, title = {Structural Variants at the LMNB1 Locus: Deciphering Pathomechanisms in Autosomal Dominant Adult-Onset Demyelinating Leukodystrophy.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.27038}, pmid = {39078102}, issn = {1531-8249}, support = {GR-2021-12373348//Ministero della Salute, Ricerca Finalizzata/ ; MNESYS (PE0000006)//Ministero dell'Universit&#xe0; e della Ricerca, National Recovery and Resilience Plan (NRRP)/ ; }, abstract = {OBJECTIVES: We aimed to elucidate the pathogenic mechanisms underlying autosomal dominant adult-onset demyelinating leukodystrophy (ADLD), and to understand the genotype/phenotype correlation of structural variants (SVs) in the LMNB1 locus.<br><br>BACKGROUND: Since the discovery of 3D genome architectures and topologically associating domains (TADs), new pathomechanisms have been postulated for SVs, regardless of gene dosage changes. ADLD is a rare genetic disease associated with duplications (classical ADLD) or noncoding deletions (atypical ADLD) in the LMNB1 locus.<br><br>METHODS: High-throughput chromosome conformation capture, RNA sequencing, histopathological analyses of postmortem brain tissues, and clinical and neuroradiological investigations were performed.<br><br>RESULTS: We collected data from >20 families worldwide carrying SVs in the LMNB1 locus and reported strong clinical variability, even among patients carrying duplications of the entire LMNB1 gene, ranging from classical and atypical ADLD to asymptomatic carriers. We showed that patients with classic ADLD always carried intra-TAD duplications, resulting in a simple gene dose gain. Atypical ADLD was caused by LMNB1 forebrain-specific misexpression due to inter-TAD deletions or duplications. The inter-TAD duplication, which extends centromerically and crosses the 2 TAD boundaries, did not cause ADLD. Our results provide evidence that astrocytes are key players in ADLD pathology.<br><br>INTERPRETATION: Our study sheds light on the 3D genome and TAD structural changes associated with SVs in the LMNB1 locus, and shows that a duplication encompassing LMNB1 is not sufficient per se to diagnose ADLD, thereby strongly affecting genetic counseling. Our study supports breaking TADs as an emerging pathogenic mechanism that should be considered when studying brain diseases. ANN NEUROL 2024.}, }
@article {pmid39061232, year = {2024}, author = {Zhou, T and Nguyen, S and Wu, J and He, B and Feng, Q}, title = {LncRNA LOC730101 Promotes Darolutamide Resistance in Prostate Cancer by Suppressing miR-1-3p.}, journal = {Cancers}, volume = {16}, number = {14}, pages = {}, doi = {10.3390/cancers16142594}, pmid = {39061232}, issn = {2072-6694}, support = {1R33AI133697-03A1/NH/NIH HHS/United States ; 1R01CA211861-05A1/NH/NIH HHS/United States ; }, abstract = {Antiandrogen is part of the standard-of-care treatment option for metastatic prostate cancer. However, prostate cancers frequently relapse, and the underlying resistance mechanism remains incompletely understood. This study seeks to investigate whether long non-coding RNAs (lncRNAs) contribute to the resistance against the latest antiandrogen drug, darolutamide. Our RNA sequencing analysis revealed significant overexpression of LOC730101 in darolutamide-resistant cancer cells compared to the parental cells. Elevated LOC730101 levels were also observed in clinical samples of metastatic castration-resistant prostate cancer (CRPC) compared to primary prostate cancer samples. Silencing LOC730101 with siRNA significantly impaired the growth of darolutamide-resistant cells. Additional RNA sequencing analysis identified a set of genes regulated by LOC730101, including key players in the cell cycle regulatory pathway. We further demonstrated that LOC730101 promotes darolutamide resistance by competitively inhibiting microRNA miR-1-3p. Moreover, by Hi-C sequencing, we found that LOC730101 is located in a topologically associating domain (TAD) that undergoes specific gene induction in darolutamide-resistant cells. Collectively, our study demonstrates the crucial role of the lncRNA LOC730101 in darolutamide resistance and its potential as a target for overcoming antiandrogen resistance in CRPC.}, }
@article {pmid39047029, year = {2024}, author = {Ling, Z and Zhang, YW and Li, SC}, title = {SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2024.0490}, pmid = {39047029}, issn = {1557-8666}, abstract = {High-throughput chromosome conformation capture (Hi-C) technology captures spatial interactions of DNA sequences into matrices, and software tools are developed to identify topologically associating domains (TADs) from the Hi-C matrices. With structural information theory, SuperTAD adopted a dynamic programming approach to find the TAD hierarchy with minimal structural entropy. However, the algorithm suffers from high time complexity. To accelerate this algorithm, we design and implement an approximation algorithm with a theoretical performance guarantee. We implemented a package, SuperTAD-Fast. Using Hi-C matrices and simulated data, we demonstrated that SuperTAD-Fast achieved great runtime improvement compared with SuperTAD. SuperTAD-Fast shows high consistency and significant enrichment of structural proteins from Hi-C data of human cell lines in comparison with the existing six hierarchical TADs detecting methods.}, }
@article {pmid39039278, year = {2024}, author = {Das, M and Semple, JI and Haemmerli, A and Volodkina, V and Scotton, J and Gitchev, T and Annan, A and Campos, J and Statzer, C and Dakhovnik, A and Ewald, CY and Mozziconacci, J and Meister, P}, title = {Condensin I folds the Caenorhabditis elegans genome.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {39039278}, issn = {1546-1718}, support = {31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {The structural maintenance of chromosome (SMC) complexes-cohesin and condensins-are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans, a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin I[DC], leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/I[DC] inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin I[DC]. C. elegans condensin I/I[DC] thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression.}, }
@article {pmid39008525, year = {2024}, author = {Maisuradze, L and King, MC and Surovtsev, IV and Mochrie, SGJ and Shattuck, MD and O'Hern, CS}, title = {Identifying topologically associating domains using differential kernels.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012221}, doi = {10.1371/journal.pcbi.1012221}, pmid = {39008525}, issn = {1553-7358}, mesh = {*Algorithms ; *Chromatin/chemistry/genetics/metabolism ; *Computational Biology/methods ; Humans ; Image Processing, Computer-Assisted/methods ; Animals ; }, abstract = {Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix [Formula: see text], where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in [Formula: see text] within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states.}, }
@article {pmid38968127, year = {2024}, author = {An, J and Brik Chaouche, R and Pereyra-Bistraín, LI and Zalzalé, H and Wang, Q and Huang, Y and He, X and Dias Lopes, C and Antunez-Sanchez, J and Bergounioux, C and Boulogne, C and Dupas, C and Gillet, C and Pérez-Pérez, JM and Mathieu, O and Bouché, N and Fragkostefanakis, S and Zhang, Y and Zheng, S and Crespi, M and Mahfouz, MM and Ariel, F and Gutierrez-Marcos, J and Raynaud, C and Latrasse, D and Benhamed, M}, title = {An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {28}, pages = {e2400737121}, doi = {10.1073/pnas.2400737121}, pmid = {38968127}, issn = {1091-6490}, support = {Project 101044399-3Dwheat//EC | European Research Council (ERC)/ ; ANR-21-CE20-0036-4D Heat Tomato//Agence Nationale de la Recherche (ANR)/ ; ANR-17-EUR-0007//Agence Nationale de la Recherche (ANR)/ ; 202108320109//China Scholarship Council (CSC)/ ; 202308620118//China Scholarship Council (CSC)/ ; }, mesh = {*Solanum lycopersicum/genetics/metabolism ; *Histones/metabolism/genetics ; *Epigenome ; Epigenesis, Genetic ; Genome, Plant ; Chromatin/metabolism/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Heterochromatin/metabolism/genetics ; Histone Code/genetics ; }, abstract = {In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.}, }
@article {pmid38967009, year = {2024}, author = {Mulero-Hernández, J and Mironov, V and Miñarro-Giménez, JA and Kuiper, M and Fernández-Breis, JT}, title = {Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae566}, pmid = {38967009}, issn = {1362-4962}, support = {FPU18/03264//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, abstract = {Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop new strategies to enable advanced data querying. Many databases have been developed to provide information about enhancers, but a schema that allows the standardized representation of data, securing interoperability between resources, has been lacking. In this work, we use knowledge graphs for the standardized representation of enhancers and topologically associating domains, together with data about their target genes, transcription factors, location on the human genome, and functional data about diseases and gene ontology annotations. We used this schema to integrate twenty-five enhancer datasets and two domain datasets, creating the most powerful integrative resource in this field to date. The knowledge graphs have been implemented using the Resource Description Framework and integrated within the open-access BioGateway knowledge network, generating a resource that contains an interoperable set of knowledge graphs (enhancers, TADs, genes, proteins, diseases, GO terms, and interactions between domains). We show how advanced queries, which combine functional and location restrictions, can be used to develop new hypotheses about functional aspects of gene expression regulation.}, }
@article {pmid38940151, year = {2024}, author = {Murtaza, G and Butaney, B and Wagner, J and Singh, R}, title = {scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Supplement_1}, pages = {i490-i500}, doi = {10.1093/bioinformatics/btae223}, pmid = {38940151}, issn = {1367-4811}, support = {1R35HG011939-01/GF/NIH HHS/United States ; }, mesh = {*Deep Learning ; *Single-Cell Analysis/methods ; *Chromatin/metabolism/chemistry ; Humans ; }, abstract = {SUMMARY: Single-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progression. Despite providing crucial insights, scHi-C data is often underutilized due to the high cost and the complexity of the experimental protocol. We present a deep learning framework, scGrapHiC, that predicts pseudo-bulk scHi-C contact maps using pseudo-bulk scRNA-seq data. Specifically, scGrapHiC performs graph deconvolution to extract genome-wide single-cell interactions from a bulk Hi-C contact map using scRNA-seq as a guiding signal. Our evaluations show that scGrapHiC, trained on seven cell-type co-assay datasets, outperforms typical sequence encoder approaches. For example, scGrapHiC achieves a substantial improvement of 23.2% in recovering cell-type-specific Topologically Associating Domains over the baselines. It also generalizes to unseen embryo and brain tissue samples. scGrapHiC is a novel method to generate cell-type-specific scHi-C contact maps using widely available genomic signals that enables the study of cell-type-specific chromatin interactions.<br><br>The GitHub link: https://github.com/rsinghlab/scGrapHiC contains the source code of scGrapHiC and associated scripts to preprocess publicly available datasets to produce the results and visualizations we have discuss in this manuscript.}, }
@article {pmid38935071, year = {2024}, author = {Chen, B and Ren, C and Ouyang, Z and Xu, J and Xu, K and Li, Y and Guo, H and Bai, X and Tian, M and Xu, X and Wang, Y and Li, H and Bo, X and Chen, H}, title = {Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {4}, pages = {}, doi = {10.1093/bib/bbae306}, pmid = {38935071}, issn = {1477-4054}, support = {62173338//National Natural Science Foundation of China/ ; 20220484198//Beijing Nova Program of Science and Technology/ ; }, mesh = {*DNA Repair ; Humans ; *DNA Breaks, Double-Stranded ; *Chromatin/metabolism/genetics ; *Gene Expression Regulation ; Transcription Factors/metabolism/genetics ; Animals ; Genomics/methods ; Genomic Instability ; Chromatin Assembly and Disassembly ; }, abstract = {Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.}, }
@article {pmid38927609, year = {2024}, author = {Zhu, H and Liu, T and Wang, Z}, title = {C2c: Predicting Micro-C from Hi-C.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/genes15060673}, pmid = {38927609}, issn = {2073-4425}, support = {1R35GM137974/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; Humans ; Computational Biology/methods ; Neural Networks, Computer ; Micrococcal Nuclease/metabolism/genetics ; Nucleosomes/genetics ; Software ; }, abstract = {MOTIVATION: High-resolution Hi-C data, capable of detecting chromatin features below the level of Topologically Associating Domains (TADs), significantly enhance our understanding of gene regulation. Micro-C, a variant of Hi-C incorporating a micrococcal nuclease (MNase) digestion step to examine interactions between nucleosome pairs, has been developed to overcome the resolution limitations of Hi-C. However, Micro-C experiments pose greater technical challenges compared to Hi-C, owing to the need for precise MNase digestion control and higher-resolution sequencing. Therefore, developing computational methods to derive Micro-C data from existing Hi-C datasets could lead to better usage of a large amount of existing Hi-C data in the scientific community and cost savings.<br><br>RESULTS: We developed C2c ("high" or upper case C to "micro" or lower case c), a computational tool based on a residual neural network to learn the mapping between Hi-C and Micro-C contact matrices and then predict Micro-C contact matrices based on Hi-C contact matrices. Our evaluation results show that the predicted Micro-C contact matrices reveal more chromatin loops than the input Hi-C contact matrices, and more of the loops detected from predicted Micro-C match the promoter-enhancer interactions. Furthermore, we found that the mutual loops from real and predicted Micro-C better match the ChIA-PET data compared to Hi-C and real Micro-C loops, and the predicted Micro-C leads to more TAD-boundaries detected compared to the Hi-C data. The website URL of C2c can be found in the Data Availability Statement.}, }
@article {pmid38895201, year = {2024}, author = {Wong, EWP and Sahin, M and Yang, R and Lee, U and Zhan, YA and Misra, R and Tomas, F and Alomran, N and Polyzos, A and Lee, CJ and Trieu, T and Fundichely, AM and Wiesner, T and Rosowicz, A and Cheng, S and Liu, C and Lallo, M and Merghoub, T and Hamard, PJ and Koche, R and Khurana, E and Apostolou, E and Zheng, D and Chen, Y and Leslie, CS and Chi, P}, title = {TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.31.596845}, pmid = {38895201}, abstract = {Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.}, }
@article {pmid38871723, year = {2024}, author = {Sun, W and Xiong, D and Ouyang, J and Xiao, X and Jiang, Y and Wang, Y and Li, S and Xie, Z and Wang, J and Tang, Z and Zhang, Q}, title = {Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5048}, pmid = {38871723}, issn = {2041-1723}, support = {82171056//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Translocation, Genetic ; *Chromatin/metabolism/genetics ; *Iris/metabolism ; Male ; Female ; *Pedigree ; Chromosomes, Human, Pair 6/genetics ; Chromosomes, Human, Pair 18/genetics ; Induced Pluripotent Stem Cells/metabolism ; Adult ; Iris Diseases/genetics/metabolism/pathology ; Genetic Linkage ; }, abstract = {Despite the advent of genomic sequencing, molecular diagnosis remains unsolved in approximately half of patients with Mendelian disorders, largely due to unclarified functions of noncoding regions and the difficulty in identifying complex structural variations. In this study, we map a unique form of central iris hypoplasia in a large family to 6q15-q23.3 and 18p11.31-q12.1 using a genome-wide linkage scan. Long-read sequencing reveals a balanced translocation t(6;18)(q22.31;p11.22) with intergenic breakpoints. By performing Hi-C on induced pluripotent stem cells from a patient, we identify two chromatin topologically associating domains spanning across the breakpoints. These alterations lead the ectopic chromatin interactions between APCDD1 on chromosome 18 and enhancers on chromosome 6, resulting in upregulation of APCDD1. Notably, APCDD1 is specifically localized in the iris of human eyes. Our findings demonstrate that noncoding structural variations can lead to Mendelian diseases by disrupting the 3D genome structure and resulting in altered gene expression.}, }
@article {pmid38826443, year = {2024}, author = {Aharonoff, A and Kim, J and Washington, A and Ercan, S}, title = {SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.21.595224}, pmid = {38826443}, abstract = {UNLABELLED: Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans , for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegan s dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae , which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained.<br><br>SIGNIFICANCE STATEMENT: X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus . Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.}, }
@article {pmid38810546, year = {2024}, author = {Bhattacharya, M and Lyda, SF and Lei, EP}, title = {Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization.}, journal = {Current opinion in genetics &amp; development}, volume = {87}, number = {}, pages = {102208}, doi = {10.1016/j.gde.2024.102208}, pmid = {38810546}, issn = {1879-0380}, abstract = {Chromatin insulators are DNA-protein complexes that promote specificity of enhancer-promoter interactions and maintain distinct transcriptional states through control of 3D genome organization. In this review, we highlight recent work visualizing how mammalian CCCTC-binding factor acts as a boundary to dynamic DNA loop extrusion mediated by cohesin. We also discuss new studies in both mammals and Drosophila that elucidate biological redundancy of chromatin insulator function and interplay with transcription with respect to topologically associating domain formation. Finally, we present novel concepts in spatiotemporal regulation of chromatin insulator function during differentiation and development and possible consequences of disrupted insulator activity on cellular proliferation.}, }
@article {pmid38783373, year = {2024}, author = {Zagirova, D and Kononkova, A and Vaulin, N and Khrameeva, E}, title = {From compartments to loops: understanding the unique chromatin organization in neuronal cells.}, journal = {Epigenetics &amp; chromatin}, volume = {17}, number = {1}, pages = {18}, pmid = {38783373}, issn = {1756-8935}, support = {21-74-10102//Russian Science Foundation/ ; }, abstract = {The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.}, }
@article {pmid38782890, year = {2024}, author = {Xu, J and Xu, X and Huang, D and Luo, Y and Lin, L and Bai, X and Zheng, Y and Yang, Q and Cheng, Y and Huang, A and Shi, J and Bo, X and Gu, J and Chen, H}, title = {A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4376}, pmid = {38782890}, issn = {2041-1723}, support = {62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20220484198//Beijing Nova Program/ ; 20220484198//Beijing Nova Program/ ; 20220484198//Beijing Nova Program/ ; }, mesh = {*Benchmarking ; *Chromatin/chemistry ; Humans ; Computational Biology/methods ; Software ; Chromatin Assembly and Disassembly ; }, abstract = {Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.}, }
@article {pmid38778427, year = {2024}, author = {Sui, P and Wang, Z and Zhang, P and Pan, F}, title = {Three-dimensional chromatin landscapes in MLLr AML.}, journal = {Experimental hematology &amp; oncology}, volume = {13}, number = {1}, pages = {56}, pmid = {38778427}, issn = {2162-3619}, abstract = {Rearrangements of the mixed lineage leukemia (MLLr) gene are frequently associated with aggressive acute myeloid leukemia (AML). However, the treatment options are limited due to the genomic complexity and dynamics of 3D structure, which regulate oncogene transcription and leukemia development. Here, we carried out an integrative analysis of 3D genome structure, chromatin accessibility, and gene expression in gene-edited MLL-AF9 AML samples. Our data revealed profound MLLr-specific alterations of chromatin accessibility, A/B compartments, topologically associating domains (TAD), and chromatin loops in AML. The local 3D configuration of the AML genome was rewired specifically at loci associated with AML-specific gene expression. Together, we demonstrate that MLL-AF9 fusion disrupts the 3D chromatin landscape, potentially contributing to the dramatic transcriptome remodeling in MLLr AML.}, }
@article {pmid38775198, year = {2024}, author = {Moindrot, B and Imaizumi, Y and Feil, R}, title = {Differential 3D genome architecture and imprinted gene expression: cause or consequence?.}, journal = {Biochemical Society transactions}, volume = {}, number = {}, pages = {}, doi = {10.1042/BST20230143}, pmid = {38775198}, issn = {1470-8752}, abstract = {Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.}, }
@article {pmid38766012, year = {2024}, author = {Irastorza-Azcarate, I and Kukalev, A and Kempfer, R and Thieme, CJ and Mastrobuoni, G and Markowski, J and Loof, G and Sparks, TM and Brookes, E and Natarajan, KN and Sauer, S and Fisher, AG and Nicodemi, M and Ren, B and Schwarz, RF and Kempa, S and Pombo, A}, title = {Extensive folding variability between homologous chromosomes in mammalian cells.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.08.591087}, pmid = {38766012}, abstract = {Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.}, }
@article {pmid38764013, year = {2024}, author = {Zhang, B and Long, Y and Pei, L and Huang, X and Li, B and Han, B and Zhang, M and Lindsey, K and Zhang, X and Wang, M and Yang, X}, title = {Drought response revealed by chromatin organization variation and transcriptional regulation in cotton.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {114}, pmid = {38764013}, issn = {1741-7007}, mesh = {*Gossypium/genetics/physiology ; *Droughts ; *Gene Expression Regulation, Plant ; *Chromatin/metabolism ; Stress, Physiological/genetics ; Genes, Plant ; }, abstract = {BACKGROUND: Cotton is a major world cash crop and an important source of natural fiber, oil, and protein. Drought stress is becoming a restrictive factor affecting cotton production. To facilitate the development of drought-tolerant cotton varieties, it is necessary to study the molecular mechanism of drought stress response by exploring key drought-resistant genes and related regulatory factors.<br><br>RESULTS: In this study, two cotton varieties, ZY007 (drought-sensitive) and ZY168 (drought-tolerant), showing obvious phenotypic differences under drought stress, were selected. A total of 25,898 drought-induced genes were identified, exhibiting significant enrichment in pathways related to plant stress responses. Under drought induction, At subgenome expression bias was observed at the whole-genome level, which may be due to stronger inhibition of Dt subgenome expression. A gene co-expression module that was significantly associated with drought resistance was identified. About 90% of topologically associating domain (TAD) boundaries were stable, and 6613 TAD variation events were identified between the two varieties under drought. We identified 92 genes in ZY007 and 98 in ZY168 related to chromatin 3D structural variation and induced by drought stress. These genes are closely linked to the cotton response to drought stress through canonical hormone-responsive pathways, modulation of kinase and phosphatase activities, facilitation of calcium ion transport, and other related molecular mechanisms.<br><br>CONCLUSIONS: These results lay a foundation for elucidating the molecular mechanism of the cotton drought response and provide important regulatory locus and gene resources for the future molecular breeding of drought-resistant cotton varieties.}, }
@article {pmid38755928, year = {2024}, author = {Yuan, T and Yan, H and Bailey, MLP and Williams, JF and Surovtsev, I and King, MC and Mochrie, SGJ}, title = {Effect of loops on the mean-square displacement of Rouse-model chromatin.}, journal = {Physical review. E}, volume = {109}, number = {4-1}, pages = {044502}, doi = {10.1103/PhysRevE.109.044502}, pmid = {38755928}, issn = {2470-0053}, mesh = {*Chromatin/metabolism/genetics/chemistry ; Models, Molecular ; }, abstract = {Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.}, }
@article {pmid38753319, year = {2024}, author = {Barozzi, I and Slaven, N and Canale, E and Lopes, R and Amorim Monteiro Barbosa, I and Bleu, M and Ivanoiu, D and Pacini, C and Mensa, E and Chambers, A and Bravaccini, S and Ravaioli, S and Gyorffy, B and Dieci, MV and Pruneri, G and Galli, GG and Magnani, L}, title = {A functional survey of the regulatory landscape of estrogen-receptor-positive breast cancer evolution.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {}, doi = {10.1158/2159-8290.CD-23-1157}, pmid = {38753319}, issn = {2159-8290}, abstract = {Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer (HDBC), potentially explaining ~40% of relapses. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of non-coding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies triggers the emergence of transient features which could ultimately be exploited to hinder the adaptive process.}, }
@article {pmid38743310, year = {2024}, author = {Semeigazin, A and Iida, S and Minami, K and Tamura, S and Ide, S and Higashi, K and Toyoda, A and Kurokawa, K and Maeshima, K}, title = {Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells.}, journal = {Histochemistry and cell biology}, volume = {}, number = {}, pages = {}, pmid = {38743310}, issn = {1432-119X}, support = {JP23KJ0996//Japan Society for the Promotion of Science/ ; JP23KJ0998//Japan Society for the Promotion of Science/ ; JP22H05606//Japan Society for the Promotion of Science/ ; JP23K17398//Japan Society for the Promotion of Science/ ; JPMJSP2104//Japan Science and Technology Agency/ ; JPMJSP2104//Japan Science and Technology Agency/ ; }, abstract = {Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs) with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.}, }
@article {pmid38712032, year = {2024}, author = {Loke, P and Zhao, M and Jankovic, D and Hornick, K and Link, V and Souza, COS and Belkaid, Y and Lack, J}, title = {Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3759654/v1}, pmid = {38712032}, abstract = {How macrophages in the tissue environment integrate multiple stimuli will depend on the genetic background of the host, but this is poorly understood. Here, we investigated C57BL/6 and BALB/c strain specific in vivo IL-4 activation of tissue-resident macrophages (TRMs) from the peritoneal cavity. C57BL/6 TRMs are more transcriptionally responsive to IL-4 stimulation, with a greater association of induced genes with super enhancers, induced enhancers, and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling revealed BL/6 specific enrichment of NF-κB, IRF, and STAT motifs. Additionally, IL-4-activated BL/6 TRMs demonstrated an augmented synergistic response upon in vitro lipopolysaccharide (LPS) exposure compared to BALB/c TRMs, despite naïve BALB/c TRMs displaying a more robust transcriptional response to LPS than naïve BL/6 TRMs. Single-cell RNA sequencing (scRNA-seq) analysis of mixed bone marrow chimeric mice indicated that transcriptional differences between BL/6 and BALB/c TRMs, and synergy between IL-4 and LPS, are cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming resulting in strain specific synergistic responses to LPS exposure.}, }
@article {pmid38705995, year = {2024}, author = {Afanasyev, AY and Kim, Y and Tolokh, IS and Sharakhov, IV and Onufriev, AV}, title = {The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.}, journal = {Epigenetics &amp; chromatin}, volume = {17}, number = {1}, pages = {13}, pmid = {38705995}, issn = {1756-8935}, support = {MCB-1715207//Directorate for Biological Sciences/ ; GM14459//Office of Extramural Research, National Institutes of Health/ ; }, mesh = {Animals ; *Nuclear Lamina/metabolism ; *Drosophila melanogaster/metabolism ; *Chromatin/metabolism ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE.<br><br>RESULTS: In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These&#xa0;include the possibility&#xa0;that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase.<br><br>CONCLUSIONS: At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.}, }
@article {pmid38697116, year = {2024}, author = {Liu, C and Nagashima, H and Fernando, N and Bass, V and Gopalakrishnan, J and Signorella, S and Montgomery, W and Lim, AI and Harrison, O and Reich, L and Yao, C and Sun, HW and Brooks, SR and Jiang, K and Nagarajan, V and Zhao, Y and Jung, S and Phillips, R and Mikami, Y and Lareau, CA and Kanno, Y and Jankovic, D and Aryee, MJ and Pękowska, A and Belkaid, Y and O'Shea, J and Shih, HY}, title = {A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2024.04.007}, pmid = {38697116}, issn = {1097-4180}, abstract = {Cytokine expression during T cell differentiation is a highly regulated process that involves long-range promoter-enhancer and CTCF-CTCF contacts at cytokine loci. Here, we investigated the impact of dynamic chromatin loop formation within the topologically associating domain (TAD) in regulating the expression of interferon gamma (IFN-γ) and interleukin-22 (IL-22); these cytokine loci are closely located in the genome and are associated with complex enhancer landscapes, which are selectively active in type 1 and type 3 lymphocytes. In situ Hi-C analyses revealed inducible TADs that insulated Ifng and Il22 enhancers during Th1 cell differentiation. Targeted deletion of a 17 bp boundary motif of these TADs imbalanced Th1- and Th17-associated immunity, both in vitro and in vivo, upon Toxoplasma gondii infection. In contrast, this boundary element was dispensable for cytokine regulation in natural killer cells. Our findings suggest that precise cytokine regulation relies on lineage- and developmental stage-specific interactions of 3D chromatin architectures and enhancer landscapes.}, }
@article {pmid38696651, year = {2024}, author = {Daly, AF and Beckers, A}, title = {The Genetic Pathophysiology and Clinical Management of the TADopathy, X-Linked Acrogigantism.}, journal = {Endocrine reviews}, volume = {}, number = {}, pages = {}, doi = {10.1210/endrev/bnae014}, pmid = {38696651}, issn = {1945-7189}, abstract = {Pituitary gigantism is a rare manifestation of chronic growth hormone (GH) excess that begins before closure of the growth plates. Nearly half of pituitary gigantism patients have an identifiable genetic cause. X-linked acrogigantism (X-LAG; 10% of pituitary gigantism) typically begins during infancy and can lead to the tallest individuals described. In the 10 years since its discovery, about 40 patients have been identified. Patients with X-LAG usually develop mixed GH and prolactin macroadenomas with occasional hyperplasia that secrete copious amounts of GH, and frequently prolactin. Circulating GH releasing hormone (GHRH) is also elevated in a proportion of patients. X-LAG is caused by constitutive or sporadic mosaic duplications at chromosome Xq26.3 that disrupt the normal chromatin architecture of a topologically associating domain (TAD) around the orphan G protein coupled receptor (GPCR), GPR101. This leads to the formation of a neoTAD in which GPR101 over-expression is driven by ectopic enhancers ("TADopathy"). X-LAG has been seen in three families due to transmission of the duplication from affected mothers to sons. GPR101 is a constitutively active receptor with an unknown natural ligand that signals via multiple G proteins and protein kinases A and C to promote GH/prolactin hypersecretion. Treatment of X-LAG is challenging due to the young patient population and resistance to somatostatin analogs; the GH receptor antagonist pegvisomant is often an effective option. GH, insulin-like growth factor 1 (IGF-1) and prolactin hypersecretion and physical overgrowth can be controlled before definitive adult gigantism occurs, often at the cost of permanent hypopituitarism.}, }
@article {pmid38685685, year = {2024}, author = {Liu, H and Pan, Z and Lin, X and Chen, L and Yang, Q and Zhang, W and Dai, L and Zhang, Y and Li, W and Chen, Y and Peng, K and Wanggou, S and Zeng, F and Li, X}, title = {A potassium-chloride co-transporter with altered genome architecture functions as a suppressor in glioma.}, journal = {Journal of cellular and molecular medicine}, volume = {28}, number = {9}, pages = {e18352}, doi = {10.1111/jcmm.18352}, pmid = {38685685}, issn = {1582-4934}, support = {82270825//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Glioma/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; *Cell Proliferation/genetics ; Cell Line, Tumor ; *Brain Neoplasms/genetics/pathology/metabolism ; *Symporters/genetics/metabolism ; Cell Movement/genetics ; Prognosis ; Receptors, GABA-A/metabolism/genetics ; *K Cl- Cotransporters ; }, abstract = {Gliomas, the most lethal tumours in brain, have a poor prognosis despite accepting standard treatment. Limited benefits from current therapies can be attributed to genetic, epigenetic and microenvironmental cues that affect cell programming and drive tumour heterogeneity. Through the analysis of Hi-C data, we identified a potassium-chloride co-transporter SLC12A5 associated with disrupted topologically associating domain which was downregulated in tumour tissues. Multiple independent glioma cohorts were included to analyse the characterization of SLC12A5 and found it was significantly associated with pathological features, prognostic value, genomic alterations, transcriptional landscape and drug response. We constructed two SLC12A5 overexpression cell lines to verify the function of SLC12A5 that suppressed tumour cell proliferation and migration in vitro. In addition, SLC12A5 was also positively associated with GABAA receptor activity and negatively associated with pro-tumour immune signatures and immunotherapy response. Collectively, our study provides a comprehensive characterization of SLC12A5 in glioma and supports SLC12A5 as a potential suppressor of disease progression.}, }
@article {pmid38669773, year = {2024}, author = {Wang, X and Yue, F}, title = {Hijacked enhancer-promoter and silencer-promoter loops in cancer.}, journal = {Current opinion in genetics &amp; development}, volume = {86}, number = {}, pages = {102199}, doi = {10.1016/j.gde.2024.102199}, pmid = {38669773}, issn = {1879-0380}, abstract = {Recent work has shown that besides inducing fusion genes, structural variations (SVs) can also contribute to oncogenesis by disrupting the three-dimensional genome organization and dysregulating gene expression. At the chromatin-loop level, SVs can relocate enhancers or silencers from their original genomic loci to activate oncogenes or repress tumor suppressor genes. On a larger scale, different types of alterations in topologically associating domains (TADs) have been reported in cancer, such as TAD expansion, shuffling, and SV-induced neo-TADs. Furthermore, the transformation from normal cells to cancerous cells is usually coupled with active or repressive compartmental switches, and cancer-specific compartments have been proposed. This review discusses the sites, and the other latest advances in studying how SVs disrupt higher-order genome structure in cancer, which in turn leads to oncogene dysregulation. We also highlight the clinical implications of these changes and the challenges ahead in this field.}, }
@article {pmid38669177, year = {2024}, author = {Kuffler, L and Skelly, DA and Czechanski, A and Fortin, HJ and Munger, SC and Baker, CL and Reinholdt, LG and Carter, GW}, title = {Imputation of 3D genome structure by genetic-epigenetic interaction modeling in mice.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.88222}, pmid = {38669177}, issn = {2050-084X}, support = {R01GM115518/GM/NIGMS NIH HHS/United States ; R35GM133724/GM/NIGMS NIH HHS/United States ; P40OD011102/NH/NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Epigenesis, Genetic ; *Chromatin/metabolism/genetics ; *Genome ; Genetic Variation ; Embryonic Stem Cells/metabolism ; }, abstract = {Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. Analyses of these interactions have previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. Here, we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. We establish the extent and structure of genotype-by-epigenotype interaction using embryonic stem cells derived from Diversity Outbred mice. This mouse population segregates millions of variants from eight inbred founders, enabling precision genetic mapping with extensive genotypic and phenotypic diversity. With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. Our results demonstrate that statistical interactions between genetic variants and chromatin accessibility are common throughout the genome. We found that these interactions occur within the local area of the affected gene, and that this locality corresponds to topologically associated domains (TADs). The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. We confirmed this finding with CTCF ChIP-seq that revealed strain-specific binding in the inbred founder mice. In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF-binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. These findings provide evidence that genetic and epigenetic factors operate within the context of 3D chromatin structure.}, }
@article {pmid38663040, year = {2024}, author = {Martitz, A and Schulz, EG}, title = {Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation.}, journal = {Current opinion in genetics &amp; development}, volume = {86}, number = {}, pages = {102198}, doi = {10.1016/j.gde.2024.102198}, pmid = {38663040}, issn = {1879-0380}, abstract = {Genomes are organised through hierarchical structures, ranging from local kilobase-scale cis-regulatory contacts to large chromosome territories. Most notably, (sub)-compartments partition chromosomes according to transcriptional activity, while topologically associating domains (TADs) define cis-regulatory landscapes. The inactive X chromosome in mammals has provided unique insights into the regulation and function of the three-dimensional (3D) genome. Concurrent with silencing of the majority of genes and major alterations of its chromatin state, the X chromosome undergoes profound spatial rearrangements at multiple scales. These include the emergence of megadomains, alterations of the compartment structure and loss of the majority of TADs. Moreover, the Xist locus, which orchestrates X-chromosome inactivation, has provided key insights into regulation and function of regulatory domains. This review provides an overview of recent insights into the control of these structural rearrangements and contextualises them within a broader understanding of 3D genome organisation.}, }
@article {pmid38410476, year = {2024}, author = {Martins, F and Machado, AL and Ribeiro, A and Oliveira, SM and Carvalho, J and Matthiesen, R and Backman, V and Velho, S}, title = {KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3752760/v2}, pmid = {38410476}, support = {R01 CA228272/CA/NCI NIH HHS/United States ; U54 CA261694/CA/NCI NIH HHS/United States ; U54 CA268084/CA/NCI NIH HHS/United States ; }, abstract = {Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity.}, }
@article {pmid38654598, year = {2024}, author = {Banerjee, A and Zhang, S and Bahar, I}, title = {Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.}, journal = {Briefings in functional genomics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bfgp/elae014}, pmid = {38654598}, issn = {2041-2657}, support = {R01 GM139297/GF/NIH HHS/United States ; }, abstract = {Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.}, }
@article {pmid38643172, year = {2024}, author = {Baudic, M and Murata, H and Bosada, FM and Melo, US and Aizawa, T and Lindenbaum, P and van der Maarel, LE and Guedon, A and Baron, E and Fremy, E and Foucal, A and Ishikawa, T and Ushinohama, H and Jurgens, SJ and Choi, SH and Kyndt, F and Le Scouarnec, S and Wakker, V and Thollet, A and Rajalu, A and Takaki, T and Ohno, S and Shimizu, W and Horie, M and Kimura, T and Ellinor, PT and Petit, F and Dulac, Y and Bru, P and Boland, A and Deleuze, JF and Redon, R and Le Marec, H and Le Tourneau, T and Gourraud, JB and Yoshida, Y and Makita, N and Vieyres, C and Makiyama, T and Mundlos, S and Christoffels, VM and Probst, V and Schott, JJ and Barc, J}, title = {TAD boundary deletion causes PITX2-related cardiac electrical and structural defects.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3380}, pmid = {38643172}, issn = {2041-1723}, support = {R21006NN, RPV21014NNA//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.}, }
@article {pmid38613389, year = {2024}, author = {Farhadova, S and Ghousein, A and Charon, F and Surcis, C and Gomez-Velazques, M and Roidor, C and Di Michele, F and Borensztein, M and De Sario, A and Esnault, C and Noordermeer, D and Moindrot, B and Feil, R}, title = {The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae247}, pmid = {38613389}, issn = {1362-4962}, support = {ANR-18-CE12-0022-02//Agence National de Recherche/ ; ANR-10-LABX-12-01//LabEx EPIGENMED-an ANR 'Investissement d'avenir' programme/ ; EQU202103012763//Fondation pour la Recherche M&#xe9;dicale/ ; 19CS145-00//PlanCancer/ ; //CNRS-INSERM ATIP-Avenir Programme/ ; //Azerbaijan National Academy of Sciences/ ; //Ministry of Education/ ; //University of Montpellier/ ; //La Ligue Nationale Contre le Cancer/ ; }, abstract = {The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain's imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5'-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.}, }
@article {pmid38589516, year = {2024}, author = {Xiong, K and Zhang, R and Ma, J}, title = {scGHOST: identifying single-cell 3D genome subcompartments.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {38589516}, issn = {1548-7105}, support = {UM1HG011593//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HG012303//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Single-cell Hi-C (scHi-C) technologies allow for probing of genome-wide cell-to-cell variability in three-dimensional (3D) genome organization from individual cells. Computational methods have been developed to reveal single-cell 3D genome features based on scHi-C, including A/B compartments, topologically associating domains and chromatin loops. However, no method exists for annotating single-cell subcompartments, which is important for understanding chromosome spatial localization in single cells. Here we present scGHOST, a single-cell subcompartment annotation method using graph embedding with constrained random walk sampling. Applications of scGHOST to scHi-C data and contact maps derived from single-cell 3D genome imaging demonstrate reliable identification of single-cell subcompartments, offering insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from complex tissues, scGHOST identifies cell-type-specific or allele-specific subcompartments linked to gene transcription across various cell types and developmental stages, suggesting functional implications of single-cell subcompartments. scGHOST is an effective method for annotating single-cell 3D genome subcompartments in a broad range of biological contexts.}, }
@article {pmid38567720, year = {2024}, author = {Funaya, S and Takahashi, Y and Suzuki, MG and Suzuki, Y and Aoki, F}, title = {H3.1/3.2 regulate the initial progression of the gene expression program.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae214}, pmid = {38567720}, issn = {1362-4962}, support = {19H05752//Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {In mice, transcription from the zygotic genome is initiated at the mid-one-cell stage, and occurs promiscuously in many areas of the genome, including intergenic regions. Regulated transcription from selected genes is established during the two-cell stage. This dramatic change in the gene expression pattern marks the initiation of the gene expression program and is essential for early development. We investigated the involvement of the histone variants H3.1/3.2 in the regulation of changes in gene expression pattern during the two-cell stage. Immunocytochemistry analysis showed low nuclear deposition of H3.1/3.2 in the one-cell stage, followed by a rapid increase in the late two-cell stage. Where chromatin structure is normally closed between the one- and two-cell stages, it remained open until the late two-cell stage when H3.1/3.2 were knocked down by small interfering RNA. Hi-C analysis showed that the formation of the topologically associating domain was disrupted in H3.1/3.2 knockdown (KD) embryos. Promiscuous transcription was also maintained in the late two-cell stage in H3.1/3.2 KD embryos. These results demonstrate that H3.1/3.2 are involved in the initial process of the gene expression program after fertilization, through the formation of a closed chromatin structure to execute regulated gene expression during the two-cell stage.}, }
@article {pmid38565950, year = {2024}, author = {Ramírez-Cuéllar, J and Ferrari, R and Sanz, RT and Valverde-Santiago, M and García-García, J and Nacht, AS and Castillo, D and Le Dily, F and Neguembor, MV and Malatesta, M and Bonnin, S and Marti-Renom, MA and Beato, M and Vicent, GP}, title = {LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {}, pmid = {38565950}, issn = {1460-2075}, support = {PID2019-105173RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2022-137045OB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2020-115696RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; 4DGenome" nr: 609989//EC | European Research Council (ERC)/ ; 201820I131//MEC | Consejo Superior de Investigaciones Cient&#xed;ficas (CSIC)/ ; MIUR: 2018-2022 MUR:2023-2027//Italian Ministry for University and Research/ ; 2013-2017//Centro de Excelencia Severo Ochoa/ ; }, abstract = {The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.}, }
@article {pmid38561401, year = {2024}, author = {Serra, F and Nieto-Aliseda, A and Fanlo-Escudero, L and Rovirosa, L and Cabrera-Pasadas, M and Lazarenkov, A and Urmeneta, B and Alcalde-Merino, A and Nola, EM and Okorokov, AL and Fraser, P and Graupera, M and Castillo, SD and Sardina, JL and Valencia, A and Javierre, BM}, title = {p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2821}, pmid = {38561401}, issn = {2041-1723}, support = {CP22/00127//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 4823998//European Hematology Association (EHA)/ ; PID2021-125277OB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; }, abstract = {Activation of the p53 tumor suppressor triggers a transcriptional program to control cellular response to stress. However, the molecular mechanisms by which p53 controls gene transcription are not completely understood. Here, we uncover the critical role of spatio-temporal genome architecture in this process. We demonstrate that p53 drives direct and indirect changes in genome compartments, topologically associating domains, and DNA loops prior to one hour of its activation, which escort the p53 transcriptional program. Focusing on p53-bound enhancers, we report 340 genes directly regulated by p53 over a median distance of 116 kb, with 74% of these genes not previously identified. Finally, we showcase that p53 controls transcription of distal genes through newly formed and pre-existing enhancer-promoter loops in a cohesin dependent manner. Collectively, our findings demonstrate a previously unappreciated architectural role of p53 as regulator at distinct topological layers and provide a reliable set of new p53 direct target genes that may help designs of cancer therapies.}, }
@article {pmid38553796, year = {2024}, author = {Li, M and Yang, J and Xiao, R and Liu, Y and Hu, J and Li, T and Wu, P and Zhang, M and Huang, Y and Sun, Y and Li, C}, title = {The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells.}, journal = {Cell proliferation}, volume = {}, number = {}, pages = {e13639}, doi = {10.1111/cpr.13639}, pmid = {38553796}, issn = {1365-2184}, support = {2016YFA0100103//National Key Research and Development Program of China/ ; 2021YFA1100300//National Key Research and Development Program of China/ ; 2021-I2M-1-019//CAMS Innovation Fund for Medical Sciences/ ; 2016-I2M-3-002//CAMS Innovation Fund for Medical Sciences/ ; 32288102//National Natural Science Foundation of China/ ; 32025006//National Natural Science Foundation of China/ ; }, abstract = {Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.}, }
@article {pmid38502563, year = {2024}, author = {Jeong, D and Shi, G and Li, X and Thirumalai, D}, title = {Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.88564}, pmid = {38502563}, issn = {2050-084X}, support = {CHE 2320256//National Science Foundation/ ; F-0019//Welch Foundation/ ; }, abstract = {Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.}, }
@article {pmid38495565, year = {2024}, author = {Wall, BPG and Nguyen, M and Harrell, JC and Dozmorov, MG}, title = {Machine and deep learning methods for predicting 3D genome organization.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {38495565}, issn = {2331-8422}, abstract = {Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.}, }
@article {pmid38490101, year = {2024}, author = {Mizokami, H and Okabe, A and Choudhary, R and Mima, M and Saeda, K and Fukuyo, M and Rahmutulla, B and Seki, M and Goh, BC and Kondo, S and Dochi, H and Moriyama-Kita, M and Misawa, K and Hanazawa, T and Tan, P and Yoshizaki, T and Fullwood, MJ and Kaneda, A}, title = {Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma.}, journal = {EBioMedicine}, volume = {102}, number = {}, pages = {105057}, doi = {10.1016/j.ebiom.2024.105057}, pmid = {38490101}, issn = {2352-3964}, abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor endemic to Southern China and Southeast Asia. While previous studies have revealed a low frequency of gene mutations in NPC, its epigenomic aberrations are not fully elucidated apart from DNA hypermethylation. Epigenomic rewiring and enhancer dysregulation, such as enhancer hijacking due to genomic structural changes or extrachromosomal DNA, drive cancer progression.<br><br>METHODS: We conducted Hi-C, 4C-seq, ChIP-seq, and RNA-seq analyses to comprehensively elucidate the epigenome and interactome of NPC using C666-1 EBV(+)-NPC cell lines, NP69T immortalized nasopharyngeal epithelial cells, clinical NPC biopsy samples, and in&#xa0;vitro EBV infection in HK1 and NPC-TW01 EBV(-) cell lines.<br><br>FINDINGS: In C666-1, the EBV genome significantly interacted with inactive B compartments of host cells; the significant association of EBV-interacting regions (EBVIRs) with B compartment was confirmed using clinical NPC and in&#xa0;vitro EBV infection model. EBVIRs in C666-1 showed significantly higher levels of active histone modifications compared with NP69T. Aberrant activation of EBVIRs after EBV infection was validated using in&#xa0;vitro EBV infection models. Within the EBVIR-overlapping topologically associating domains, 14 H3K4me3(+) genes were significantly upregulated in C666-1. Target genes of EBVIRs including PLA2G4A, PTGS2 and CITED2, interacted with the enhancers activated in EBVIRs and were highly expressed in NPC, and their knockdown significantly reduced cell proliferation.<br><br>INTERPRETATION: The EBV genome contributes to NPC tumorigenesis through "enhancer infestation" by interacting with the inactive B compartments of the host genome and aberrantly activating enhancers.<br><br>FUNDING: The funds are listed in the Acknowledgements section.}, }
@article {pmid38481440, year = {2024}, author = {Caruso, M and Mazzatenta, D and Asioli, S and Costanza, G and Trivellin, G and Franke, M and Abboud, D and Hanson, J and Raverot, V and Pétrossians, P and Beckers, A and Cappa, M and Daly, AF}, title = {Case report: Management of pediatric gigantism caused by the TADopathy, X-linked acrogigantism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1345363}, pmid = {38481440}, issn = {1664-2392}, abstract = {X-linked acrogigantism (X-LAG) is a rare form of pituitary gigantism that is associated with growth hormone (GH) and prolactin-secreting pituitary adenomas/pituitary neuroendocrine tumors (PitNETs) that develop in infancy. It is caused by a duplication on chromosome Xq26.3 that leads to the misexpression of the gene GPR101, a constitutively active stimulator of pituitary GH and prolactin secretion. GPR101 normally exists within its own topologically associating domain (TAD) and is insulated from surrounding regulatory elements. X-LAG is a TADopathy in which the duplication disrupts a conserved TAD border, leading to a neo-TAD in which ectopic enhancers drive GPR101 over-expression, thus causing gigantism. Here we trace the full diagnostic and therapeutic pathway of a female patient with X-LAG from 4C-seq studies demonstrating the neo-TAD through medical and surgical interventions and detailed tumor histopathology. The complex nature of treating young children with X-LAG is illustrated, including the achievement of hormonal control using a combination of neurosurgery and adult doses of first-generation somatostatin analogs.}, }
@article {pmid38473917, year = {2024}, author = {Plaisancié, J and Chesneau, B and Fares-Taie, L and Rozet, JM and Pechmeja, J and Noero, J and Gaston, V and Bailleul-Forestier, I and Calvas, P and Chassaing, N}, title = {Structural Variant Disrupting the Expression of the Remote FOXC1 Gene in a Patient with Syndromic Complex Microphthalmia.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, doi = {10.3390/ijms25052669}, pmid = {38473917}, issn = {1422-0067}, abstract = {Ocular malformations (OMs) arise from early defects during embryonic eye development. Despite the identification of over 100 genes linked to this heterogeneous group of disorders, the genetic cause remains unknown for half of the individuals following Whole-Exome Sequencing. Diagnosis procedures are further hampered by the difficulty of studying samples from clinically relevant tissue, which is one of the main obstacles in OMs. Whole-Genome Sequencing (WGS) to screen for non-coding regions and structural variants may unveil new diagnoses for OM individuals. In this study, we report a patient exhibiting a syndromic OM with a de novo 3.15 Mb inversion in the 6p25 region identified by WGS. This balanced structural variant was located 100 kb away from the FOXC1 gene, previously associated with ocular defects in the literature. We hypothesized that the inversion disrupts the topologically associating domain of FOXC1 and impairs the expression of the gene. Using a new type of samples to study transcripts, we were able to show that the patient presented monoallelic expression of FOXC1 in conjunctival cells, consistent with the abolition of the expression of the inverted allele. This report underscores the importance of investigating structural variants, even in non-coding regions, in individuals affected by ocular malformations.}, }
@article {pmid38455359, year = {2023}, author = {Pathak, RU and Phanindhar, K and Mishra, RK}, title = {Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1326933}, doi = {10.3389/fmolb.2023.1326933}, pmid = {38455359}, issn = {2296-889X}, abstract = {The hierarchical structure of eukaryotic genomes has regulatory layers, one of them being epigenetic "indexing" of the genome that leads to cell-type-specific patterns of gene expression. By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using scaffold/matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large-scale genome-wide mapping of S/MARs has begun to uncover these aspects of genome organization. A recent genome-wide study showed the association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that the multitude of TE-derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. In this study, we provide an insight that TE-driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs, as elements that can hop through the genome along with regulatory capabilities, may provide an active mechanism of genome evolution leading to the emergence of novel features in biological systems. The significance is that a genome-wide study mapping developmental S/MARs reveals an intriguing link between these elements and TEs. This article highlights the potential of the TE-S/MAR combination to drive evolution by restructuring and shaping the genome.}, }
@article {pmid38452764, year = {2024}, author = {Kim, KL and Rahme, GJ and Goel, VY and El Farran, CA and Hansen, AS and Bernstein, BE}, title = {Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2024.02.007}, pmid = {38452764}, issn = {1097-4164}, abstract = {Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.}, }
@article {pmid38449288, year = {2024}, author = {Liu, E and Lyu, H and Liu, Y and Fu, L and Cheng, X and Yin, X}, title = {Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae138}, pmid = {38449288}, issn = {1367-4811}, abstract = {MOTIVATION: Topologically associating domains (TADs) are fundamental building blocks of three-dimensional genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity.<br><br>RESULTS: We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels.<br><br>AVAILABILITY: scKTLD is freely available at https://github.com/lhqxinghun/scKTLD.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid38448979, year = {2024}, author = {Liu, Y and Zheng, Z and Wang, C and Wang, Y and Sun, X and Ren, Z and Yang, X and Yang, X}, title = {Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {40}, pmid = {38448979}, issn = {1674-9782}, support = {32372910 and 32102567//the National Science Foundation of China/ ; 2022KJXX-13, 2023-YBNY-144 and K3031223077//Program for Shaanxi Science and Technology/ ; 2022GD-TSLD-46-0302//Program for Shaanxi Science and Technology/ ; }, abstract = {BACKGROUND: Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate. Three-dimensional (3D) chromatin architecture takes part in disease processing by regulating transcriptional reprogramming. The study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver (FLS) and reveal their effect on hepatic transcriptional reprogramming in laying hens.<br><br>RESULTS: Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposition as well as higher total triglyceride and cholesterol in serum. A/B compartment switching, topologically associating domain (TAD) and chromatin loop changes are identified by high-throughput/resolution chromosome conformation capture (HiC) technology. Targeted genes of these alternations in hepatic 3D genome organization significantly enrich pathways related to lipid metabolism and hepatic damage. H3K27ac differential peaks and differential expression genes (DEGs) identified through RNA-seq analysis are also enriched in these pathways. Notably, certain DEGs are found to correspond with changes in 3D chromatin structure and H3K27ac binding in their promoters. DNA motif analysis reveals that candidate transcription factors are implicated in regulating transcriptional reprogramming. Furthermore, disturbed folate metabolism is observed, as evidenced by lower folate levels and altered enzyme expression.<br><br>CONCLUSION: Our findings establish a link between transcriptional reprogramming changes and 3D chromatin structure variations during early FLS formation, which provides candidate transcription factors and folate as targets for FLS prevention or treatment.}, }
@article {pmid38432398, year = {2024}, author = {Fraile, A and Cebrián, J and Thuissard-Vasallo, I and Pérez-Martín, S and Casado, R and Gil-Fournier, B and Alonso-Martín, J and Tamargo, J and Caballero, R and Delpón, E and Cosío, FG}, title = {Coexistent HCN4 and GATA5 rare variants and Atrial Fibrillation in a large Spanish Family.}, journal = {The Canadian journal of cardiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cjca.2024.02.024}, pmid = {38432398}, issn = {1916-7075}, abstract = {BACKGROUND: Familial association of atrial fibrillation (AF) can involve single gene variants related to known arrhythmogenic mechanisms; however, genome-wide association studies often disclose complex genetic variants in familial and non-familial AF, making it difficult to relate to known pathogenetic mechanisms.<br><br>METHODS: The finding of 4 siblings with AF led to studying 47 members of a family. Long-term Holter monitoring (298 hours average) ruled out silent AFWhole-exome sequencing was performed and variants shared by the index cases were filtered and prioritized according to current recommendations. HCN4 currents (IHCN4) were recorded in Chinese hamster ovary cells expressing human p.P1163H and/or native Hcn4 channels using the patch-clamp technique and topologically associated domain analysis of GATA5 variant carriers were performed.<br><br>RESULTS: The clinical study diagnosed 2 more AF cases. Five family members carried the heterozygous p.P1163H, HCN4 variant, 14 the intronic 20,61040536,G,A GATA5 rare variant, and 9 carried both variants (HCN4+GATA5). Five of the 6 AF cases (onset age ranging 33-70 years) carried both variants and one the GATA5 variant alone. Multivariate analysis showed that the presence of HCN4+GATA5 variants significantly and independently increased AF risk [OR=32.740 (1.812-591.408)] and not age, hypertension or overweight. Functional testing showed that IHcn4 generated by heterozygous p.P1163H were normal. Topologically associating domain analysis suggested that GATA5 could affect the expression of many genes, including those encoding microRNA-1.<br><br>CONCLUSION: The coincidence of two rare gene variants was independently associated with AF, but functional studies do not allow the postulation of the arrhythmogenic mechanism(s) involved.}, }
@article {pmid38402218, year = {2024}, author = {Torres, DE and Kramer, HM and Tracanna, V and Fiorin, GL and Cook, DE and Seidl, MF and Thomma, BPHJ}, title = {Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1701}, pmid = {38402218}, issn = {2041-1723}, support = {project 831.15.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; LT000627/2014-L//Human Frontier Science Program (HFSP)/ ; 2018-67013-28492//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, abstract = {The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.}, }
@article {pmid38355805, year = {2024}, author = {Patta, I and Zand, M and Lee, L and Mishra, S and Bortnick, A and Lu, H and Prusty, A and McArdle, S and Mikulski, Z and Wang, HY and Cheng, CS and Fisch, KM and Hu, M and Murre, C}, title = {Nuclear morphology is shaped by loop-extrusion programs.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38355805}, issn = {1476-4687}, abstract = {It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces[1-3]. However, how polymorphonuclear structures are assembled remains unknown[4]. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin[5]-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted in enrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.}, }
@article {pmid38346246, year = {2024}, author = {Liu, S and Athreya, A and Lao, Z and Zhang, B}, title = {From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.}, journal = {Annual review of biophysics}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biophys-030822-032650}, pmid = {38346246}, issn = {1936-1238}, abstract = {Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo. Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid38280381, year = {2024}, author = {Nakamura, T and Ueda, J and Mizuno, S and Honda, K and Kazuno, AA and Yamamoto, H and Hara, T and Takata, A}, title = {Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100488}, doi = {10.1016/j.xgen.2024.100488}, pmid = {38280381}, issn = {2666-979X}, abstract = {Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.}, }
@article {pmid38254945, year = {2023}, author = {Murtaza, G and Jain, A and Hughes, M and Wagner, J and Singh, R}, title = {A Comprehensive Evaluation of Generalizability of Deep Learning-Based Hi-C Resolution Improvement Methods.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/genes15010054}, pmid = {38254945}, issn = {2073-4425}, support = {1R35HG011939-01/NH/NIH HHS/United States ; GR5245041/NIST/NIST DOC/United States ; }, abstract = {Hi-C is a widely used technique to study the 3D organization of the genome. Due to its high sequencing cost, most of the generated datasets are of a coarse resolution, which makes it impractical to study finer chromatin features such as Topologically Associating Domains (TADs) and chromatin loops. Multiple deep learning-based methods have recently been proposed to increase the resolution of these datasets by imputing Hi-C reads (typically called upscaling). However, the existing works evaluate these methods on either synthetically downsampled datasets, or a small subset of experimentally generated sparse Hi-C datasets, making it hard to establish their generalizability in the real-world use case. We present our framework-Hi-CY-that compares existing Hi-C resolution upscaling methods on seven experimentally generated low-resolution Hi-C datasets belonging to various levels of read sparsities originating from three cell lines on a comprehensive set of evaluation metrics. Hi-CY also includes four downstream analysis tasks, such as TAD and chromatin loops recall, to provide a thorough report on the generalizability of these methods. We observe that existing deep learning methods fail to generalize to experimentally generated sparse Hi-C datasets, showing a performance reduction of up to 57%. As a potential solution, we find that retraining deep learning-based methods with experimentally generated Hi-C datasets improves performance by up to 31%. More importantly, Hi-CY shows that even with retraining, the existing deep learning-based methods struggle to recover biological features such as chromatin loops and TADs when provided with sparse Hi-C datasets. Our study, through the Hi-CY framework, highlights the need for rigorous evaluation in the future. We identify specific avenues for improvements in the current deep learning-based Hi-C upscaling methods, including but not limited to using experimentally generated datasets for training.}, }
@article {pmid38244545, year = {2024}, author = {Wahl, N and Espeso-Gil, S and Chietera, P and Nagel, A and Laighneach, A and Morris, DW and Rajarajan, P and Akbarian, S and Dechant, G and Apostolova, G}, title = {SATB2 organizes the 3D genome architecture of cognition in cortical neurons.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2023.12.024}, pmid = {38244545}, issn = {1097-4164}, abstract = {The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.}, }
@article {pmid38238628, year = {2024}, author = {Hung, TC and Kingsley, DM and Boettiger, AN}, title = {Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {38238628}, issn = {1546-1718}, support = {DP2GM132935A//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01DK127419//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.}, }
@article {pmid38218905, year = {2024}, author = {Hua, D and Gu, M and Zhang, X and Du, Y and Xie, H and Qi, L and Du, X and Bai, Z and Zhu, X and Tian, D}, title = {DiffDomain enables identification of structurally reorganized topologically associating domains.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {502}, pmid = {38218905}, issn = {2041-1723}, support = {2022A1515010043//Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province)/ ; KCXFZ20211020172545006//Shenzhen Science and Technology Innovation Commission/ ; 12171198//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20210101147JC//Department of Science and Technology of Jilin Province (Jilin Province Science and Technology Department)/ ; }, abstract = {Topologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the early stages of development. Here, we present DiffDomain, an algorithm leveraging high-dimensional random matrix theory to identify structurally reorganized TADs using high-throughput chromosome conformation capture (Hi-C) contact maps. Method comparison using multiple real Hi-C datasets reveals that DiffDomain outperforms alternative methods for false positive rates, true positive rates, and identifying a new subtype of reorganized TADs. Applying DiffDomain to Hi-C data from different cell types and disease states demonstrates its biological relevance. Identified reorganized TADs are associated with structural variations and epigenomic changes such as changes in CTCF binding sites. By applying to a single-cell Hi-C data from mouse neuronal development, DiffDomain can identify reorganized TADs between cell types with reasonable reproducibility using pseudo-bulk Hi-C data from as few as 100 cells per condition. Moreover, DiffDomain reveals differential cell-to-population variability and heterogeneous cell-to-cell variability in TADs. Therefore, DiffDomain is a statistically sound method for better comparative analysis of TADs using both Hi-C and single-cell Hi-C data.}, }
@article {pmid38213897, year = {2023}, author = {Rosen, J and Lee, L and Abnousi, A and Chen, J and Wen, J and Hu, M and Li, Y}, title = {HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {931-939}, pmid = {38213897}, issn = {2001-0370}, abstract = {High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization. Most recently, Hi-C-derived enrichment-based technologies, including HiChIP and PLAC-seq, offer attractive alternatives due to their high signal-to-noise ratio and low cost. While a series of computational tools have been developed for Hi-C data, methods tailored for HiChIP and PLAC-seq data are still under development. Here we present HPTAD, a computational method to identify topologically associating domains (TADs) from HiChIP and PLAC-seq data. We performed comprehensive benchmark analysis to demonstrate its superior performance over existing TAD callers designed for Hi-C data. HPTAD is freely available at https://github.com/yunliUNC/HPTAD.}, }
@article {pmid38206813, year = {2024}, author = {Zhang, M and Huang, H and Li, J and Wu, Q}, title = {ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry.}, journal = {Cell reports}, volume = {43}, number = {1}, pages = {113663}, doi = {10.1016/j.celrep.2023.113663}, pmid = {38206813}, issn = {2211-1247}, abstract = {The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.}, }
@article {pmid37748139, year = {2024}, author = {Tang, B and Wang, X and He, H and Chen, R and Qiao, G and Yang, Y and Xu, Z and Wang, L and Dong, Q and Yu, J and Zhang, MQ and Shi, M and Wang, J}, title = {Aging-disturbed FUS phase transition impairs hematopoietic stem cells by altering chromatin structure.}, journal = {Blood}, volume = {143}, number = {2}, pages = {124-138}, doi = {10.1182/blood.2023020539}, pmid = {37748139}, issn = {1528-0020}, abstract = {Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity. The molecular mechanisms behind this phenomenon are not fully understood. Here, we observed that the expression of FUS is increased in aged HSCs, and enforced FUS recapitulates the phenotype of aged HSCs through arginine-glycine-glycine-mediated aberrant FUS phase transition. By using Fus-gfp mice, we observed that FUShigh HSCs exhibit compromised FUS mobility and resemble aged HSCs both functionally and transcriptionally. The percentage of FUShigh HSCs is increased upon physiological aging and replication stress, and FUSlow HSCs of aged mice exhibit youthful function. Mechanistically, FUShigh HSCs exhibit a different global chromatin organization compared with FUSlow HSCs, which is observed in aged HSCs. Many topologically associating domains (TADs) are merged in aged HSCs because of the compromised binding of CCCTC-binding factor with chromatin, which is invoked by aberrant FUS condensates. It is notable that the transcriptional alteration between FUShigh and FUSlow HSCs originates from the merged TADs and is enriched in HSC aging-related genes. Collectively, this study reveals for the first time that aberrant FUS mobility promotes HSC aging by altering chromatin structure.}, }
@article {pmid38168424, year = {2023}, author = {Li, Y and Xiao, P and Boadu, F and Goldkamp, AK and Nirgude, S and Cheng, J and Hagen, DE and Kalish, JM and Rivera, RM}, title = {The counterpart congenital overgrowth syndromes Beckwith-Wiedemann Syndrome in human and large offspring syndrome in bovine involve alterations in DNA methylation, transcription, and chromatin configuration.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.14.23299981}, pmid = {38168424}, abstract = {Beckwith-Wiedemann Syndrome (BWS, OMIM #130650) is a congenital epigenetic disorder in humans which affects approximately 1 in 10,340 children. The incidence is likely an underestimation as the condition is usually recognized based on observable phenotypes at birth. BWS children have up to a 28% risk of developing tumors and currently, only 80% of patients can be corroborated molecularly (epimutations/variants). It is unknown how the subtypes of this condition are molecularly similar/dissimilar globally, therefore there is a need to deeply characterize the syndrome at the molecular level. Here we characterize the methylome, transcriptome and chromatin configuration of 18 BWS individuals together with the animal model of the condition, the bovine large offspring syndrome (LOS). Sex specific comparisons are performed for a subset of the BWS patients and LOS. Given that this epigenetic overgrowth syndrome has been characterized as a loss-of-imprinting condition, parental allele-specific comparisons were performed using the bovine animal model. In general, the differentially methylated regions (DMRs) detected in BWS and LOS showed significant enrichment for CTCF binding sites. Altered chromosome compartments in BWS and LOS were positively correlated with gene expression changes, and the promoters of differentially expressed genes showed significant enrichment for DMRs, differential topologically associating domains, and differential A/B compartments in some comparisons of BWS subtypes and LOS. We show shared regions of dysregulation between BWS and LOS, including several HOX gene clusters, and also demonstrate that altered DNA methylation differs between the clinically epigenetically identified BWS patients and those identified as having DNA variants (i.e. CDKN1C microdeletion). Lastly, we highlight additional genes and genomic regions that have the potential to serve as targets for biomarker development to improve current molecular methodologies. In summary, our results suggest that genome-wide alternation of chromosome architecture, which is partially caused by DNA methylation changes, also contribute to the development of BWS and LOS.}, }
@article {pmid38167349, year = {2024}, author = {Sun, L and Zhou, J and Xu, X and Liu, Y and Ma, N and Liu, Y and Nie, W and Zou, L and Deng, XW and He, H}, title = {Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {35}, pmid = {38167349}, issn = {2041-1723}, abstract = {Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.}, }
@article {pmid38134876, year = {2023}, author = {Malachowski, T and Chandradoss, KR and Boya, R and Zhou, L and Cook, AL and Su, C and Pham, K and Haws, SA and Kim, JH and Ryu, HS and Ge, C and Luppino, JM and Nguyen, SC and Titus, KR and Gong, W and Wallace, O and Joyce, EF and Wu, H and Rojas, LA and Phillips-Cremins, JE}, title = {Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.}, journal = {Cell}, volume = {186}, number = {26}, pages = {5840-5858.e36}, doi = {10.1016/j.cell.2023.11.019}, pmid = {38134876}, issn = {1097-4172}, abstract = {Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.}, }
@article {pmid38129077, year = {2023}, author = {Jessberger, G and Várnai, C and Stocsits, RR and Tang, W and Stary, G and Peters, JM}, title = {Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.277865.123}, pmid = {38129077}, issn = {1549-5469}, abstract = {Paternal genomes are compacted during spermiogenesis and decompacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in Xenopus egg extracts. In pronuclei, chromatin compartmentalization increases, but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, and cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.}, }
@article {pmid38102116, year = {2023}, author = {Xiao, M and Kondo, S and Nomura, M and Kato, S and Nishimura, K and Zang, W and Zhang, Y and Akashi, T and Viny, A and Shigehiro, T and Ikawa, T and Yamazaki, H and Fukumoto, M and Tanaka, A and Hayashi, Y and Koike, Y and Aoyama, Y and Ito, H and Nishikawa, H and Kitamura, T and Kanai, A and Yokoyama, A and Fujiwara, T and Goyama, S and Noguchi, H and Lee, SC and Toyoda, A and Hinohara, K and Abdel-Wahab, O and Inoue, D}, title = {BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8372}, pmid = {38102116}, issn = {2041-1723}, support = {21ck0106697h0001//Japan Agency for Medical Research and Development (AMED)/ ; JP20H00537//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20H03717//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF (ncBAF). While cBAF and PBAF regulate fates of multiple cell types, roles for ncBAF in hematopoietic stem cells (HSCs) have not been investigated. Motivated by recent discovery of disrupted expression of BRD9, an essential component of ncBAF, in multiple cancers, including clonal hematopoietic disorders, we evaluate here the role of BRD9 in normal and malignant HSCs. BRD9 loss enhances chromatin accessibility, promoting myeloid lineage skewing while impairing B cell development. BRD9 significantly colocalizes with CTCF, whose chromatin recruitment is augmented by BRD9 loss, leading to altered chromatin state and expression of myeloid-related genes within intact topologically associating domains. These data uncover ncBAF as critical for cell fate specification in HSCs via three-dimensional regulation of gene expression and illuminate roles for ncBAF in normal and malignant hematopoiesis.}, }
@article {pmid38092881, year = {2023}, author = {Fok, ET and Moorlag, SJCFM and Negishi, Y and Groh, LA and Dos Santos, JC and Gräwe, C and Monge, VV and Craenmehr, DDD and van Roosmalen, M and da Cunha Jolvino, DP and Migliorini, LB and Neto, AS and Severino, P and Vermeulen, M and Joosten, LAB and Netea, MG and Fanucchi, S and Mhlanga, MM}, title = {A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {38092881}, issn = {1546-1718}, abstract = {Inflammation is characterized by a biphasic cycle consisting initially of a proinflammatory phase that is subsequently resolved by anti-inflammatory processes. Interleukin-1β (IL-1β) is a master regulator of proinflammation and is encoded within the same topologically associating domain (TAD) as IL-37, which is an anti-inflammatory cytokine that opposes the function of IL-1β. Within this TAD, we identified a long noncoding RNA called AMANZI, which negatively regulates IL-1β expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced proinflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL-1β and IL-37, thereby regulating two functionally opposed states of inflammation from within a single TAD.}, }
@article {pmid38084924, year = {2023}, author = {Balasubramanian, D and Borges Pinto, P and Grasso, A and Vincent, S and Tarayre, H and Lajoignie, D and Ghavi-Helm, Y}, title = {Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad1183}, pmid = {38084924}, issn = {1362-4962}, support = {Enhancer3D 759708/ERC_/European Research Council/International ; }, abstract = {Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.}, }
@article {pmid38076897, year = {2023}, author = {Rossini, R and Oshaghi, M and Nekrasov, M and Bellanger, A and Domaschenz, R and Dijkwel, Y and Abdelhalim, M and Collas, P and Tremethick, D and Paulsen, J}, title = {Multi-level 3D genome organization deteriorates during breast cancer progression.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.26.568711}, pmid = {38076897}, abstract = {Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.}, }
@article {pmid38061928, year = {2023}, author = {Long, Y and Wendel, JF and Zhang, X and Wang, M}, title = {Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2023.11.009}, pmid = {38061928}, issn = {1878-4372}, abstract = {Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.}, }
@article {pmid38049665, year = {2023}, author = {Leeman-Neill, RJ and Song, D and Bizarro, J and Wacheul, L and Rothschild, G and Singh, S and Yang, Y and Sarode, AY and Gollapalli, K and Wu, L and Zhang, W and Chen, Y and Lauring, MC and Whisenant, DE and Bhavsar, S and Lim, J and Swerdlow, SH and Bhagat, G and Zhao, Q and Berchowitz, LE and Lafontaine, DLJ and Wang, J and Basu, U}, title = {Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {38049665}, issn = {1546-1718}, support = {R01AI134988//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; RO1AI143897//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI099195//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; DOD W81XWH-18-1-0394//U.S. Department of Defense (United States Department of Defense)/ ; GM124633//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32CA265828//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Whole-genome sequencing of longitudinal tumor pairs representing transformation of follicular lymphoma to high-grade B cell lymphoma with MYC and BCL2 rearrangements (double-hit lymphoma) identified coding and noncoding genomic alterations acquired during lymphoma progression. Many of these transformation-associated alterations recurrently and focally occur at topologically associating domain resident regulatory DNA elements, including H3K4me3 promoter marks located within H3K27ac super-enhancer clusters in B cell non-Hodgkin lymphoma. One region found to undergo recurrent alteration upon transformation overlaps a super-enhancer affecting the expression of the PAX5/ZCCHC7 gene pair. ZCCHC7 encodes a subunit of the Trf4/5-Air1/2-Mtr4 polyadenylation-like complex and demonstrated copy number gain, chromosomal translocation and enhancer retargeting-mediated transcriptional upregulation upon lymphoma transformation. Consequently, lymphoma cells demonstrate nucleolar dysregulation via altered noncoding 5.8S ribosomal RNA processing. We find that a noncoding mutation acquired during lymphoma progression affects noncoding rRNA processing, thereby rewiring protein synthesis leading to oncogenic changes in the lymphoma proteome.}, }
@article {pmid38017545, year = {2023}, author = {Llinàs-Arias, P and Ensenyat-Mendez, M and Íñiguez-Muñoz, S and Orozco, JIJ and Valdez, B and Salomon, MP and Matsuba, C and Solivellas-Pieras, M and Bedoya-López, AF and Sesé, B and Mezger, A and Ormestad, M and Unzueta, F and Strand, SH and Boiko, AD and Hwang, ES and Cortés, J and DiNome, ML and Esteller, M and Lupien, M and Marzese, DM}, title = {Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors.}, journal = {Molecular cancer}, volume = {22}, number = {1}, pages = {190}, pmid = {38017545}, issn = {1476-4598}, support = {CD22/00026//Instituto de Salud Carlos III/ ; CPII22/00004//Instituto de Salud Carlos III/ ; IMP21/10//IDISBA - Impetus Call/ ; Margalida Comas//Govern de les Illes Balears/ ; }, abstract = {BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive subtype that exhibits a high incidence of distant metastases and lacks targeted therapeutic options. Here we explored how the epigenome contributes to matrix metalloprotease (MMP) dysregulation impacting tumor invasion, which is the first step of the metastatic process.<br><br>METHODS: We combined RNA expression and chromatin interaction data to identify insulator elements potentially associated with MMP gene expression and invasion. We employed CRISPR/Cas9 to disrupt the CCCTC-Binding Factor (CTCF) binding site on an insulator element downstream of the MMP8 gene (IE8) in two TNBC cellular models. We characterized these models by combining Hi-C, ATAC-seq, and RNA-seq with functional experiments to determine invasive ability. The potential of our findings to predict the progression of ductal carcinoma in situ (DCIS), was tested in data from clinical specimens.<br><br>RESULTS: We explored the clinical relevance of an insulator element located within the Chr11q22.2 locus, downstream of the MMP8 gene (IE8). This regulatory element resulted in a topologically associating domain (TAD) boundary that isolated nine MMP genes into two anti-correlated expression clusters. This expression pattern was associated with worse relapse-free (HR&#x2009;=&#x2009;1.57 [1.06&#x2009;-&#x2009;2.33]; p&#x2009;=&#x2009;0.023) and overall (HR&#x2009;=&#x2009;2.65 [1.31&#x2009;-&#x2009;5.37], p&#x2009;=&#x2009;0.005) survival of TNBC patients. After CRISPR/Cas9-mediated disruption of IE8, cancer cells showed a switch in the MMP expression signature, specifically downregulating the pro-invasive MMP1 gene and upregulating the antitumorigenic MMP8 gene, resulting in reduced invasive ability and collagen degradation. We observed that the MMP expression pattern predicts DCIS that eventually progresses into invasive ductal carcinomas (AUC&#x2009;=&#x2009;0.77, p&#x2009;<&#x2009;0.01).<br><br>CONCLUSION: Our study demonstrates how the activation of an IE near the MMP8 gene determines the regional transcriptional regulation of MMP genes with opposing functional activity, ultimately influencing the invasive properties of aggressive forms of breast cancer.}, }
@article {pmid38017297, year = {2023}, author = {Jehangir, M and Ahmad, SF and Singchat, W and Panthum, T and Thong, T and Aramsirirujiwet, P and Lisachov, A and Muangmai, N and Han, K and Koga, A and Duengkae, P and Srikulnath, K}, title = {Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {31}, number = {4}, pages = {34}, pmid = {38017297}, issn = {1573-6849}, support = {P-20-52605//National Science and Technology Development Agency (NSTDA)/ ; }, abstract = {Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.}, }
@article {pmid38014261, year = {2023}, author = {Zhao, H and Lin, Y and Lin, E and Liu, F and Shu, L and Jing, D and Wang, B and Wang, M and Shan, F and Zhang, L and Lam, JC and Midla, SC and Giardine, BM and Keller, CA and Hardison, RC and Blobel, GA and Zhang, H}, title = {Genome folding principles revealed in condensin-depleted mitotic chromosomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.09.566494}, pmid = {38014261}, abstract = {During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co- depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1Π and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensin-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.}, }
@article {pmid38013620, year = {2023}, author = {Singh, AK and Walavalkar, K and Tavernari, D and Ciriello, G and Notani, D and Sabarinathan, R}, title = {Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers.}, journal = {Molecular oncology}, volume = {}, number = {}, pages = {}, doi = {10.1002/1878-0261.13559}, pmid = {38013620}, issn = {1878-0261}, abstract = {HPV infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome-wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and TADs. HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long-range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi-C and 4C-seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~500kb apart), leading to allele-specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.}, }
@article {pmid37976174, year = {2023}, author = {Siqueira, E and Kim, BH and Reser, L and Chow, R and Delaney, K and Esteller, M and Ross, MM and Shabanowitz, J and Hunt, DF and Guil, S and Ausiö, J}, title = {Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells.}, journal = {Epigenetics}, volume = {18}, number = {1}, pages = {2276425}, doi = {10.1080/15592294.2023.2276425}, pmid = {37976174}, issn = {1559-2308}, abstract = {An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.}, }
@article {pmid37963468, year = {2023}, author = {He, J and Yan, A and Chen, B and Huang, J and Kee, K}, title = {3D genome remodeling and homologous pairing during meiotic prophase of mouse oogenesis and spermatogenesis.}, journal = {Developmental cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.devcel.2023.10.009}, pmid = {37963468}, issn = {1878-1551}, abstract = {During meiosis, the chromatin and transcriptome undergo prominent switches. Although recent studies have explored the genome reorganization during spermatogenesis, the chromatin remodeling in oogenesis and characteristics of homologous pairing remain largely elusive. We comprehensively compared chromatin structures and transcriptomes at successive substages of meiotic prophase in both female and male mice using low-input high-through chromosome conformation capture (Hi-C) and RNA sequencing (RNA-seq). Compartments and topologically associating domains (TADs) gradually disappeared and slowly recovered in both sexes. We found that homologs adopted different sex-conserved pairing strategies prior to and after the leptotene-to-zygotene transition, changing from long interspersed nuclear element (LINE)-enriched compartments B to short interspersed nuclear element (SINE)-enriched compartments A. We complemented marker genes and predicted the sex-specific meiotic sterile genes for each substage. This study provides valuable insights into the similarities and distinctions between sexes in chromosome architecture, homologous pairing, and transcriptome during meiotic prophase of both oogenesis and spermatogenesis.}, }
@article {pmid37922325, year = {2023}, author = {Zhu, Y and Rosenfeld, MG and Suh, Y}, title = {Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {45}, pages = {e2313285120}, doi = {10.1073/pnas.2313285120}, pmid = {37922325}, issn = {1091-6490}, abstract = {The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here, we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize multirestriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantitatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gauge regulatory interaction networks, identifying >20-fold more enhancer:promoter (E:P) loops than in situ Hi-C. In addition to vastly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically associating domain boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high-resolution interactome maps required for characterizing fine-gauge regulatory chromatin interactions in analysis of development, homeostasis, and disease.}, }
@article {pmid37907089, year = {2023}, author = {Chu, X and Wang, J}, title = {Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.}, journal = {Open biology}, volume = {13}, number = {11}, pages = {230175}, doi = {10.1098/rsob.230175}, pmid = {37907089}, issn = {2046-2441}, abstract = {Cell cycle is known to be regulated by the underlying gene network. Chromosomes, which serve as the scaffold for gene expressions, undergo significant structural reorganizations during mitosis. Understanding the mechanism of the cell cycle from the chromosome structural perspective remains a grand challenge. In this study, we applied an integrated theoretical approach to investigate large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition. We observed that the chromosome structural expansion and adaptation of the structural asphericity do not occur synchronously and attributed this behaviour to the unique unloading sequence of the two types of condensins. Furthermore, we observed that the coherent motions between the chromosomal loci are primarily enhanced within the topologically associating domains (TADs) as cells progress to the G1 phase, suggesting that TADs can be considered as both structural and dynamical units for organizing the three-dimensional chromosome. Our analysis also reveals that the quantified pathways of chromosome structural reorganization during the mitosis-to-G1 phase transition exhibit high stochasticity at the single-cell level and show nonlinear behaviours in changing TADs and contacts formed at the long-range regions. Our findings offer valuable insights into large-scale chromosome structural dynamics after mitosis.}, }
@article {pmid37898735, year = {2023}, author = {Gao, GF and Li, P and Leonard, WJ}, title = {Co-localization of clusters of TCR-regulated genes with TAD rearrangements.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {650}, pmid = {37898735}, issn = {1471-2164}, support = {Z99HL999999/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Gene expression has long been known to be influenced by the relative proximity of DNA regulatory elements. Topologically associating domains (TADs) are self-interacting genomic regions involved in regulating gene expression by controlling the proximity of these elements. Prior studies of TADs and their biological roles have revealed correlations between TAD changes and cellular differentiation. Here, we used Hi-C and RNA-seq data to correlate TCR-induced changes in TAD structure and gene expression in human CD4[+] T cells.<br><br>RESULTS: We developed a pipeline, Differentially Expressed Gene Enrichment Finder (DEGEF), that identifies regions of differentially expressed gene enrichment. Using DEGEF, we found that TCR-regulated genes cluster non-uniformly across the genome and that these clusters preferentially localized in regions of TAD rearrangement. Interestingly, clusters of upregulated genes preferentially formed new Hi-C contacts compared to downregulated clusters, suggesting that TCR-activated CD4[+] T cells may regulate genes by changing stimulatory contacts rather than inhibitory contacts.<br><br>CONCLUSIONS: Our observations support a significant relationship between TAD rearrangements and changes in local gene expression. These findings indicate potentially important roles for TAD rearrangements in shaping their local regulatory environments and thus driving differential expression of nearby genes during CD4[+] T cell activation. Moreover, they provide new insights into global mechanisms that regulate gene expression.}, }
@article {pmid37889077, year = {2023}, author = {Song, C and Zhang, G and Mu, X and Feng, C and Zhang, Q and Song, S and Zhang, Y and Yin, M and Zhang, H and Tang, H and Li, C}, title = {eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad925}, pmid = {37889077}, issn = {1362-4962}, support = {62171166//National Natural Science Foundation of China/ ; 20210002-1005 USCAT-2021-01//Affiliated Hospital of University of South China for Advanced Talents/ ; 2019M661311//China Postdoctoral Science Foundation/ ; 2023JJ30547//Natural Science Foundation of Hunan Province/ ; 20201920//Scientific Research Fund Project of Hunan Provincial Health Commission/ ; 2020SK4008//Construction of Innovative Provinces in Hunan/ ; 20214310NHYCG03//University of South China/ ; }, abstract = {Enhancer RNAs (eRNAs) transcribed from distal active enhancers serve as key regulators in gene transcriptional regulation. The accumulation of eRNAs from multiple sequencing assays has led to an urgent need to comprehensively collect and process these data to illustrate the regulatory landscape of eRNAs. To address this need, we developed the eRNAbase (http://bio.liclab.net/eRNAbase/index.php) to store the massive available resources of human and mouse eRNAs and provide comprehensive annotation and analyses for eRNAs. The current version of eRNAbase cataloged 10 399 928 eRNAs from 1012 samples, including 858 human samples and 154 mouse samples. These eRNAs were first identified and uniformly processed from 14 eRNA-related experiment types manually collected from GEO/SRA and ENCODE. Importantly, the eRNAbase provides detailed and abundant (epi)genetic annotations in eRNA regions, such as super enhancers, enhancers, common single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, CRISPR/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, methylation sites, chromatin interactions regions, topologically associating domains and RNA spatial interactions. Furthermore, the eRNAbase provides users with three novel analyses including eRNA-mediated pathway regulatory analysis, eRNA-based variation interpretation analysis and eRNA-mediated TF-target gene analysis. Hence, eRNAbase is a powerful platform to query, browse and visualize regulatory cues associated with eRNAs.}, }
@article {pmid37886958, year = {2023}, author = {Fischer, EF and Pilarczyk, G and Hausmann, M}, title = {Microscopic Analysis of Heterochromatin, Euchromatin and Cohesin in Cancer Cell Models and under Anti-Cancer Treatment.}, journal = {Current issues in molecular biology}, volume = {45}, number = {10}, pages = {8152-8172}, doi = {10.3390/cimb45100515}, pmid = {37886958}, issn = {1467-3045}, support = {02 NUK 058A//Federal Ministry of Education and Research/ ; }, abstract = {The spatial organization of euchromatin (EC) and heterochromatin (HC) appears as a cell-type specific network, which seems to have an impact on gene regulation and cell fate. The spatial organization of cohesin should thus also be characteristic for a cell type since it is involved in a TAD (topologically associating domain) formation, and thus in gene regulation or DNA repair processes. Based on the previous hypotheses and results on the general importance of heterochromatin organization on genome functions in particular, the configurations of these organizational units (EC represented by H3K4me3-positive regions, HC represented by H3K9me3-positive regions, cohesins) are investigated in the cell nuclei of different cancer and non-cancerous cell types and under different anti-cancer treatments. Confocal microscopic images of the model cell systems were used and analyzed using analytical processes of quantification created in Fiji, an imaging tool box well established in different fields of science. Human fibroblasts, breast cancer and glioblastoma cells as well as murine embryonal terato-carcinoma cells were used as these cell models and compared according to the different parameters of spatial arrangements. In addition, proliferating, quiescent and from the quiescent state reactivated fibroblasts were analyzed. In some selected cases, the cells were treated with X-rays or azacitidine. Heterogeneous results were obtained by the analyses of the configurations of the three different organizational units: granulation and a loss of H3K4me3-positive regions (EC) occurred after irradiation with 4 Gy or azacitidine treatment. While fibroblasts responded to irradiation with an increase in cohesin and granulation, in breast cancer cells, it resulted in decreases in cohesin and changes in granulation. H3K9me3-positive regions (HC) in fibroblasts experienced increased granulation, whereas in breast cancer cells, the amount of such regions increased. After azacitidine treatment, murine stem cells showed losses of cohesin and granulation and an increase in the granulation of H3K9me3-positive regions. Fibroblasts that were irradiated with 2 Gy only showed irregularities in structural amounts and granulation. Quiescent fibroblasts contained less euchromatin-related H3K4me3-positive signals and cohesin levels as well as higher heterochromatin-related H3K9me3-positive signals than non-quiescent ones. In general, fibroblasts responded more intensely to X-ray irradiation than breast cancer cells. The results indicate the usefulness of model cell systems and show that, in general, characteristic differences initially existing in chromatin and cohesin organizations result in specific responses to anti-cancer treatment.}, }
@article {pmid37884483, year = {2023}, author = {Lee, H and Seo, PJ}, title = {Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis.}, journal = {Nucleic acids research}, volume = {51}, number = {19}, pages = {10261-10277}, doi = {10.1093/nar/gkad710}, pmid = {37884483}, issn = {1362-4962}, support = {NRF-2022R1A2B5B02001266//Basic Science Research/ ; NRF-2022R1A4A3024451//Basic Research Laboratory/ ; //National Research Foundation of Korea/ ; }, abstract = {Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.}, }
@article {pmid37882064, year = {2023}, author = {Sreenivas, P and Wang, L and Wang, M and Challa, A and Modi, P and Hensch, NR and Gryder, B and Chou, HC and Zhao, XR and Sunkel, B and Moreno-Campos, R and Khan, J and Stanton, BZ and Ignatius, MS}, title = {A SNAI2/CTCF Interaction is Required for NOTCH1 Expression in Rhabdomyosarcoma.}, journal = {Molecular and cellular biology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/10985549.2023.2256640}, pmid = {37882064}, issn = {1098-5549}, abstract = {Rhabdomyosarcoma (RMS) is a pediatric malignancy of the muscle with characteristics of cells blocked in differentiation. NOTCH1 is an oncogene that promotes self-renewal and blocks differentiation in the fusion negative-RMS sub-type. However, how NOTCH1 expression is transcriptionally maintained in tumors is unknown. Analyses of SNAI2 and CTCF chromatin binding and HiC analyses revealed a conserved SNAI2/CTCF overlapping peak downstream of the NOTCH1 locus marking a sub-topologically associating domain (TAD) boundary. Deletion of the SNAI2-CTCF peak showed that it is essential for NOTCH1 expression and viability of FN-RMS cells. Reintroducing constitutively activated NOTCH1-ΔE in cells with the SNAI2-CTCF peak deleted restored cell-viability. Ablation of SNAI2 using CRISPR/Cas9 reagents resulted in the loss of majority of RD and SMS-CTR FN-RMS cells. However, the few surviving clones that repopulate cultures have recovered NOTCH1. Cells that re-establish NOTCH1 expression after SNAI2 ablation are unable to differentiate robustly as SNAI2 shRNA knockdown cells; yet, SNAI2-ablated cells continued to be exquisitely sensitive to ionizing radiation. Thus, we have uncovered a novel mechanism by which SNAI2 and CTCF maintenance of a sub-TAD boundary promotes rather than represses NOTCH1 expression. Further, we demonstrate that SNAI2 suppression of apoptosis post-radiation is independent of SNAI2/NOTCH1 effects on self-renewal and differentiation.}, }
@article {pmid37865700, year = {2023}, author = {Messina, O and Raynal, F and Gurgo, J and Fiche, JB and Pancaldi, V and Nollmann, M}, title = {3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6678}, pmid = {37865700}, issn = {2041-1723}, support = {episcope//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {In mammals, insulators contribute to the regulation of loop extrusion to organize chromatin into topologically associating domains. In Drosophila the role of insulators in 3D genome organization is, however, under current debate. Here, we addressed this question by combining bioinformatics analysis and multiplexed chromatin imaging. We describe a class of Drosophila insulators enriched at regions forming preferential chromatin interactions genome-wide. Notably, most of these 3D interactions do not involve TAD borders. Multiplexed imaging shows that these interactions occur infrequently, and only rarely involve multiple genomic regions coalescing together in space in single cells. Finally, we show that non-border preferential 3D interactions enriched in this class of insulators are present before TADs and transcription during Drosophila development. Our results are inconsistent with insulators forming stable hubs in single cells, and instead suggest that they fine-tune existing 3D chromatin interactions, providing an additional regulatory layer for transcriptional regulation.}, }
@article {pmid37853125, year = {2023}, author = {Arnould, C and Rocher, V and Saur, F and Bader, AS and Muzzopappa, F and Collins, S and Lesage, E and Le Bozec, B and Puget, N and Clouaire, T and Mangeat, T and Mourad, R and Ahituv, N and Noordermeer, D and Erdel, F and Bushell, M and Marnef, A and Legube, G}, title = {Chromatin compartmentalization regulates the response to DNA damage.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37853125}, issn = {1476-4687}, abstract = {The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated[1,2], the contribution of chromosome folding to these processes remains unclear[3]. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1. This compartment forms by a mechanism that is consistent with polymer-polymer phase separation rather than liquid-liquid phase separation. The D compartment arises mostly in G1 phase, is independent of cohesin and is enhanced after pharmacological inhibition of DNA-dependent protein kinase (DNA-PK) or R-loop accumulation. Importantly, R-loop-enriched DNA-damage-responsive genes physically localize to the D compartment, and this contributes to their optimal activation, providing a function for DSB clustering in the DNA damage response. However, DSB-induced chromosome reorganization comes at the expense of an increased rate of translocations, also observed in cancer genomes. Overall, we characterize how DSB-induced compartmentalization orchestrates the DNA damage response and highlight the critical impact of chromosome architecture in genomic instability.}, }
@article {pmid37845234, year = {2023}, author = {Calandrelli, R and Wen, X and Charles Richard, JL and Luo, Z and Nguyen, TC and Chen, CJ and Qi, Z and Xue, S and Chen, W and Yan, Z and Wu, W and Zaleta-Rivera, K and Hu, R and Yu, M and Wang, Y and Li, W and Ma, J and Ren, B and Zhong, S}, title = {Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6519}, pmid = {37845234}, issn = {2041-1723}, support = {DP1DK126138//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U54DK107977//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01GM138852//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM136922//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01HD107206//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; DP1HD087990//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; U01CA200147//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; UM1HG011593//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; UM1HG011585//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U01HL156059//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; }, abstract = {The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.}, }
@article {pmid37811140, year = {2023}, author = {Bonaglia, MC and Salvo, E and Sironi, M and Bertuzzo, S and Errichiello, E and Mattina, T and Zuffardi, O}, title = {Case Report: Decrypting an interchromosomal insertion associated with Marfan's syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1244983}, pmid = {37811140}, issn = {1664-8021}, abstract = {Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.}, }
@article {pmid37790381, year = {2023}, author = {Hristov, BH and Noble, WS and Bertero, A}, title = {Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.21.558852}, pmid = {37790381}, abstract = {Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans -contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes co-regulated by the same trans -acting element (i.e., a transcription or splicing factor) co-localize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same transcription factor interact with one another in trans , especially those bound by transcription factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA binding proteins correlates with trans interaction of the encoding loci. These findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.}, }
@article {pmid37787451, year = {2023}, author = {Parodi, L and Comeau, ME and Georgakis, MK and Mayerhofer, E and Chung, J and Falcone, GJ and Malik, R and Demel, SL and Worrall, BB and Koch, S and Testai, FD and Kittner, SJ and McCauley, JL and Hall, CE and Mayson, DJ and Elkind, MS and James, ML and Woo, D and Rosand, J and Langefeld, CD and Anderson, CD}, title = {Deep resequencing of the 1q22 locus in non-lobar intracerebral hemorrhage.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.26814}, pmid = {37787451}, issn = {1531-8249}, abstract = {OBJECTIVE: Genome-wide association studies have identified 1q22 as a susceptibility locus for cerebral small vessel diseases (CSVDs), including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study we performed targeted high-depth sequencing of 1q22 in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown.<br><br>METHODS: 95,000 base pairs spanning 1q22, including SEMA4A, SLC25A44 and PMF1/PMF1-BGLAP were sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and RIFT analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, ChIP-Seq and ChIA-PET databases. Multivariable Mendelian randomization (MVMR) assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at 1q22 could be causally related to ICH risk.<br><br>RESULTS: Common and rare variant analyses prioritized variants in SEMA4A 5'-UTR and PMF1 intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that 1q22 is spatially organized in a single chromatin loop and that the genes therein belong to the same Topologically Associating Domain. ChIP-Seq and ChIA-PET data analysis highlighted the presence of long-range interactions between the SEMA4A-promoter and PMF1-enhancer regions prioritized by association testing. MVMR analyses demonstrated that PMF1 overexpression could be causally related to non-lobar ICH risk.<br><br>INTERPRETATION: Altered promoter-enhancer interactions leading to PMF1 overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non-lobar ICH risk at 1q22, offering a potential new target for prevention of ICH and CSVD. This article is protected by copyright. All rights reserved.}, }
@article {pmid37774974, year = {2023}, author = {Kaur, P and Lu, X and Xu, Q and Irvin, EM and Pappas, C and Zhang, H and Finkelstein, IJ and Shi, Z and Tao, YJ and Yu, H and Wang, H}, title = {High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {105296}, doi = {10.1016/j.jbc.2023.105296}, pmid = {37774974}, issn = {1083-351X}, abstract = {3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains (TADs) and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. In this study, high-speed atomic force microscopy (HS-AFM) imaging reveals that cohesin-NIPBL captures DNA through arm extension, assisted by feet (shorter protrusions), and followed by transfer of DNA to its lower compartment (SMC heads, RAD21, SA1 and NIPBL). While binding at the lower compartment, arm extension leads to the capture of a second DNA segment and the initiation of a DNA loop that is independent of ATP hydrolysis. The feet are likely contributed by the C-terminal domains of SA1 and NIPBL and can transiently bind to DNA to facilitate the loading of the cohesin complex onto DNA. Furthermore, HS-AFM imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results advance our understanding of cohesin by establishing direct experimental evidence for a multi-step DNA binding mechanism mediated by dynamic protein conformational changes.}, }
@article {pmid37762117, year = {2023}, author = {Yang, J and Zhu, X and Wang, R and Li, M and Tang, Q}, title = {Revisiting Assessment of Computational Methods for Hi-C Data Analysis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, doi = {10.3390/ijms241813814}, pmid = {37762117}, issn = {1422-0067}, support = {2021ZDZX0008//Qianzi Tang/ ; }, abstract = {The performances of algorithms for Hi-C data preprocessing, the identification of topologically associating domains, and the detection of chromatin interactions and promoter-enhancer interactions have been mostly evaluated using semi-quantitative or synthetic data approaches, without utilizing the most recent methods, since 2017. In this study, we comprehensively evaluated 24 popular state-of-the-art methods for the complete end-to-end pipeline of Hi-C data analysis, using manually curated or experimentally validated benchmark datasets, including a CRISPR dataset for promoter-enhancer interaction validation. Our results indicate that, although no single method exhibited superior performance in all situations, HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances of most evaluation metrics for preprocessing, topologically associating domain identification, and chromatin interaction/promoter-enhancer interaction detection, respectively. The comprehensive comparison presented in this manuscript provides a reference for researchers to choose Hi-C analysis tools that best suit their needs.}, }
@article {pmid37726281, year = {2023}, author = {Nakato, R and Sakata, T and Wang, J and Nagai, LAE and Nagaoka, Y and Oba, GM and Bando, M and Shirahige, K}, title = {Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5647}, pmid = {37726281}, issn = {2041-1723}, support = {JP23gm6310012h0004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJCR18S5//MEXT | Japan Science and Technology Agency (JST)/ ; }, abstract = {Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.}, }
@article {pmid37725346, year = {2023}, author = {He, X and Huang, X and Long, Y and Liu, Z and Chang, X and Zhang, X and Wang, M}, title = {Tcbf: A novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad576}, pmid = {37725346}, issn = {1367-4811}, abstract = {SUMMARY: TAD boundaries are essential for organizing the chromatin spatial structure and regulating gene expression in eukaryotes. However, for large-scale pan-3D genome research, identifying conserved and specific TAD boundaries across different species or individuals is computationally challenging. Here, we present Tcbf, a rapid and powerful Python/R tool that integrates gene synteny blocks and homologous sequences to automatically detect conserved and specific TAD boundaries among multiple species, which can efficiently analyze huge genome datasets, greatly reduce the computational burden and enable pan-3D genome research.<br><br>Tcbf is implemented by Python/R and is available at https://github.com/TcbfGroup/Tcbf under the MIT license.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37705115, year = {2023}, author = {Oprescu, SN and Baumann, N and Chen, X and Sun, Q and Zhao, Y and Yue, F and Wang, H and Kuang, S}, title = {Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle.}, journal = {Skeletal muscle}, volume = {13}, number = {1}, pages = {15}, pmid = {37705115}, issn = {2044-5040}, support = {F31AR077424/NH/NIH HHS/United States ; R01AR078695/NH/NIH HHS/United States ; }, abstract = {Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associating domains. Unexpectedly, Myod1[Cre]-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7[CreER]- or Rosa26[CreER]- driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remains to be elucidated.}, }
@article {pmid37699887, year = {2023}, author = {Chang, LH and Ghosh, S and Papale, A and Luppino, JM and Miranda, M and Piras, V and Degrouard, J and Edouard, J and Poncelet, M and Lecouvreur, N and Bloyer, S and Leforestier, A and Joyce, EF and Holcman, D and Noordermeer, D}, title = {Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5615}, pmid = {37699887}, issn = {2041-1723}, support = {SPF201909009328//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; SPF201909009284//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; }, abstract = {Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.}, }
@article {pmid37608075, year = {2023}, author = {Chen, Y and Zhou, T and Liao, Z and Gao, W and Wu, J and Zhang, S and Li, Y and Liu, H and Zhou, H and Xu, C and Su, P}, title = {Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf.}, journal = {Cell death and differentiation}, volume = {}, number = {}, pages = {}, pmid = {37608075}, issn = {1476-5403}, support = {92068105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172376//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82102518//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072385//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021M693630//China Postdoctoral Science Foundation/ ; }, abstract = {Proper development of the limb bud relies on the concordance of various signals, but its molecular mechanisms have not yet been fully illustrated. Here we report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. Its ablation in the limb bud results in limbless forelimbs and severe deformities of the hindlimbs. In terms of mechanism, hnRNPK functions as a transcription activator for the vital genes involved in the three regulatory axes of limb bud development. Simultaneously, for the first time we elucidate that hnRNPK binds to and coordinates with the insulator protein CCCTC binding factor (CTCF) to maintain a three-dimensional chromatin architecture. Ablation of hnRNPK weakens the binding strength of CTCF to topologically associating domain (TAD) boundaries, then leading to the loose TADs, and decreased interactions between promoters and enhancers, and further decreased transcription of developmental genes. Our study establishes a fundamental and novel role of hnRNPK in regulating limb bud development.}, }
@article {pmid37603403, year = {2023}, author = {Agarwal, A and Korsak, S and Choudhury, A and Plewczynski, D}, title = {The dynamic role of cohesin in maintaining human genome architecture.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2200240}, doi = {10.1002/bies.202200240}, pmid = {37603403}, issn = {1521-1878}, abstract = {Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.}, }
@article {pmid37592325, year = {2023}, author = {Yan, T and Wang, K and Feng, K and Gao, X and Jin, Y and Wu, H and Zhang, W and Wei, L}, title = {Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {129}, pmid = {37592325}, issn = {2731-3654}, abstract = {BACKGROUND: Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.<br><br>RESULTS: Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the 'fatty acid metabolism', 'response to stress', 'carbon fixation' and 'photosynthesis' functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.<br><br>CONCLUSIONS: Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.}, }
@article {pmid37576549, year = {2023}, author = {Tav, C and Fournier, &#xc9; and Fournier, M and Khadangi, F and Baguette, A and Côté, MC and Silveira, MAD and Bérubé-Simard, FA and Bourque, G and Droit, A and Bilodeau, S}, title = {Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1237092}, pmid = {37576549}, issn = {1664-8021}, abstract = {Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.}, }
@article {pmid37559123, year = {2023}, author = {Lyu, J and Chen, C}, title = {LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {184}, pmid = {37559123}, issn = {1474-760X}, abstract = {Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.}, }
@article {pmid37550699, year = {2023}, author = {Deng, L and Zhou, Q and Zhou, J and Zhang, Q and Jia, Z and Zhu, G and Cheng, S and Cheng, L and Yin, C and Yang, C and Shen, J and Nie, J and Zhu, JK and Li, G and Zhao, L}, title = {3D organization of regulatory elements for transcriptional regulation in Arabidopsis.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {181}, pmid = {37550699}, issn = {1474-760X}, support = {32222063//National Natural Science Foundation of China/ ; 32188102//National Natural Science Foundation of China/ ; 31930032//National Natural Science Foundation of China/ ; 2662021PY005//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.<br><br>RESULTS: Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression.<br><br>CONCLUSION: The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.}, }
@article {pmid37536338, year = {2023}, author = {Mohana, G and Dorier, J and Li, X and Mouginot, M and Smith, RC and Malek, H and Leleu, M and Rodriguez, D and Khadka, J and Rosa, P and Cousin, P and Iseli, C and Restrepo, S and Guex, N and McCabe, BD and Jankowski, A and Levine, MS and Gambetta, MC}, title = {Chromosome-level organization of the regulatory genome in the Drosophila nervous system.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2023.07.008}, pmid = {37536338}, issn = {1097-4172}, abstract = {Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.}, }
@article {pmid37537310, year = {2023}, author = {Tettey, TT and Rinaldi, L and Hager, GL}, title = {Long-range gene regulation in hormone-dependent cancer.}, journal = {Nature reviews. Cancer}, volume = {}, number = {}, pages = {}, pmid = {37537310}, issn = {1474-1768}, abstract = {The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.}, }
@article {pmid37516964, year = {2023}, author = {Oka, M and Otani, M and Miyamoto, Y and Oshima, R and Adachi, J and Tomonaga, T and Asally, M and Nagaoka, Y and Tanaka, K and Toyoda, A and Ichikawa, K and Morishita, S and Isono, K and Koseki, H and Nakato, R and Ohkawa, Y and Yoneda, Y}, title = {Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure.}, journal = {Cell reports}, volume = {42}, number = {8}, pages = {112884}, doi = {10.1016/j.celrep.2023.112884}, pmid = {37516964}, issn = {2211-1247}, abstract = {NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure.}, }
@article {pmid37498561, year = {2023}, author = {Wang, Y and Guo, Z and Cheng, J}, title = {Single-cell Hi-C data Enhancement with Deep Residual and Generative Adversarial Networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad458}, pmid = {37498561}, issn = {1367-4811}, abstract = {MOTIVATION: The spatial genome organization of a eukaryotic cell is important for its function. The development of single-cell technologies for probing the three-dimensional (3D) genome conformation, especially single-cell chromosome conformation capture techniques (ScHi-C), has enabled us to understand genome function better than before. However, due to extreme sparsity and high noise associated with single-cell Hi-C data, it is still difficult to study genome structure and function using the HiC-data of one single cell.<br><br>RESULTS: In this work, we developed a deep learning method ScHiCEDRN based on deep residual networks and generative adversarial networks for the imputation and enhancement of Hi-C data of a single cell. In terms of both image evaluation and Hi-C reproducibility metrics, ScHiCEDRN outperforms the four deep learning methods (DeepHiC, HiCPlus, HiCSR, and Loopenhance) on enhancing the raw single-cell Hi-C data of human and Drosophila. The experiments also show that it can generate single-cell Hi-C data more suitable for identifying topologically associating domain (TAD) boundaries and reconstructing 3D chromosome structures than the existing methods. Moreover, ScHiCEDRN's performance generalizes well across different single cells and cell types, and it can be applied to improving population Hi-C data.<br><br>AVAILABILITY: The source code of ScHiCEDRN is available at the GitHub repository: https://github.com/BioinfoMachineLearning/ScHiCEDRN.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37478379, year = {2023}, author = {Liu, T and Wang, Z}, title = {HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad263}, pmid = {37478379}, issn = {1477-4054}, support = {/GM/NIGMS NIH HHS/United States ; R35GM137974/NH/NIH HHS/United States ; }, abstract = {The Hi-C experiments have been extensively used for the studies of genomic structures. In the last few years, spatiotemporal Hi-C has largely contributed to the investigation of genome dynamic reorganization. However, computationally modeling and forecasting spatiotemporal Hi-C data still have not been seen in the literature. We present HiC4D for dealing with the problem of forecasting spatiotemporal Hi-C data. We designed and benchmarked a novel network and named it residual ConvLSTM (ResConvLSTM), which is a combination of residual network and convolutional long short-term memory (ConvLSTM). We evaluated our new ResConvLSTM networks and compared them with the other five methods, including a naïve network (NaiveNet) that we designed as a baseline method and four outstanding video-prediction methods from the literature: ConvLSTM, spatiotemporal LSTM (ST-LSTM), self-attention LSTM (SA-LSTM) and simple video prediction (SimVP). We used eight different spatiotemporal Hi-C datasets for the blind test, including two from mouse embryogenesis, one from somatic cell nuclear transfer (SCNT) embryos, three embryogenesis datasets from different species and two non-embryogenesis datasets. Our evaluation results indicate that our ResConvLSTM networks almost always outperform the other methods on the eight blind-test datasets in terms of accurately predicting the Hi-C contact matrices at future time-steps. Our benchmarks also indicate that all of the methods that we benchmarked can successfully recover the boundaries of topologically associating domains called on the experimental Hi-C contact matrices. Taken together, our benchmarks suggest that HiC4D is an effective tool for predicting spatiotemporal Hi-C data. HiC4D is publicly available at both http://dna.cs.miami.edu/HiC4D/ and https://github.com/zwang-bioinformatics/HiC4D/.}, }
@article {pmid37467757, year = {2023}, author = {Senapati, S and Irshad, IU and Sharma, AK and Kumar, H}, title = {Fundamental insights into the correlation between chromosome configuration and transcription.}, journal = {Physical biology}, volume = {}, number = {}, pages = {}, doi = {10.1088/1478-3975/ace8e5}, pmid = {37467757}, issn = {1478-3975}, abstract = {Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain (TAD), and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research. .}, }
@article {pmid37461500, year = {2023}, author = {Goudarzi, S and Pagadala, M and Klie, A and Talwar, JV and Carter, H}, title = {Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.07.04.547722}, pmid = {37461500}, abstract = {Cancer is a highly heterogeneous disease caused by genetic and epigenetic alterations in normal cells. A recent study uncovered methylation quantitative trait loci (meQTLs) associated with different levels of local DNA methylation in cancers. Here, we investigated whether the distribution of cancer meQTLs reflected functional organization of the genome in the form of chromatin topologically associated domains (TADs), and evaluated whether cancer meQTLs near known driver genes have the potential to influence cancer risk or progression. At TAD boundaries, we observed differences in the distribution of meQTLs when one or both of the adjacent TADs was transcriptionally active, with higher densities near inactive TADs. Furthermore, we found differences in cancer meQTL distributions in active versus inactive TADs and observed an enrichment of meQTLs in active TADs near tumor suppressors, whereas there was a depletion of such meQTLs near oncogenes. Several meQTLs were associated with cancer risk in the UKBioBank, and we were able to reproduce breast cancer risk associations in the DRIVE cohort. Survival analysis in TCGA implicated a number of meQTLs in 13 tumor types. In 10 of these, polygenic meQTL scores were associated with increased hazard in a CoxPH analysis. Risk and survival-associated meQTLs tended to affect cancer genes involved in DNA damage repair and cellular adhesion and reproduced cancer-specific associations reported in prior literature. In summary, this study provides evidence that genetic variants that influence local DNA methylation are affected by chromatin structure and can impact tumor evolution.}, }
@article {pmid37453058, year = {2023}, author = {Kim, K and Kim, M and Lee, AJ and Song, SH and Kang, JK and Eom, J and Kang, GH and Bae, JM and Min, S and Kim, Y and Lim, Y and Kim, HS and Kim, YJ and Kim, TY and Jung, I}, title = {Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer.}, journal = {Cell reports}, volume = {42}, number = {7}, pages = {112778}, doi = {10.1016/j.celrep.2023.112778}, pmid = {37453058}, issn = {2211-1247}, abstract = {The regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation remains unclear. This study investigated SV-mediated gene dysregulation by profiling 3D cancer genome maps from 40 patients with colorectal cancer (CRC). We developed a machine learning-based method for spatial characterization of the altered 3D cancer genome. This revealed a frequent establishment of "de novo chromatin contacts" that can span multiple topologically associating domains (TADs) in addition to the canonical TAD fusion/shuffle model. Using this information, we precisely identified super-enhancer (SE)-hijacking and its clonal characteristics. Clonal SE-hijacking genes, such as TOP2B, are recurrently associated with cell-cycle/DNA-processing functions, which can potentially be used as CRC prognostic markers. Oncogene activation and increased drug resistance due to SE-hijacking were validated by reconstructing the patient's SV using CRISPR-Cas9. Collectively, the spatial and clonality-resolved analysis of the 3D cancer genome reveals regulatory principles of large-scale SVs in oncogene activation and their clinical implications.}, }
@article {pmid37445616, year = {2023}, author = {Lee, EG and Leong, L and Chen, S and Tulloch, J and Yu, CE}, title = {APOE Locus-Associated Mitochondrial Function and Its Implication in Alzheimer's Disease and Aging.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, doi = {10.3390/ijms241310440}, pmid = {37445616}, issn = {1422-0067}, support = {BX000933 and BX004823//U.S. Department of Veterans Affairs Office of Research and Development Biomedical Laboratory Research Program/ ; }, abstract = {The Apolipoprotein E (APOE) locus has garnered significant clinical interest because of its association with Alzheimer's disease (AD) and longevity. This genetic association appears across multiple genes in the APOE locus. Despite the apparent differences between AD and longevity, both conditions share a commonality of aging-related changes in mitochondrial function. This commonality is likely due to accumulative biological effects partly exerted by the APOE locus. In this study, we investigated changes in mitochondrial structure/function-related markers using oxidative stress-induced human cellular models and postmortem brains (PMBs) from individuals with AD and normal controls. Our results reveal a range of expressional alterations, either upregulated or downregulated, in these genes in response to oxidative stress. In contrast, we consistently observed an upregulation of multiple APOE locus genes in all cellular models and AD PMBs. Additionally, the effects of AD status on mitochondrial DNA copy number (mtDNA CN) varied depending on APOE genotype. Our findings imply a potential coregulation of APOE locus genes possibly occurring within the same topologically associating domain (TAD) of the 3D chromosome conformation. The coordinated expression of APOE locus genes could impact mitochondrial function, contributing to the development of AD or longevity. Our study underscores the significant role of the APOE locus in modulating mitochondrial function and provides valuable insights into the underlying mechanisms of AD and aging, emphasizing the importance of this locus in clinical research.}, }
@article {pmid37438531, year = {2023}, author = {Park, DS and Nguyen, SC and Isenhart, R and Shah, PP and Kim, W and Barnett, RJ and Chandra, A and Luppino, JM and Harke, J and Wai, M and Walsh, PJ and Abdill, RJ and Yang, R and Lan, Y and Yoon, S and Yunker, R and Kanemaki, MT and Vahedi, G and Phillips-Cremins, JE and Jain, R and Joyce, EF}, title = {High-throughput Oligopaint screen identifies druggable 3D genome regulators.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37438531}, issn = {1476-4687}, abstract = {The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions[1-3]. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.}, }
@article {pmid37433821, year = {2023}, author = {Kadam, S and Kumari, K and Manivannan, V and Dutta, S and Mitra, MK and Padinhateeri, R}, title = {Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4108}, pmid = {37433821}, issn = {2041-1723}, support = {BT/HRD/NBA/39/12/2018-19//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; }, abstract = {Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.}, }
@article {pmid37426677, year = {2023}, author = {Liu, H and Tsai, H and Yang, M and Li, G and Bian, Q and Ding, G and Wu, D and Dai, J}, title = {Three-dimensional genome structure and function.}, journal = {MedComm}, volume = {4}, number = {4}, pages = {e326}, pmid = {37426677}, issn = {2688-2663}, abstract = {Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.}, }
@article {pmid37418545, year = {2023}, author = {Onrust-van Schoonhoven, A and de Bruijn, MJW and Stikker, B and Brouwer, RWW and Braunstahl, GJ and van IJcken, WFJ and Graf, T and Huylebroeck, D and Hendriks, RW and Stik, G and Stadhouders, R}, title = {3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction.}, journal = {Science immunology}, volume = {8}, number = {85}, pages = {eadg3917}, doi = {10.1126/sciimmunol.adg3917}, pmid = {37418545}, issn = {2470-9468}, abstract = {Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4[+] memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.}, }
@article {pmid37398486, year = {2023}, author = {Syed, SA and Shqillo, K and Nand, A and Zhan, Y and Dekker, J and Imbalzano, AN}, title = {Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.13.544859}, pmid = {37398486}, abstract = {Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.}, }
@article {pmid37387127, year = {2023}, author = {Zhang, Y and Blanchette, M}, title = {Reference panel-guided super-resolution inference of Hi-C data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {Supplement_1}, pages = {i386-i393}, doi = {10.1093/bioinformatics/btad266}, pmid = {37387127}, issn = {1367-4811}, support = {//Genome Quebec/ ; //Canada and Genome Quebec/ ; }, abstract = {MOTIVATION: Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types.<br><br>RESULTS: Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains.<br><br>https://github.com/BlanchetteLab/RefHiC.}, }
@article {pmid37386239, year = {2023}, author = {Pandupuspitasari, NS and Khan, FA and Huang, C and Ali, A and Yousaf, MR and Shakeel, F and Putri, EM and Negara, W and Muktiani, A and Prasetiyono, BWHE and Kustiawan, L and Wahyuni, DS}, title = {Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease.}, journal = {Functional &amp; integrative genomics}, volume = {23}, number = {3}, pages = {214}, pmid = {37386239}, issn = {1438-7948}, abstract = {In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.}, }
@article {pmid37381832, year = {2023}, author = {Zhang, Y and Cao, X and Gao, Z and Ma, X and Wang, Q and Xu, X and Cai, X and Zhang, Y and Zhang, Z and Wei, G and Wen, B}, title = {MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {e57550}, doi = {10.15252/embr.202357550}, pmid = {37381832}, issn = {1469-3178}, support = {2021YFA1100203//MOST | National Key Research and Development Program of China (NKPs)/ ; 32130019//MOST | National Natural Science Foundation of China (NSFC)/ ; }, abstract = {Long interspersed nuclear elements (LINEs) play essential roles in shaping chromatin states, while the factors that cooperate with LINEs and their roles in higher-order chromatin organization remain poorly understood. Here, we show that MATR3, a nuclear matrix protein, interplays with antisense LINE1 (AS L1) RNAs to form a meshwork via phase separation, providing a dynamic platform for chromatin spatial organization. MATR3 and AS L1 RNAs affect the nuclear localization of each other. After MATR3 depletion, the chromatin, particularly H3K27me3-modified chromatin, redistributes in the cell nuclei. Topologically associating domains (TADs) that highly transcribe MATR3-associated AS L1 RNAs show decreased intra-TAD interactions in both AML12 and ES cells. MATR3 depletion increases the accessibility of H3K27me3 domains adjacent to MATR3-associated AS L1, without affecting H3K27me3 modifications. Furthermore, amyotrophic lateral sclerosis (ALS)-associated MATR3 mutants alter biophysical features of the MATR3-AS L1 RNA meshwork and cause an abnormal H3K27me3 staining. Collectively, we reveal a role of the meshwork formed by MATR3 and AS L1 RNAs in gathering chromatin in the nucleus.}, }
@article {pmid37381036, year = {2023}, author = {Sun, Y and Xu, X and Zhao, W and Zhang, Y and Chen, K and Li, Y and Wang, X and Zhang, M and Xue, B and Yu, W and Hou, Y and Wang, C and Xie, W and Li, C and Kong, D and Wang, S and Sun, Y}, title = {RAD21 is the core subunit of the cohesin complex involved in directing genome organization.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {155}, pmid = {37381036}, issn = {1474-760X}, support = {21825401//National Natural Science Foundation of China/ ; No. 2022YFA1303103//National Key Research and Development Program of China Stem Cell and Translational Research/ ; }, abstract = {BACKGROUND: The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we use super-resolution imaging to reveal the unique role of cohesin subunit RAD21 in cohesin loading and chromatin structure regulation.<br><br>RESULTS: We directly visualize that up-regulation of RAD21 leads to excessive chromatin loop extrusion into a vermicelli-like morphology with RAD21 clustered into foci and excessively loaded cohesin bow-tying a TAD to form a beads-on-a-string-type pattern. In contrast, up-regulation of the other four cohesin subunits results in even distributions. Mechanistically, we identify that the essential role of RAD21 is attributed to the RAD21-loader interaction, which facilitates the cohesin loading process rather than increasing the abundance of cohesin complex upon up-regulation of RAD21. Furthermore, Hi-C and genomic analysis reveal how RAD21 up-regulation affects genome-wide higher-order chromatin structure. Accumulated contacts are shown at TAD corners while inter-TAD interactions increase after vermicelli formation. Importantly, we find that in breast cancer cells, the expression of RAD21 is aberrantly high with poor patient survival and RAD21 forms beads in the nucleus. Up-regulated RAD21 in HeLa cells leads to compartment switching and up-regulation of cancer-related genes.<br><br>CONCLUSIONS: Our results provide key insights into the molecular mechanism by which RAD21 facilitates the cohesin loading process and provide an explanation to how cohesin and loader work cooperatively to promote chromatin extrusion, which has important implications in construction of three-dimensional genome organization.}, }
@article {pmid37325549, year = {2023}, author = {Wang, M and Sreenivas, P and Sunkel, BD and Wang, L and Ignatius, M and Stanton, BZ}, title = {The 3D chromatin landscape of rhabdomyosarcoma.}, journal = {NAR cancer}, volume = {5}, number = {3}, pages = {zcad028}, pmid = {37325549}, issn = {2632-8674}, abstract = {Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with a lack of precision therapy options for patients. We hypothesized that with a general paucity of known mutations in RMS, chromatin structural driving mechanisms are essential for tumor proliferation. Thus, we carried out high-depth in situ Hi-C in representative cell lines and patient-derived xenografts (PDXs) to define chromatin architecture in each major RMS subtype. We report a comprehensive 3D chromatin structural analysis and characterization of fusion-positive (FP-RMS) and fusion-negative RMS (FN-RMS). We have generated spike-in in situ Hi-C chromatin interaction maps for the most common FP-RMS and FN-RMS cell lines and compared our data with PDX models. In our studies, we uncover common and distinct structural elements in large Mb-scale chromatin compartments, tumor-essential genes within variable topologically associating domains and unique patterns of structural variation. Our high-depth chromatin interactivity maps and comprehensive analyses provide context for gene regulatory events and reveal functional chromatin domains in RMS.}, }
@article {pmid37322110, year = {2023}, author = {Rekaik, H and Lopez-Delisle, L and Hintermann, A and Mascrez, B and Bochaton, C and Mayran, A and Duboule, D}, title = {Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {37322110}, issn = {1546-1718}, abstract = {During development, Hox genes are temporally activated according to their relative positions on their clusters, contributing to the proper identities of structures along the rostrocaudal axis. To understand the mechanism underlying this Hox timer, we used mouse embryonic stem cell-derived stembryos. Following Wnt signaling, the process involves transcriptional initiation at the anterior part of the cluster and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, that is, with an asymmetric distribution favoring the anterior part of the cluster. Chromatin extrusion then occurs with successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time delay in the activation of more posterior-located genes due to long-range contacts with a flanking topologically associating domain. Mutant stembryos support this model and reveal that the presence of evolutionary conserved and regularly spaced intergenic CTCF sites controls the precision and the pace of this temporal mechanism.}, }
@article {pmid37302180, year = {2023}, author = {da Costa-Nunes, JA and Noordermeer, D}, title = {TADs: Dynamic structures to create stable regulatory functions.}, journal = {Current opinion in structural biology}, volume = {81}, number = {}, pages = {102622}, doi = {10.1016/j.sbi.2023.102622}, pmid = {37302180}, issn = {1879-033X}, abstract = {Mammalian chromosomes are organized at different length scales within the cell nucleus. Topologically Associating Domains (TADs) are structural units of 3D genome organization with functions in gene regulation, DNA replication, recombination and repair. Whereas TADs were initially interpreted as insulated domains, recent studies are revealing that these domains should be interpreted as dynamic collections of actively extruding loops. This process of loop extrusion is subsequently blocked at dedicated TAD boundaries, thereby promoting intra-domain interactions over their surroundings. In this review, we discuss how mammalian TAD structure can emerge from this dynamic process and we discuss recent evidence that TAD boundaries can have regulatory functions.}, }
@article {pmid37292994, year = {2023}, author = {Xiong, K and Zhang, R and Ma, J}, title = {scGHOST: Identifying single-cell 3D genome subcompartments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.24.542032}, pmid = {37292994}, abstract = {New single-cell Hi-C (scHi-C) technologies enable probing of the genome-wide cell-to-cell variability in 3D genome organization from individual cells. Several computational methods have been developed to reveal single-cell 3D genome features based on scHi-C data, including A/B compartments, topologically-associating domains, and chromatin loops. However, no scHi-C analysis method currently exists for annotating single-cell subcompartments, which are crucial for providing a more refined view of large-scale chromosome spatial localization in single cells. Here, we present SCGHOST, a single-cell subcompartment annotation method based on graph embedding with constrained random walk sampling. Applications of SCGHOST to scHi-C data and single-cell 3D genome imaging data demonstrate the reliable identification of single-cell subcompartments and offer new insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from the human prefrontal cortex, SCGHOST identifies cell type-specific subcompartments that are strongly connected to cell type-specific gene expression, suggesting the functional implications of single-cell subcompartments. Overall, SCGHOST is an effective new method for single-cell 3D genome subcompartment annotation based on scHi-C data for a broad range of biological contexts.}, }
@article {pmid37279476, year = {2023}, author = {Peng, X and Li, Y and Zou, M and Kong, X and Sheng, Y}, title = {CATAD: exploring topologically associating domains from an insight of core-attachment structure.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad204}, pmid = {37279476}, issn = {1477-4054}, abstract = {Identifying topologically associating domains (TADs), which are considered as the basic units of chromosome structure and function, can facilitate the exploration of the 3D-structure of chromosomes. Methods have been proposed to identify TADs by detecting the boundaries of TADs or identifying the closely interacted regions as TADs, while the possible inner structure of TADs is seldom investigated. In this study, we assume that a TAD is composed of a core and its surrounding attachments, and propose a method, named CATAD, to identify TADs based on the core-attachment structure model. In CATAD, the cores of TADs are identified based on the local density and cosine similarity, and the surrounding attachments are determined based on boundary insulation. CATAD was applied to the Hi-C data of two human cell lines and two mouse cell lines, and the results show that the boundaries of TADs identified by CATAD are significantly enriched by structural proteins, histone modifications, transcription start sites and enzymes. Furthermore, CATAD outperforms other methods in many cases, in terms of the average peak, boundary tagged ratio and fold change. In addition, CATAD is robust and rarely affected by the different resolutions of Hi-C matrices. Conclusively, identifying TADs based on the core-attachment structure is useful, which may inspire researchers to explore TADs from the angles of possible spatial structures and formation process.}, }
@article {pmid37277355, year = {2023}, author = {Kessler, S and Minoux, M and Joshi, O and Ben Zouari, Y and Ducret, S and Ross, F and Vilain, N and Salvi, A and Wolff, J and Kohler, H and Stadler, MB and Rijli, FM}, title = {A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3242}, pmid = {37277355}, issn = {2041-1723}, abstract = {Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.}, }
@article {pmid37259205, year = {2023}, author = {Gu, J and Li, S and Zhu, B and Liang, Q and Chen, B and Tang, X and Chen, C and Wu, DD and Li, Y}, title = {Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13818}, pmid = {37259205}, issn = {1755-0998}, abstract = {Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.}, }
@article {pmid37254808, year = {2023}, author = {Li, D and Zhao, XY and Zhou, S and Hu, Q and Wu, F and Lee, HY}, title = {Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad468}, pmid = {37254808}, issn = {1362-4962}, abstract = {Mammalian erythroid development can be divided into three stages: hematopoietic stem and progenitor cell (HSPC), erythroid progenitor (Ery-Pro), and erythroid precursor (Ery-Pre). However, the mechanisms by which the 3D genome changes to establish the stage-specific transcription programs that are critical for erythropoiesis remain unclear. Here, we analyze the chromatin landscape at multiple levels in defined populations from primary human erythroid culture. While compartments and topologically associating domains remain largely unchanged, ∼50% of H3K27Ac-marked enhancers are dynamic in HSPC versus Ery-Pre. The enhancer anchors of enhancer-promoter loops are enriched for occupancy of respective stage-specific transcription factors (TFs), indicating these TFs orchestrate the enhancer connectome rewiring. The master TF of erythropoiesis, GATA1, is found to occupy most erythroid gene promoters at the Ery-Pro stage, and mediate conspicuous local rewiring through acquiring binding at the distal regions in Ery-Pre, promoting productive erythroid transcription output. Knocking out GATA1 binding sites precisely abrogates local rewiring and corresponding gene expression. Interestingly, knocking down GATA1 can transiently revert the cell state to an earlier stage and prolong the window of progenitor state. This study reveals mechanistic insights underlying chromatin rearrangements during development by integrating multidimensional chromatin landscape analyses to associate with transcription output and cellular states.}, }
@article {pmid37254161, year = {2023}, author = {Tolokh, IS and Kinney, NA and Sharakhov, IV and Onufriev, AV}, title = {Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.}, journal = {Epigenetics &amp; chromatin}, volume = {16}, number = {1}, pages = {21}, pmid = {37254161}, issn = {1756-8935}, support = {R01 GM144596/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult.<br><br>RESULTS: We have developed a coarse-grained dynamical model of D.&#xa0;melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. The simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same&#xa0;strong effect on the predicted positioning of individual TADs&#xa0;-- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region.<br><br>CONCLUSIONS: A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.}, }
@article {pmid37250307, year = {2023}, author = {Hamba, Y and Kamatani, T and Miya, F and Boroevich, KA and Tsunoda, T}, title = {Topologically associating domain underlies tissue specific expression of long intergenic non-coding RNAs.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106640}, pmid = {37250307}, issn = {2589-0042}, abstract = {Accumulating evidence indicates that long intergenic non-coding RNAs (lincRNAs) show more tissue-specific expression patterns than protein-coding genes (PCGs). However, although lincRNAs are subject to canonical transcriptional regulation like PCGs, the molecular basis for the specificity of their expression patterns remains unclear. Here, using expression data and coordinates of topologically associating domains (TADs) in human tissues, we show that lincRNA loci are significantly enriched in the more internal region of TADs compared to PCGs and that lincRNAs within TADs have higher tissue specificity than those outside TADs. Based on these, we propose an analytical framework to interpret transcriptional status using lincRNA as an indicator. We applied it to hypertrophic cardiomyopathy data and found disease-specific transcriptional regulation: ectopic expression of keratin at the TAD level and derepression of myocyte differentiation-related genes by E2F1 with down-regulation of LINC00881. Our results provide understanding of the function and regulation of lincRNAs according to genomic structure.}, }
@article {pmid37193952, year = {2023}, author = {Zhang, X and Yu, G and Dai, Y and Zhang, H and Wang, K and Han, J}, title = {High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon.}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {260}, pmid = {37193952}, issn = {1471-2229}, abstract = {BACKGROUND: The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear.<br><br>RESULTS: In this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated&#x2009;~&#x2009;1.5&#xa0;kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response.<br><br>CONCLUSIONS: Our study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.}, }
@article {pmid37162822, year = {2023}, author = {Parodi, L and Comeau, ME and Georgakis, MK and Mayerhofer, E and Chung, J and Falcone, GJ and Malik, R and Demel, SL and Worrall, BB and Koch, S and Testai, FD and Kittner, SJ and McCauley, JL and Hall, CE and Mayson, DJ and Elkind, MS and James, ML and Woo, D and Rosand, J and Langefeld, CD and Anderson, CD}, title = {Deep resequencing of the 1q22 locus in non-lobar intracerebral hemorrhage.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.18.23288754}, pmid = {37162822}, abstract = {OBJECTIVE: Genome-wide association studies have identified 1q22 as a susceptibility locus for cerebral small vessel diseases (CSVDs), including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study we performed targeted high-depth sequencing of 1q22 in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown.<br><br>METHODS: 95,000 base pairs spanning 1q22 , including SEMA4A, SLC25A44 and PMF1 / PMF1-BGLAP were sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and RIFT analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, ChIP-Seq and ChIA-PET databases. Multivariable Mendelian randomization (MVMR) assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at 1q22 could be causally related to ICH risk.<br><br>RESULTS: Common and rare variant analyses prioritized variants in SEMA4A 5'-UTR and PMF1 intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that 1q22 is spatially organized in a single chromatin loop and that the genes therein belong to the same Topologically Associating Domain. ChIP-Seq and ChIA-PET data analysis highlighted the presence of long-range interactions between the SEMA4A -promoter and PMF1 -enhancer regions prioritized by association testing. MVMR analyses demonstrated that PMF1 overexpression could be causally related to non-lobar ICH risk.<br><br>INTERPRETATION: Altered promoter-enhancer interactions leading to PMF1 overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non-lobar ICH risk at 1q22 , offering a potential new target for prevention of ICH and CSVD.}, }
@article {pmid37162225, year = {2023}, author = {Li, A and Zeng, G and Wang, H and Li, X and Zhang, Z}, title = {DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2300366}, doi = {10.1002/advs.202300366}, pmid = {37162225}, issn = {2198-3844}, abstract = {Topologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state-of-the-art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.}, }
@article {pmid37139561, year = {2023}, author = {Liu, J and Li, P and Sun, J and Guo, J}, title = {LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad165}, pmid = {37139561}, issn = {1477-4054}, abstract = {With the development of chromosome conformation capture technique, the study of spatial conformation of a genome based on Hi-C technique has made a quantum leap. Previous studies reveal that genomes are folded into hierarchy of three-dimensional (3D) structures associated with topologically associating domains (TADs), and detecting TAD boundaries is of great significance in the chromosome-level analysis of 3D genome architecture. In this paper, we propose a novel TAD identification method, LPAD, which first extracts node correlations from global interactions of chromosomes based on the random walk with restart and then builds an undirected graph from Hi-C contact matrix. Next, LPAD designs a label propagation-based approach to discover communities and generates TADs. Experimental results verify the effectiveness and quality of TAD detections compared with existing methods. Furthermore, experimental evaluation of chromatin immunoprecipitation sequencing data shows that LPAD performs high enrichment of histone modifications remarkably nearby the TAD boundaries, and these results demonstrate LPAD's advantages on TAD identification accuracy.}, }
@article {pmid37116707, year = {2023}, author = {Liu, P and Li, D and Zhang, J and He, M and Gao, D and Wang, Y and Lin, Y and Pan, D and Li, P and Wang, T and Li, J and Kong, F and Zeng, B and Lu, L and Ma, J and Long, K and Li, G and Tang, Q and Jin, L and Li, M}, title = {Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {104757}, doi = {10.1016/j.jbc.2023.104757}, pmid = {37116707}, issn = {1083-351X}, abstract = {Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is essential for understanding human-specific metabolic regulation, but the functional importance and evolutionary dynamics of three-dimensional (3D) genome organizations of ATs are not well defined. Here, we compared the 3D genome architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation in ATs at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI), which have not been described previously. We found promoter-enhancer interaction (PEI) are much more evolutionarily dynamic with respect to compartmentalization and topologically associating domain (TAD). Compared to conserved PEIs, human-specific PEIs are enriched for human-specific sequence and the binding motifs of their potential mediators (transcription factors) are less conserved. Our data also demonstrated that genes involved in the evolutionarily dynamics of chromatin organization have weaker transcriptional conservation than those associated with conserved chromatin organization. Furthermore, the genes involved in energy metabolism and the maintenance of metabolic homeostasis are enriched in human-specific chromatin organization, while housekeeping genes, health-related genes and genetic variations are enriched in evolutionarily conserved compared to human-specific chromatin organization. Finally, we showed extensively divergent human-specific 3D genome organizations among one subcutaneous and three visceral ATs. Together, these findings provide a global overview of 3D genome architecture dynamics between ATs from human and mammalian models, and new insights into understanding the regulatory evolution of human ATs.}, }
@article {pmid37104607, year = {2023}, author = {Keough, KC and Whalen, S and Inoue, F and Przytycki, PF and Fair, T and Deng, C and Steyert, M and Ryu, H and Lindblad-Toh, K and Karlsson, E and ,  and Nowakowski, T and Ahituv, N and Pollen, A and Pollard, KS and Andrews, G and Armstrong, JC and Bianchi, M and Birren, BW and Bredemeyer, KR and Breit, AM and Christmas, MJ and Clawson, H and Damas, J and Di Palma, F and Diekhans, M and Dong, MX and Eizirik, E and Fan, K and Fanter, C and Foley, NM and Forsberg-Nilsson, K and Garcia, CJ and Gatesy, J and Gazal, S and Genereux, DP and Goodman, L and Grimshaw, J and Halsey, MK and Harris, AJ and Hickey, G and Hiller, M and Hindle, AG and Hubley, RM and Hughes, GM and Johnson, J and Juan, D and Kaplow, IM and Karlsson, EK and Keough, KC and Kirilenko, B and Koepfli, KP and Korstian, JM and Kowalczyk, A and Kozyrev, SV and Lawler, AJ and Lawless, C and Lehmann, T and Levesque, DL and Lewin, HA and Li, X and Lind, A and Lindblad-Toh, K and Mackay-Smith, A and Marinescu, VD and Marques-Bonet, T and Mason, VC and Meadows, JRS and Meyer, WK and Moore, JE and Moreira, LR and Moreno-Santillan, DD and Morrill, KM and Muntané, G and Murphy, WJ and Navarro, A and Nweeia, M and Ortmann, S and Osmanski, A and Paten, B and Paulat, NS and Pfenning, AR and Phan, BN and Pollard, KS and Pratt, HE and Ray, DA and Reilly, SK and Rosen, JR and Ruf, I and Ryan, L and Ryder, OA and Sabeti, PC and Schäffer, DE and Serres, A and Shapiro, B and Smit, AFA and Springer, M and Srinivasan, C and Steiner, C and Storer, JM and Sullivan, KAM and Sullivan, PF and Sundström, E and Supple, MA and Swofford, R and Talbot, JE and Teeling, E and Turner-Maier, J and Valenzuela, A and Wagner, F and Wallerman, O and Wang, C and Wang, J and Weng, Z and Wilder, AP and Wirthlin, ME and Xue, JR and Zhang, X}, title = {Three-dimensional genome rewiring in loci with human accelerated regions.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6643}, pages = {eabm1696}, doi = {10.1126/science.abm1696}, pmid = {37104607}, issn = {1095-9203}, abstract = {Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.}, }
@article {pmid37099832, year = {2023}, author = {Zhang, H and Blobel, GA}, title = {Genome folding dynamics during the M-to-G1-phase transition.}, journal = {Current opinion in genetics &amp; development}, volume = {80}, number = {}, pages = {102036}, doi = {10.1016/j.gde.2023.102036}, pmid = {37099832}, issn = {1879-0380}, abstract = {All measurable features of higher-order chromosomal architecture undergo drastic reorganization as cells enter and exit mitosis. During mitosis, gene transcription is temporarily halted, the nuclear envelope is dismantled, and chromosomes undergo condensation. At this time, chromatin compartments, topologically associating domains (TADs), and loops that connect enhancers with promoters as well as CTCF/cohesin loops are dissolved. Upon G1 entry, genome organization is rebuilt in the daughter nuclei to resemble that of the mother nucleus. We survey recent studies that traced these features in relation to gene expression during the mitosis-to-G1-phase transition at high temporal resolution. Dissection of fluctuating architectural features informed the hierarchical relationships of chromosomal organization, the mechanisms by which they are formed, and their mutual (in-) dependence. These studies highlight the importance of considering the cell cycle dynamics for studies of chromosomal organization.}, }
@article {pmid37085539, year = {2023}, author = {Okonechnikov, K and Camgöz, A and Chapman, O and Wani, S and Park, DE and Hübner, JM and Chakraborty, A and Pagadala, M and Bump, R and Chandran, S and Kraft, K and Acuna-Hidalgo, R and Reid, D and Sikkink, K and Mauermann, M and Juarez, EF and Jenseit, A and Robinson, JT and Pajtler, KW and Milde, T and Jäger, N and Fiesel, P and Morgan, L and Sridhar, S and Coufal, NG and Levy, M and Malicki, D and Hobbs, C and Kingsmore, S and Nahas, S and Snuderl, M and Crawford, J and Wechsler-Reya, RJ and Davidson, TB and Cotter, J and Michaiel, G and Fleischhack, G and Mundlos, S and Schmitt, A and Carter, H and Michealraj, KA and Kumar, SA and Taylor, MD and Rich, J and Buchholz, F and Mesirov, JP and Pfister, SM and Ay, F and Dixon, JR and Kool, M and Chavez, L}, title = {3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2300}, pmid = {37085539}, issn = {2041-1723}, abstract = {Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.}, }
@article {pmid37084258, year = {2023}, author = {Wang, B and Liu, K and Li, Y and Wang, J}, title = {DFHiC: A dilated full convolution model to enhance the resolution of Hi-C data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad211}, pmid = {37084258}, issn = {1367-4811}, abstract = {MOTIVATION: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.<br><br>RESULTS: In this work, we propose a novel method, so-called DFHiC, which generates the high-resolution Hi-C matrix from the low-resolution Hi-C matrix in the framework of the dilated convolutional neural network. The dilated convolution is able to effectively explore the global patterns in the overall Hi-C matrix by taking advantage of the information of the Hi-C matrix in a way of the longer genomic distance. Consequently, DFHiC can improve the resolution of the Hi-C matrix reliably and accurately. More importantly, the super-resolution Hi-C data enhanced by DFHiC is more in line with the real high-resolution Hi-C data than those done by the other existing methods, in terms of both chromatin significant interactions and identifying topologically associating domains (TADs).<br><br>AVAILABILITY: https://github.com/BinWangCSU/DFHiC.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37081156, year = {2023}, author = {Rajderkar, S and Barozzi, I and Zhu, Y and Hu, R and Zhang, Y and Li, B and Alcaina Caro, A and Fukuda-Yuzawa, Y and Kelman, G and Akeza, A and Blow, MJ and Pham, Q and Harrington, AN and Godoy, J and Meky, EM and von Maydell, K and Hunter, RD and Akiyama, JA and Novak, CS and Plajzer-Frick, I and Afzal, V and Tran, S and Lopez-Rios, J and Talkowski, ME and Lloyd, KCK and Ren, B and Dickel, DE and Visel, A and Pennacchio, LA}, title = {Topologically associating domain boundaries are required for normal genome function.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {435}, pmid = {37081156}, issn = {2399-3642}, abstract = {Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes[1-3], but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.}, }
@article {pmid37076620, year = {2023}, author = {Davidson, IF and Barth, R and Zaczek, M and van der Torre, J and Tang, W and Nagasaka, K and Janissen, R and Kerssemakers, J and Wutz, G and Dekker, C and Peters, JM}, title = {CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37076620}, issn = {1476-4687}, abstract = {In eukaryotes, genomic DNA is extruded into loops by cohesin[1]. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)[2,3] that have important roles in gene regulation and recombination during development and disease[1,4-7]. How CTCF establishes TAD boundaries and to what extent these are permeable to cohesin is unclear[8]. Here, to address these questions, we visualize interactions of single CTCF and cohesin molecules on DNA in vitro. We show that CTCF is sufficient to block diffusing cohesin, possibly reflecting how cohesive cohesin accumulates at TAD boundaries, and is also sufficient to block loop-extruding cohesin, reflecting how CTCF establishes TAD boundaries. CTCF functions asymmetrically, as predicted; however, CTCF is dependent on DNA tension. Moreover, CTCF regulates cohesin's loop-extrusion activity by changing its direction and by inducing loop shrinkage. Our data indicate that CTCF is not, as previously assumed, simply a barrier to cohesin-mediated loop extrusion but is an active regulator of this process, whereby the permeability of TAD boundaries can be modulated by DNA tension. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.}, }
@article {pmid37070946, year = {2023}, author = {Yin, X and Romero-Campero, FJ and Yang, M and Baile, F and Cao, Y and Shu, J and Luo, L and Wang, D and Sun, S and Yan, P and Gong, Z and Mo, X and Qin, G and Calonje, M and Zhou, Y}, title = {Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koad112}, pmid = {37070946}, issn = {1532-298X}, abstract = {Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.}, }
@article {pmid37063858, year = {2023}, author = {Guo, M and Yao, Z and Jiang, C and Songyang, Z and Gan, L and Xiong, Y}, title = {Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1161522}, pmid = {37063858}, issn = {1664-3224}, abstract = {BACKGROUNDS: Hepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive.<br><br>METHODS: We applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization.<br><br>RESULTS: We found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure.<br><br>CONCLUSION: Our work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.}, }
@article {pmid37055796, year = {2023}, author = {Cheng, J and Cao, X and Wang, X and Wang, J and Yue, B and Sun, W and Huang, Y and Lan, X and Ren, G and Lei, C and Chen, H}, title = {Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {59}, pmid = {37055796}, issn = {1674-9782}, abstract = {BACKGROUND: Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China. Three-dimensional genome structure is confirmed to be an important layer of transcription regulation. Although genome-wide interaction data of several livestock species have already been produced, the genome structure states and its regulatory rules in cattle muscle are still limited.<br><br>RESULTS: Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle (Bos taurus). We showed that compartments, topologically associating domains (TADs), and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development. Furthermore, we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps. We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.<br><br>CONCLUSIONS: Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology, which will benefit the progress of genetic improvement of beef cattle.}, }
@article {pmid37047368, year = {2023}, author = {Mao, A and Chen, C and Portillo-Ledesma, S and Schlick, T}, title = {Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, doi = {10.3390/ijms24076395}, pmid = {37047368}, issn = {1422-0067}, support = {R35-GM122562/NH/NIH HHS/United States ; }, abstract = {In humans and other eukaryotes, DNA is condensed into chromatin fibers that are further wound into chromosomes. This organization allows regulatory elements in the genome, often distant from each other in the linear DNA, to interact and facilitate gene expression through regions known as topologically associating domains (TADs). CCCTC-binding factor (CTCF) is one of the major components of TAD formation and is responsible for recruiting a partner protein, cohesin, to perform loop extrusion and facilitate proper gene expression within TADs. Because single-residue CTCF mutations have been linked to the development of a variety of cancers in humans, we aim to better understand how these mutations affect the CTCF structure and its interaction with DNA. To this end, we compare all-atom molecular dynamics simulations of a wildtype CTCF-DNA complex to those of eight different cancer-linked CTCF mutant sequences. We find that most mutants have lower binding energies compared to the wildtype protein, leading to the formation of less stable complexes. Depending on the type and position of the mutation, this loss of stability can be attributed to major changes in the electrostatic potential, loss of hydrogen bonds between the CTCF and DNA, and/or destabilization of specific zinc fingers. Interestingly, certain mutations in specific fingers can affect the interaction with the DNA of other fingers, explaining why mere single mutations can impair CTCF function. Overall, these results shed mechanistic insights into experimental observations and further underscore CTCF's importance in the regulation of chromatin architecture and gene expression.}, }
@article {pmid37041182, year = {2023}, author = {Tan, ZW and Toong, PJ and Guarnera, E and Berezovsky, IN}, title = {Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {5906}, pmid = {37041182}, issn = {2045-2322}, abstract = {We tackle here genomic mechanisms of a rapid onset and recovery from anosmia-a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin structure in mice, we hypothesized that the disruption of the OR gene expression and, respectively, deficiency of the OR function can be caused by chromatin reorganization taking place upon SARS-CoV-2 infection. We obtained chromatin ensemble reconstructions from COVID-19 patients and control samples using our original computational framework for the whole-genome 3D chromatin ensemble reconstruction. Specifically, we used megabase-scale structural units and effective interactions between them obtained in the Markov State modelling of the Hi-C contact network as an unput in the stochastic embedding procedure of the whole-genome 3D chromatin ensemble reconstruction. We have also developed here a new procedure for analyzing fine structural hierarchy with (sub)TAD-size units in local chromatin regions, which we apply here to parts of chromosomes containing OR genes and corresponding regulatory elements. We observed structural modifications in COVID-19 patients on different levels of chromatin organization, from the alteration of whole genome structure and chromosomal intermingling to reorganization of contacts between chromatin loops at the level of topologically associating domains. While complementary data on known regulatory elements point to potential pathology-associated changes within the overall picture of chromatin alterations, further investigation using additional epigenetic factors mapped on 3D reconstructions with improved resolution will be required for better understanding of anosmia caused by SARS-CoV-2 infection.}, }
@article {pmid37041138, year = {2023}, author = {Melo, US and Jatzlau, J and Prada-Medina, CA and Flex, E and Hartmann, S and Ali, S and Schöpflin, R and Bernardini, L and Ciolfi, A and Moeinzadeh, MH and Klever, MK and Altay, A and Vallecillo-García, P and Carpentieri, G and Delledonne, M and Ort, MJ and Schwestka, M and Ferrero, GB and Tartaglia, M and Brusco, A and Gossen, M and Strunk, D and Geißler, S and Mundlos, S and Stricker, S and Knaus, P and Giorgio, E and Spielmann, M}, title = {Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2034}, pmid = {37041138}, issn = {2041-1723}, abstract = {Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in which signaling pathways such as BMP, TGFβ and WNT are known key players in driving ectopic bone formation. Identifying novel genes and pathways related to the mineralization process are important steps for future gene therapy in bone disorders. In this study, we detect an inter-chromosomal insertional duplication in a female proband disrupting a topologically associating domain and causing an ultra-rare progressive form of heterotopic ossification. This structural variant lead to enhancer hijacking and misexpression of ARHGAP36 in fibroblasts, validated here by orthogonal in vitro studies. In addition, ARHGAP36 overexpression inhibits TGFβ, and activates hedgehog signaling and genes/proteins related to extracellular matrix production. Our work on the genetic cause of this heterotopic ossification case has revealed that ARHGAP36 plays a role in bone formation and metabolism, outlining first details of this gene contributing to bone-formation and -disease.}, }
@article {pmid37017672, year = {2023}, author = {Fritz, AJ and Ghule, PN and Toor, R and Dillac, L and Perelman, J and Boyd, J and Lian, JB and Gordon, JAR and Frietze, S and Van Wijnen, A and Stein, JL and Stein, GS}, title = {Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle.}, journal = {Critical reviews in eukaryotic gene expression}, volume = {33}, number = {3}, pages = {85-97}, doi = {10.1615/CritRevEukaryotGeneExpr.2022046190}, pmid = {37017672}, issn = {1045-4403}, abstract = {Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.}, }
@article {pmid37016431, year = {2023}, author = {Narang, S and Evensen, NA and Saliba, J and Pierro, J and Loh, ML and Brown, PA and Kolekar, P and Mulder, H and Shao, Y and Easton, J and Ma, X and Tsirigos, A and Carroll, WL}, title = {NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {64}, pmid = {37016431}, issn = {1474-760X}, abstract = {BACKGROUND: The NSD2 p.E1099K (EK) mutation is shown to be enriched in patients with relapsed acute lymphoblastic leukemia (ALL), indicating a role in clonal evolution and drug resistance.<br><br>RESULTS: To uncover 3D chromatin architecture-related mechanisms underlying drug resistance, we perform Hi-C on three B-ALL cell lines heterozygous for NSD2 EK. The NSD2 mutation leads to widespread remodeling of the 3D genome, most dramatically in terms of compartment changes with a strong bias towards A compartment shifts. Systematic integration of the Hi-C data with previously published ATAC-seq, RNA-seq, and ChIP-seq data show an expansion in H3K36me2 and a shrinkage in H3K27me3 within A compartments as well as increased gene expression and chromatin accessibility. These results suggest that NSD2 EK plays a prominent role in chromatin decompaction through enrichment of H3K36me2. In contrast, we identify few changes in intra-topologically associating domain activity. While compartment changes vary across cell lines, a common core of decompacting loci are shared, driving the expression of genes/pathways previously implicated in drug resistance. We further perform RNA sequencing on a cohort of matched diagnosis/relapse ALL patients harboring the relapse-specific NSD2 EK mutation. Changes in patient gene expression upon relapse significantly correlate with core compartment changes, further implicating the role of NSD2 EK in genome decompaction.<br><br>CONCLUSIONS: In spite of cell-context-dependent changes mediated by EK, there appears to be a shared transcriptional program dependent on compartment shifts which could explain phenotypic differences across EK cell lines. This core program is an attractive target for therapeutic intervention.}, }
@article {pmid37012431, year = {2023}, author = {Dozmorov, MG and Marshall, MA and Rashid, NS and Grible, JM and Valentine, A and Olex, AL and Murthy, K and Chakraborty, A and Reyna, J and Figueroa, DS and Hinojosa-Gonzalez, L and Da-Inn Lee, E and Baur, BA and Roy, S and Ay, F and Harrell, JC}, title = {Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {5420}, pmid = {37012431}, issn = {2045-2322}, support = {R35-GM128938/GM/NIGMS NIH HHS/United States ; R35-GM128938/GM/NIGMS NIH HHS/United States ; 1R01CA246182-01A1/CA/NCI NIH HHS/United States ; CCR19608826/KOMEN/Susan G. Komen/United States ; }, abstract = {Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.}, }
@article {pmid37000624, year = {2023}, author = {Wang, B and Ji, L and Bian, Q}, title = {SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.}, journal = {Cell reports}, volume = {42}, number = {4}, pages = {112323}, doi = {10.1016/j.celrep.2023.112323}, pmid = {37000624}, issn = {2211-1247}, abstract = {Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.}, }
@article {pmid36996812, year = {2023}, author = {Chen, LF and Long, HK and Park, M and Swigut, T and Boettiger, AN and Wysocka, J}, title = {Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2023.03.009}, pmid = {36996812}, issn = {1097-4164}, abstract = {Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.}, }
@article {pmid36990727, year = {2023}, author = {Aldersey, JE and Liu, N and Tearle, R and Low, WY and Breen, J and Williams, JL and Bottema, CDK}, title = {Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue.}, journal = {Animal genetics}, volume = {}, number = {}, pages = {}, doi = {10.1111/age.13322}, pmid = {36990727}, issn = {1365-2052}, abstract = {Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300-kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus- and Brahman-specific Hi-C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus- and Brahman-specific Hi-C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.}, }
@article {pmid36941615, year = {2023}, author = {Li, X and Wang, J and Yu, Y and Li, G and Wang, J and Li, C and Zeng, Z and Li, N and Zhang, Z and Dong, Q and Yu, Y and Wang, X and Wang, T and Grover, CE and Wang, B and Liu, B and Wendel, JF and Gong, L}, title = {Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae).}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {56}, pmid = {36941615}, issn = {1741-7007}, abstract = {BACKGROUND: Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species.<br><br>RESULTS: Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), including Gossypium arboreum, Gossypium raimondii, and Gossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved in Gossypioides and Gossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestral in-cis interactions.<br><br>CONCLUSIONS: Our findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.}, }
@article {pmid36914797, year = {2023}, author = {Li, D and Wu, F and Zhou, S and Huang, XJ and Lee, HY}, title = {Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis.}, journal = {Nature structural &amp; molecular biology}, volume = {}, number = {}, pages = {}, pmid = {36914797}, issn = {1545-9985}, abstract = {Mammalian erythropoiesis involves progressive chromatin compaction and subsequent enucleation in terminal differentiation, but the mechanisms underlying the three-dimensional chromatin reorganization remain obscure. Here, we systematically analyze the higher-order chromatin in purified populations of primary human erythroblasts. Our results reveal that heterochromatin regions undergo substantial compression, with H3K9me3 markers relocalizing to the nuclear periphery and forming a significant number of long-range interactions, and that ~58% of the topologically associating domain (TAD) boundaries are disrupted, while certain TADs enriched for markers of the active transcription state and erythroid master regulators, GATA1 and KLF1, are selectively maintained during terminal erythropoiesis. Finally, we demonstrate that GATA1 is involved in safeguarding selected essential chromatin domains during terminal erythropoiesis. Our study therefore delineates the molecular characteristics of a development-driven chromatin compaction process, which reveals transcription competence as a key indicator of the selected domain maintenance to ensure appropriate gene expression during the extreme compaction of chromatin.}, }
@article {pmid36894325, year = {2023}, author = {Dang, D and Zhang, SW and Duan, R and Zhang, S}, title = {Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.277187.122}, pmid = {36894325}, issn = {1549-5469}, abstract = {Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization, and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. Obvious inconsistencies among the TADs identified by different methods indeed make the statistical and biological properties of TADs overly depend on the method we chose rather than on the data. To this end, we employ the consensus structural information captured by these methods to define the TAD separation landscape for decoding the consensus domain organization of the 3D genome. We demonstrate that the TAD separation landscape could be used to compare domain boundaries across multiple cell types for discovering conserved and divergent topological structures, decipher three types of boundary regions with diverse biological features, and identify Consensus TADs (ConsTADs). We illustrate that these analyses could deepen our understanding of the relationships between the topological domains and chromatin states, gene expression, and DNA replication timing.}, }
@article {pmid36869353, year = {2023}, author = {Richer, S and Tian, Y and Schoenfelder, S and Hurst, L and Murrell, A and Pisignano, G}, title = {Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {40}, pmid = {36869353}, issn = {1474-760X}, support = {MR/P000711/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available.<br><br>RESULTS: We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs).<br><br>CONCLUSIONS: This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.}, }
@article {pmid36842325, year = {2023}, author = {Karpinska, MA and Oudelaar, AM}, title = {The role of loop extrusion in enhancer-mediated gene activation.}, journal = {Current opinion in genetics &amp; development}, volume = {79}, number = {}, pages = {102022}, doi = {10.1016/j.gde.2023.102022}, pmid = {36842325}, issn = {1879-0380}, abstract = {Gene expression patterns in complex multicellular organisms are regulated by enhancers, which communicate with their target gene promoters in three-dimensional (3D) chromatin structures. Despite advances in our understanding of the mechanisms that organize mammalian genomes into compartments and topologically associating domains (TADs), it is not well understood how specific interactions between enhancers and promoters are controlled in this 3D context. In this review, we give an overview of recent evidence that shows that a process of loop extrusion plays an important role in the regulation of enhancer-promoter communication and discuss recent insights into the molecular mechanism by which loop extrusion contributes to enhancer-mediated gene activation.}, }
@article {pmid36840746, year = {2023}, author = {Sabaté, T and Lelandais, B and Bertrand, E and Zimmer, C}, title = {Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad034}, pmid = {36840746}, issn = {1362-4962}, abstract = {Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of loop formation can be quantified from fixed cell images alone, while the lifetime of loops and the speed of extrusion can be estimated from dynamic live-cell data. Our delineation of appropriate imaging conditions and the proposed analytical methods lay the groundwork for a systematic quantitative characterization of loop extrusion in fixed or living cells.}, }
@article {pmid36800432, year = {2023}, author = {Zhao, Y and Ding, Y and He, L and Zhou, Q and Chen, X and Li, Y and Alfonsi, MV and Wu, Z and Sun, H and Wang, H}, title = {Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging.}, journal = {Science advances}, volume = {9}, number = {7}, pages = {eabo1360}, doi = {10.1126/sciadv.abo1360}, pmid = {36800432}, issn = {2375-2548}, abstract = {Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounced when SCs become activated. Marked loss in topologically associating domain (TAD) border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can form TAD clusters and super-enhancer-containing TAD clusters orchestrate stage-specific gene expression. Furthermore, we uncover that transcription factor PAX7 is pivotal in enhancer-promoter (E-P) loop formation. We also identify cis-regulatory elements that are crucial for local chromatin organization at Pax7 locus and Pax7 expression. Lastly, we unveil that geriatric SC displays a prominent gain in long-range contacts and loss of TAD border insulation. Together, our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage development and SC aging.}, }
@article {pmid36759336, year = {2023}, author = {Kobets, VA and Ulianov, SV and Galitsyna, AA and Doronin, SA and Mikhaleva, EA and Gelfand, MS and Shevelyov, YY and Razin, SV and Khrameeva, EE}, title = {HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad044}, pmid = {36759336}, issn = {1477-4054}, abstract = {The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.}, }
@article {pmid36750787, year = {2023}, author = {Maslova, A and Plotnikov, V and Nuriddinov, M and Gridina, M and Fishman, V and Krasikova, A}, title = {Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {66}, pmid = {36750787}, issn = {1471-2164}, mesh = {Animals ; *Chickens/genetics ; Karyotype ; *Genomics ; Sex Chromosomes ; Chromosome Aberrations ; Mammals/genetics ; }, abstract = {BACKGROUND: Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line.<br><br>RESULTS: We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions&#x2009;&#x2265;&#x2009;200&#xa0;kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH.<br><br>CONCLUSIONS: In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.}, }
@article {pmid36744801, year = {2023}, author = {Yang, L and Akgol Oksuz, B and Dekker, J and Gibcus, JH}, title = {Capturing Chromosome Conformation Across Length Scales.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {191}, pages = {}, doi = {10.3791/64001}, pmid = {36744801}, issn = {1940-087X}, mesh = {*Chromosomes/genetics/metabolism ; *Chromatin/genetics ; DNA/genetics/chemistry ; Cell Nucleus/metabolism ; DNA Restriction Enzymes/metabolism ; Formaldehyde/chemistry ; Nucleic Acid Conformation ; }, abstract = {Chromosome conformation capture (3C) is used to detect three-dimensional chromatin interactions. Typically, chemical crosslinking with formaldehyde (FA) is used to fix chromatin interactions. Then, chromatin digestion with a restriction enzyme and subsequent religation of fragment ends converts three-dimensional (3D) proximity into unique ligation products. Finally, after reversal of crosslinks, protein removal, and DNA isolation, DNA is sheared and prepared for high-throughput sequencing. The frequency of proximity ligation of pairs of loci is a measure of the frequency of their colocalization in three-dimensional space in a cell population. A sequenced Hi-C library provides genome-wide information on interaction frequencies between all pairs of loci. The resolution and precision of Hi-C relies on efficient crosslinking that maintains chromatin contacts and frequent and uniform fragmentation of the chromatin. This paper describes an improved in situ Hi-C protocol, Hi-C 3.0, that increases the efficiency of crosslinking by combining two crosslinkers (formaldehyde [FA] and disuccinimidyl glutarate [DSG]), followed by finer digestion using two restriction enzymes (DpnII and DdeI). Hi-C 3.0 is a single protocol for the accurate quantification of genome folding features at smaller scales such as loops and topologically associating domains (TADs), as well as features at larger nucleus-wide scales such as compartments.}, }
@article {pmid36740586, year = {2023}, author = {Selcen, I and Prentice, E and Casaccia, P}, title = {The epigenetic landscape of oligodendrocyte lineage cells.}, journal = {Annals of the New York Academy of Sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/nyas.14959}, pmid = {36740586}, issn = {1749-6632}, abstract = {The epigenetic landscape of oligodendrocyte lineage cells refers to the cell-specific modifications of DNA, chromatin, and RNA that define a unique gene expression pattern of functionally specialized cells. Here, we focus on the epigenetic changes occurring as progenitors differentiate into myelin-forming cells and respond to the local environment. First, modifications of DNA, RNA, nucleosomal histones, key principles of chromatin organization, topologically associating domains, and local remodeling will be reviewed. Then, the relationship between epigenetic modulators and RNA processing will be explored. Finally, the reciprocal relationship between the epigenome as a determinant of the mechanical properties of cell nuclei and the target of mechanotransduction will be discussed. The overall goal is to provide an interpretative key on how epigenetic changes may account for the heterogeneity of the transcriptional profiles identified in this lineage.}, }
@article {pmid36736317, year = {2023}, author = {Costea, J and Schoeberl, UE and Malzl, D and von der Linde, M and Fitz, J and Gupta, A and Makharova, M and Goloborodko, A and Pavri, R}, title = {A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2023.01.014}, pmid = {36736317}, issn = {1097-4164}, abstract = {Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.}, }
@article {pmid36735786, year = {2023}, author = {Cavalheiro, GR and Girardot, C and Viales, RR and Pollex, T and Cao, TBN and Lacour, P and Feng, S and Rabinowitz, A and Furlong, EEM}, title = {CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eade1085}, pmid = {36735786}, issn = {2375-2548}, mesh = {Animals ; *Drosophila/genetics/metabolism ; *Drosophila Proteins/metabolism ; Genome ; Chromatin/genetics ; Chromosomes ; DNA-Binding Proteins/metabolism ; Eye Proteins/genetics/metabolism ; Microtubule-Associated Proteins/metabolism ; Nuclear Proteins/metabolism ; CCCTC-Binding Factor/genetics ; }, abstract = {The boundaries of topologically associating domains (TADs) are delimited by insulators and/or active promoters; however, how they are initially established during embryogenesis remains unclear. Here, we examined this during the first hours of Drosophila embryogenesis. DNA-FISH confirms that intra-TAD pairwise proximity is established during zygotic genome activation (ZGA) but with extensive cell-to-cell heterogeneity. Most newly formed boundaries are occupied by combinations of CTCF, BEAF-32, and/or CP190. Depleting each insulator individually from chromatin revealed that TADs can still establish, although with lower insulation, with a subset of boundaries (~10%) being more dependent on specific insulators. Some weakened boundaries have aberrant gene expression due to unconstrained enhancer activity. However, the majority of misexpressed genes have no obvious direct relationship to changes in domain-boundary insulation. Deletion of an active promoter (thereby blocking transcription) at one boundary had a greater impact than deleting the insulator-bound region itself. This suggests that cross-talk between insulators and active promoters and/or transcription might reinforce domain boundary insulation during embryogenesis.}, }
@article {pmid36719724, year = {2023}, author = {Landshammer, A and Bolondi, A and Kretzmer, H and Much, C and Buschow, R and Rose, A and Wu, HJ and Mackowiak, SD and Braendl, B and Giesselmann, P and Tornisiello, R and Parsi, KM and Huey, J and Mielke, T and Meierhofer, D and Maehr, R and Hnisz, D and Michor, F and Rinn, JL and Meissner, A}, title = {T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36719724}, issn = {2050-084X}, mesh = {Pregnancy ; Female ; Humans ; *RNA, Long Noncoding/genetics/metabolism ; Epithelial-Mesenchymal Transition ; Endoderm ; Gene Expression Regulation, Developmental ; SOXF Transcription Factors/genetics/metabolism ; Cell Differentiation/genetics ; }, abstract = {Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.}, }
@article {pmid36717722, year = {2023}, author = {Barajas-Mora, EM and Lee, L and Lu, H and Valderrama, JA and Bjanes, E and Nizet, V and Feeney, AJ and Hu, M and Murre, C}, title = {Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens.}, journal = {Nature immunology}, volume = {24}, number = {2}, pages = {320-336}, pmid = {36717722}, issn = {1529-2916}, mesh = {Mice ; Animals ; *Chromatin/genetics ; Immunoglobulin Variable Region/genetics ; Immunoglobulin kappa-Chains/genetics ; *Methicillin-Resistant Staphylococcus aureus/genetics ; B-Lymphocytes ; Epigenesis, Genetic ; }, abstract = {Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene segments that rearrange to generate antigen receptor repertoires. Here, we identified an enhancer (E34) in the murine immunoglobulin kappa (Igk) locus that instructed rearrangement of Vκ genes located in a sub-topologically associating domain, including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. We show that E34 instructs the nuclear repositioning of the E34 sub-topologically associating domain from a recombination-repressive compartment to a recombination-permissive compartment that is marked by equivalent activating histone modifications. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. We propose that the merging of Vκ genes with Jκ elements is instructed by one-dimensional epigenetic information imposed by enhancers across Vκ and Jκ genomic regions. The data also reveal how enhancers generate distinct antibody repertoires that provide protection against lethal bacterial infection.}, }
@article {pmid36708949, year = {2023}, author = {Nayak, S and Jiang, K and Hope, E and Cross, M and Overmiller, A and Naz, F and Worrell, S and Bajpai, D and Hasneen, K and Brooks, SR and Dell'Orso, S and Morasso, MI}, title = {Chromatin landscape governing murine epidermal differentiation.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2022.12.020}, pmid = {36708949}, issn = {1523-1747}, abstract = {Chromatin landscape and regulatory networks are determinant in lineage specification and differentiation. To define the temporospatial differentiation axis in murine epidermal cells in vivo, we generated datasets profiling expression dynamics (RNA-Seq), chromatin accessibility (ATAC-Seq), architecture (Hi-C), and histone modifications (ChIP-Seq) in the epidermis. We show that many differentially regulated genes are suppressed during the differentiation process, with super-enhancers (SEs) controlling differentiation-specific epigenomic changes. Our data shows the relevance of the Dlx/Klf/Grhl combinatorial regulatory network in maintaining correct temporospatial gene expression during epidermal differentiation. We determined differential open compartments, topologically associating domain (TAD) score and looping in the Basal cell (B) and Suprabasal cell (SB) epidermal fractions, with the evolutionarily conserved Epidermal Differentiation Complex (EDC) region showing distinct SB-specific TAD and loop formation that coincided with SE sites. Overall, our study provides a global genome-wide resource of chromatin dynamics that define unrecognized regulatory networks and the epigenetic control of Dlx3-bound SE elements during epidermal differentiation.}, }
@article {pmid36708167, year = {2023}, author = {Fan, S and Dang, D and Ye, Y and Zhang, SW and Gao, L and Zhang, S}, title = {scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.}, journal = {Journal of molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jmcb/mjad003}, pmid = {36708167}, issn = {1759-4685}, abstract = {Single-cell Hi-C technology provides an unprecedented opportunity to reveal chromatin structure in individual cells. However, high sequencing cost impedes the generation of biological Hi-C data with high sequencing depths and multiple replicates for downstream analysis. Here we developed a single-cell Hi-C simulator (scHi-CSim) that generates high-fidelity data for benchmarking. scHi-CSim merges neighboring cells to overcome the sparseness of data, samples interactions in distance-stratified chromosomes to maintain the heterogeneity of single cells, and estimates the empirical distribution of restriction fragments to generate simulated data. We demonstrated that scHi-CSim can generate high-fidelity data by comparing the performance of single-cell clustering and detection of chromosomal high-order structures with raw data. Furthermore, scHi-CSim is flexible to change sequencing depths and the number of simulated replicates. We showed that increasing sequencing depths could improve the accuracy of detecting topologically associating domains. We also used scHi-CSim to generate a series of simulated datasets with different sequencing depths to benchmark single-cell Hi-C clustering methods.}, }
@article {pmid36693380, year = {2023}, author = {Kim, S and Wysocka, J}, title = {Deciphering the multi-scale, quantitative cis-regulatory code.}, journal = {Molecular cell}, volume = {83}, number = {3}, pages = {373-392}, pmid = {36693380}, issn = {1097-4164}, support = {R35 GM131757/GM/NIGMS NIH HHS/United States ; }, mesh = {*Enhancer Elements, Genetic ; *Transcription Factors/genetics/metabolism ; Promoter Regions, Genetic ; Gene Expression Regulation ; Base Sequence ; Chromatin/genetics ; }, abstract = {Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.}, }
@article {pmid36658660, year = {2023}, author = {Ni, L and Liu, Y and Ma, X and Liu, T and Yang, X and Wang, Z and Liang, Q and Liu, S and Zhang, M and Wang, Z and Shen, Y and Tian, Z}, title = {Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {12}, pmid = {36658660}, issn = {1474-760X}, mesh = {*Soybeans/genetics ; *Genome ; Gene Expression Regulation ; Retroelements ; Genome, Plant ; Chromatin ; }, abstract = {BACKGROUND: High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.<br><br>RESULTS: Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations&#xa0;(SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site&#xa0;(TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation&#xa0;(PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.<br><br>CONCLUSION: Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.}, }
@article {pmid36650052, year = {2023}, author = {Islam, Z and Saravanan, B and Walavalkar, K and Farooq, U and Singh, AK and Radhakrishnan, S and Thakur, J and Pandit, A and Henikoff, S and Notani, D}, title = {Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.}, journal = {Genome research}, volume = {33}, number = {1}, pages = {1-17}, doi = {10.1101/gr.276643.122}, pmid = {36650052}, issn = {1549-5469}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Chromatin/genetics ; CCCTC-Binding Factor/metabolism ; Binding Sites ; Promoter Regions, Genetic ; *RNA ; Enhancer Elements, Genetic ; }, abstract = {Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF and MYC TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.}, }
@article {pmid36642680, year = {2023}, author = {Yeo, SJ and Ying, C and Fullwood, MJ and Tergaonkar, V}, title = {Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2022.12.003}, pmid = {36642680}, issn = {0168-9525}, abstract = {Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.}, }
@article {pmid36617663, year = {2023}, author = {Mulhair, PO and Crowley, L and Boyes, DH and Harper, A and Lewis, OT and ,  and Holland, PWH}, title = {Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera.}, journal = {Genome research}, volume = {33}, number = {1}, pages = {32-44}, doi = {10.1101/gr.277118.122}, pmid = {36617663}, issn = {1549-5469}, support = {218328/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Genes, Homeobox ; *Butterflies ; Phylogeny ; Multigene Family ; Genomics ; Evolution, Molecular ; }, abstract = {Homeobox genes encode transcription factors with essential roles in patterning and cell fate in developing animal embryos. Many homeobox genes, including Hox and NK genes, are arranged in gene clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary genome assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large order of insects. Here we analyze an extensive data set of high-quality genomes to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which the lab gene is repositioned and the ro gene is next to pb A topologically associating domain spans much of the gene cluster, suggesting deep regulatory conservation of the Hox cluster arrangement in this insect order. Most Lepidoptera have four Shx genes, divergent zen-derived loci, but these loci underwent dramatic duplication in several lineages, with some moths having over 165 homeobox loci in the Hox gene cluster; this expansion is associated with local LINE element density. In contrast, the NK gene cluster content is more stable, although there are differences in organization compared with other insects, as well as major rearrangements within butterflies. Our analysis represents the first description of homeobox gene content across the order Lepidoptera, exemplifying the potential of newly generated genome assemblies for understanding genome and gene family evolution.}, }
@article {pmid36609218, year = {2023}, author = {Zhang, L and Xu, M and Zhang, W and Zhu, C and Cui, Z and Fu, H and Ma, Y and Huang, S and Cui, J and Liang, S and Huang, L and Wang, H}, title = {Three-dimensional genome landscape comprehensively reveals patterns of spatial gene regulation in papillary and anaplastic thyroid cancers: a study using representative cell lines for each cancer type.}, journal = {Cellular &amp; molecular biology letters}, volume = {28}, number = {1}, pages = {1}, pmid = {36609218}, issn = {1689-1392}, mesh = {Humans ; Cell Line ; Chromatin/genetics ; DNA Copy Number Variations/genetics ; Homeodomain Proteins/genetics ; Methyltransferases/genetics ; *Thyroid Carcinoma, Anaplastic/genetics ; *Thyroid Neoplasms/genetics ; Transcription Factors/genetics ; Genome ; }, abstract = {BACKGROUND: Spatial chromatin structure is intricately linked with somatic aberrations, and somatic mutations of various cancer-related genes, termed co-mutations (CoMuts), occur in certain patterns during cancer initiation and progression. The functional mechanisms underlying these genetic events remain largely unclear in thyroid cancer (TC). With discrepant differentiation, papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) differ greatly in characteristics and prognosis. We aimed to reveal the spatial gene alterations and regulations between the two TC subtypes.<br><br>METHODS: We systematically investigated and compared the spatial co-mutations between ATC (8305C), PTC (BCPAP and TPC-1), and normal thyroid cells (Nthy-ori-3-1). We constructed a framework integrating whole-genome sequencing (WGS), high-throughput chromosome conformation capture (Hi-C), and transcriptome sequencing, to systematically detect the associations between the somatic co-mutations of cancer-related genes, structural variations (SVs), copy number variations (CNVs), and high-order chromatin conformation.<br><br>RESULTS: Spatial co-mutation hotspots were enriched around topologically associating domains (TADs) in TC. A common set of 227 boundaries were identified in both ATC and PTC, with significant overlaps between them. The spatial proximities of the co-mutated gene pairs in the two TC types were significantly greater than in the gene-level and overall backgrounds, and ATC cells had higher TAD contact frequency with CoMuts&#x2009;>&#x2009;10 compared with PTC cells. Compared with normal thyroid cells, in ATC the number of the created novel three-dimensional chromatin structural domains increased by 10%, and the number of shifted TADs decreased by 7%. We found five TAD blocks with CoMut genes/events specific to ATC with certain mutations in genes including MAST-NSUN4, AM129B/TRUB2, COL5A1/PPP1R26, PPP1R26/GPSM1/CCDC183, and PRAC2/DLX4. For the majority of ATC and PTC cells, the HOXA10 and HIF2&#x3b1; signals close to the transcription start sites of CoMut genes within TADs were significantly stronger than those at the background. CNV breakpoints significantly overlapped with TAD boundaries in both TC subtypes. ATCs had more CNV losses overlapping with TAD boundaries, and noncoding SVs involved in intrachromosomal SVs, amplified inversions, and tandem duplication differed between ATC and PTC. TADs with short range were more abundant in ATC than PTC. More switches of A/B compartment types existed in ATC cells compared with PTC. Gene expression was significantly synchronized, and orchestrated by complex epigenetics and regulatory elements.<br><br>CONCLUSION: Chromatin interactions and gene alterations and regulations are largely heterogeneous in TC. CNVs and complex SVs may function in the TC genome by interplaying with TADs, and are largely different between ATC and PTC. Complexity of TC genomes, which are highly organized by 3D genome-wide interactions mediating mutational and structural variations and gene activation, may have been largely underappreciated. Our comprehensive analysis may provide key evidence and targets for more customized diagnosis and treatment of TC.}, }
@article {pmid36549923, year = {2023}, author = {van Mierlo, G and Pushkarev, O and Kribelbauer, JF and Deplancke, B}, title = {Chromatin modules and their implication in genomic organization and gene regulation.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {2}, pages = {140-153}, doi = {10.1016/j.tig.2022.11.003}, pmid = {36549923}, issn = {0168-9525}, mesh = {*Chromatin/genetics ; *Gene Expression Regulation/genetics ; Genome/genetics ; Genomics ; Regulatory Sequences, Nucleic Acid/genetics ; }, abstract = {Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulating gene expression remains obscure. Recent complementary observations revealed that interactions between CREs frequently result in the formation of small-scale functional modules within topologically associating domains. Such chromatin modules likely emerge from a complex interplay between regulatory machineries assembled at CREs, including site-specific binding of transcription factors. Here, we review the methods that allow identifying chromatin modules, summarize possible mechanisms that steer CRE interactions within these modules, and discuss outstanding challenges to uncover how chromatin modules fit in our current understanding of the functional 3D genome.}, }
@article {pmid36511816, year = {2022}, author = {Kato, H and Tateishi, K and Iwadate, D and Yamamoto, K and Fujiwara, H and Nakatsuka, T and Kudo, Y and Hayakawa, Y and Ijichi, H and Otsuka, M and Kishikawa, T and Takahashi, R and Miyabayashi, K and Nakai, Y and Hirata, Y and Toyoda, A and Morishita, S and Fujishiro, M}, title = {HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers.}, journal = {Cancer science}, volume = {}, number = {}, pages = {}, doi = {10.1111/cas.15690}, pmid = {36511816}, issn = {1349-7006}, abstract = {The molecular subtypes of pancreatic cancer (PC), either classical/progenitor-like or basal/squamous-like, are currently a major topic of research because of their direct association with clinical outcomes. Some transcription factors (TFs) have been reported to be associated with these subtypes. However, the mechanisms by which these molecular signatures of PCs are established remain unknown. Epigenetic regulatory processes, supported by dynamic changes in the chromatin structure, are essential for transcriptional profiles. Previously, we reported the importance of open chromatin profiles in the biological features and transcriptional status of PCs. Here, we aimed to analyze the relationships between three-dimensional (3D) genome structures and the molecular subtypes of human PCs using Hi-C analysis. We observed a correlation of the specific elements of 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops, with the expression of related genes. We focused on HNF1B, a TF that is implicated in the progenitor subtype. Forced expression of HNF1B in squamous-type PC organoids induced the upregulation and downregulation of genes associated with progenitor and squamous subtypes, respectively. Long-range genomic interactions induced by HNF1B were accompanied by compartment modulation and H3K27ac redistribution. We also found that these HNF1B-induced changes in subtype-related gene expression required an intrinsically disordered region, suggesting a possible involvement of phase separation in compartment modulation. Thus, mapping of 3D structural changes induced by TFs, such as HNF1B, may become a useful resource for further understanding the molecular features of PCs.}, }
@article {pmid36493778, year = {2023}, author = {Alavattam, KG and Mitzelfelt, KA and Bonora, G and Fields, PA and Yang, X and Chiu, HS and Pabon, L and Bertero, A and Palpant, NJ and Noble, WS and Murry, CE}, title = {Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation.}, journal = {Stem cell reports}, volume = {18}, number = {1}, pages = {159-174}, pmid = {36493778}, issn = {2213-6711}, support = {U54 DK107979/DK/NIDDK NIH HHS/United States ; R01 HL146868/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Endothelial Cells ; *Chromatin ; Cell Differentiation/genetics ; Gene Expression Regulation ; }, abstract = {Vascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. The gene-regulatory mechanisms underpinning endothelial specialization are largely unknown, as are the roles of chromatin organization in regulating endothelial cell transcription. To investigate the relationships between chromatin organization and gene expression, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-sequencing assays at specific time points. Long-range intrachromosomal contacts increase over the course of differentiation, accompanied by widespread heteroeuchromatic compartment transitions that are tightly associated with transcription. Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene expression. Chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes essential to vascular biology. Chromatin dynamics guide transcription in endothelial cell development and promote the divergence of endothelial cells from cardiomyocytes.}, }
@article {pmid36482308, year = {2022}, author = {Yang, JY and Chang, JM}, title = {Pattern recognition of topologically associating domains using deep learning.}, journal = {BMC bioinformatics}, volume = {22}, number = {Suppl 10}, pages = {634}, pmid = {36482308}, issn = {1471-2105}, mesh = {Humans ; Animals ; Mice ; *Deep Learning ; Genomics ; }, abstract = {BACKGROUND: Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines?<br><br>RESULTS: To address the above question, we propose a novel task-TAD recognition-as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising,&#xa0;AUC&#x2009;>&#x2009;0.80,&#xa0;through cross-species and cell-type validation.<br><br>CONCLUSIONS: TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable.}, }
@article {pmid36471076, year = {2022}, author = {Mach, P and Kos, PI and Zhan, Y and Cramard, J and Gaudin, S and Tünnermann, J and Marchi, E and Eglinger, J and Zuin, J and Kryzhanovska, M and Smallwood, S and Gelman, L and Roth, G and Nora, EP and Tiana, G and Giorgetti, L}, title = {Cohesin and CTCF control the dynamics of chromosome folding.}, journal = {Nature genetics}, volume = {54}, number = {12}, pages = {1907-1918}, pmid = {36471076}, issn = {1546-1718}, mesh = {*Chromosomes/genetics ; }, abstract = {In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.}, }
@article {pmid36469845, year = {2022}, author = {Zhao, X and Zhu, S and Peng, W and Xue, HH}, title = {The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {209}, number = {12}, pages = {2269-2278}, pmid = {36469845}, issn = {1550-6606}, support = {I01 BX005771/BX/BLRD VA/United States ; R01 AI112579/AI/NIAID NIH HHS/United States ; R01 AI121080/AI/NIAID NIH HHS/United States ; R01 AI139874/AI/NIAID NIH HHS/United States ; }, mesh = {CCCTC-Binding Factor/genetics ; *Chromatin/genetics ; *Cell Cycle Proteins/metabolism ; Genome ; Chromosomes ; Cell Differentiation/genetics ; }, abstract = {T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.}, }
@article {pmid36466643, year = {2022}, author = {Wang, X and Yang, B and Zhao, W and Cao, W and Shen, Y and Li, Z and Bao, X}, title = {Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1012377}, pmid = {36466643}, issn = {1664-302X}, abstract = {Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. A high vanillin-tolerant Saccharomyces cerevisiae strain EMV-8 carrying site mutations compared to its parent strain NAN-27 was selected for the analyses. The dynamics of the chromatin structure of eukaryotic cells play a critical role in transcription and the regulation of gene expression and thus the phenotype. Consequently, Hi-C and transcriptome analyses were conducted in EMV-8 and NAN-27 in the log phase with or without vanillin stress to determine the effects of mutations and vanillin disturbance on the dynamics of three-dimensional chromosome organization and the influence of the organization on the transcriptome. The outcomes indicated that the chromosome interaction pattern disturbed by vanillin stress or genetic mutations in the log phase was similar to that in mouse cells. The short chromosomes contact the short chromosomes, and the long chromosomes contact the long chromosomes. In response to vanillin stress, the boundaries of the topologically associating domain (TAD) in the vanillin-tolerant strain EMV-8 were more stable than those in its parent strain NAN-27. The motifs of SFL1, STB3, and NHP6A/B were enriched at TAD boundaries in both EMV-8 and NAN-27 with or without vanillin, indicating that these four genes were probably related to TAD formation. The Indel mutation of YRR1, whose absence was confirmed to benefit vanillin tolerance in EMV-8, caused two new interaction sites that contained three genes, WTM2, PUP1, and ALE1, whose overexpression did not affect vanillin resistance in yeast. Overall, our results revealed that in the log phase, genetic mutations and vanillin disturbance have a negligible effect on three-dimensional chromosome organization, and the reformation or disappearance of TAD boundaries did not show an association with gene expression, which provides an example for studying yeast chromatin structure during stress tolerance using Hi-C technology.}, }
@article {pmid36465116, year = {2022}, author = {Bi, H and Hou, Y and Wang, J and Xia, Z and Wang, D and Liu, Y and Bao, H and Han, X and Ren, K and Li, E and Yue, F and Ji, P}, title = {Chromatin reconstruction during mouse terminal erythropoiesis.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105554}, pmid = {36465116}, issn = {2589-0042}, abstract = {Mammalian terminal erythropoiesis involves chromatin and nuclear condensation followed by enucleation. Late-stage erythroblasts undergo caspase-mediated nuclear opening that is important for nuclear condensation through partial histone release. It remains unknown the dynamic changes of three-dimensional (3D) genomic organization during terminal erythropoiesis. Here, we used Hi-C to determine the chromatin structural change during primary mouse erythroblast terminal differentiation. We also performed RNA-sequencing and ATAC-sequencing under the same experimental setting to further reveal the genome accessibility and gene expression changes during this process. We found that late-stage terminal erythropoiesis involves global loss of topologically associating domains and establishment of inter-chromosomal interactions of the heterochromatin regions, which are associated with globally increased chromatin accessibility and upregulation of erythroid-related genes.}, }
@article {pmid36460680, year = {2022}, author = {Zhang, Y and Blanchette, M}, title = {Reference panel guided topological structure annotation of Hi-C data.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7426}, pmid = {36460680}, issn = {2041-1723}, abstract = {Accurately annotating topological structures (e.g., loops and topologically associating domains) from Hi-C data is critical for understanding the role of 3D genome organization in gene regulation. This is a challenging task, especially at high resolution, in part due to the limited sequencing coverage of Hi-C data. Current approaches focus on the analysis of individual Hi-C data sets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available, and (ii) the vast majority of topological structures are conserved across multiple cell types. Here, we present RefHiC, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate topological structure annotation from a given study sample. We compare RefHiC against tools that do not use reference samples and find that RefHiC outperforms other programs at both topological associating domain and loop annotation across different cell types, species, and sequencing depths.}, }
@article {pmid36448318, year = {2023}, author = {Miyata, M and Yoshida, J and Takagishi, I and Horie, K}, title = {Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {30}, number = {1}, pages = {}, pmid = {36448318}, issn = {1756-1663}, mesh = {Animals ; Mice ; *CRISPR-Cas Systems ; *Mouse Embryonic Stem Cells ; Gene Editing/methods ; Genome ; Recombinational DNA Repair ; DNA End-Joining Repair ; }, abstract = {The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters and topologically associating domains. To analyse these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster in mouse embryonic stem cells using CRISPR-Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN); and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. Inversion was also detected at similar efficiency. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31-63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.}, }
@article {pmid36443333, year = {2022}, author = {Wang, Y and Mak, TSH and Dattani, S and Garcia-Barcelo, MM and Fu, AX and Yip, KY and Ngan, ES and Tam, PK and Tang, CS and Sham, PC}, title = {Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20423}, pmid = {36443333}, issn = {2045-2322}, mesh = {Humans ; *Hirschsprung Disease/genetics ; Epistasis, Genetic ; Whole Genome Sequencing ; Alleles ; Asian People ; Proto-Oncogene Proteins c-ret/genetics ; }, abstract = {Common variants in RET and NRG1 have been associated with Hirschsprung disease (HSCR), a congenital disorder characterised by incomplete innervation of distal gut, in East Asian (EA) populations. However, the allelic effects so far identified do not fully explain its heritability, suggesting the presence of epistasis, where effect of one genetic variant differs depending on other (modifier) variants. Few instances of epistasis have been documented in complex diseases due to modelling complexity and data challenges. We proposed four epistasis models to comprehensively capture epistasis for HSCR between and within RET and NRG1 loci using whole genome sequencing (WGS) data in EA samples. 65 variants within the Topologically Associating Domain (TAD) of RET demonstrated significant epistasis with the lead enhancer variant (RET+3; rs2435357). These epistatic variants formed two linkage disequilibrium (LD) clusters represented by rs2506026 and rs2506028 that differed in minor allele frequency and the best-supported epistatic model. Intriguingly, rs2506028 is in high LD with one cis-regulatory variant (rs2506030) highlighted previously, suggesting that detected epistasis might be mediated through synergistic effects on transcription regulation of RET. Our findings demonstrated the advantages of WGS data for detecting epistasis, and support the presence of interactive effects of regulatory variants in RET for HSCR.}, }
@article {pmid36409894, year = {2022}, author = {Zhao, H and Yang, M and Bishop, J and Teng, Y and Cao, Y and Beall, BD and Li, S and Liu, T and Fang, Q and Fang, C and Xin, H and Nützmann, HW and Osbourn, A and Meng, F and Jiang, J}, title = {Identification and functional validation of super-enhancers in Arabidopsis thaliana.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2215328119}, pmid = {36409894}, issn = {1091-6490}, support = {BBS/E/J/00PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Arabidopsis/genetics ; Regulatory Sequences, Nucleic Acid ; *Triterpenes ; Chromatin/genetics ; Mammals/genetics ; }, abstract = {Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131-157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.}, }
@article {pmid36357311, year = {2022}, author = {Yancoskie, MN and Maritz, C and van Eijk, P and Reed, SH and Naegeli, H}, title = {To incise or not and where: SET-domain methyltransferases know.}, journal = {Trends in biochemical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibs.2022.10.003}, pmid = {36357311}, issn = {0968-0004}, abstract = {The concept of the histone code posits that histone modifications regulate gene functions once interpreted by epigenetic readers. A well-studied case is trimethylation of lysine 4 of histone H3 (H3K4me3), which is enriched at gene promoters. However, H3K4me3 marks are not needed for the expression of most genes, suggesting extra roles, such as influencing the 3D genome architecture. Here, we highlight an intriguing analogy between the H3K4me3-dependent induction of double-strand breaks in several recombination events and the impact of this same mark on DNA incisions for the repair of bulky lesions. We propose that Su(var)3-9, Enhancer-of-zeste and Trithorax (SET)-domain methyltransferases generate H3K4me3 to guide nucleases into chromatin spaces, the favorable accessibility of which ensures that DNA break intermediates are readily processed, thereby safeguarding genome stability.}, }
@article {pmid36331876, year = {2022}, author = {Kim, J and Jimenez, DS and Ragipani, B and Zhang, B and Street, LA and Kramer, M and Albritton, SE and Winterkorn, LH and Morao, AK and Ercan, S}, title = {Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36331876}, issn = {2050-084X}, support = {R35 GM130311/GM/NIGMS NIH HHS/United States ; T32 HD007520/HD/NICHD NIH HHS/United States ; R33 EB019784/EB/NIBIB NIH HHS/United States ; R01 DC005991/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Gene Expression Regulation ; Dosage Compensation, Genetic ; X Chromosome/genetics ; }, abstract = {Condensins are molecular motors that compact DNA via linear translocation. In Caenorhabditis elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of recruitment elements on the X-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a 'super rex' composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to the formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.}, }
@article {pmid36325618, year = {2022}, author = {Attou, A and Zülske, T and Wedemann, G}, title = {Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.}, journal = {Biophysical journal}, volume = {121}, number = {24}, pages = {4788-4799}, pmid = {36325618}, issn = {1542-0086}, mesh = {CCCTC-Binding Factor/chemistry/genetics/metabolism ; *Nucleosomes ; Protein Binding ; *Cell Cycle Proteins/metabolism ; Chromatin ; }, abstract = {The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.}, }
@article {pmid36323253, year = {2022}, author = {Zhu, X and Qi, C and Wang, R and Lee, JH and Shao, J and Bei, L and Xiong, F and Nguyen, PT and Li, G and Krakowiak, J and Koh, SP and Simon, LM and Han, L and Moore, TI and Li, W}, title = {Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization.}, journal = {Cell reports}, volume = {41}, number = {5}, pages = {111576}, pmid = {36323253}, issn = {2211-1247}, support = {R21 GM132778/GM/NIGMS NIH HHS/United States ; R01 HG011633/HG/NHGRI NIH HHS/United States ; R01 CA262623/CA/NCI NIH HHS/United States ; K01 HL143111/HL/NHLBI NIH HHS/United States ; U01 HL156059/HL/NHLBI NIH HHS/United States ; R01 GM136922/GM/NIGMS NIH HHS/United States ; K22 CA204468/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Nuclear Pore Complex Proteins/genetics ; *Nuclear Proteins/genetics ; Transcription Factors/genetics ; Nuclear Pore ; Genome ; Chromatin ; Cell Cycle Proteins/genetics ; }, abstract = {The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&amp;Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.}, }
@article {pmid36318264, year = {2023}, author = {Wang, Y and Song, C and Zhao, J and Zhang, Y and Zhao, X and Feng, C and Zhang, G and Zhu, J and Wang, F and Qian, F and Zhou, L and Zhang, J and Bai, X and Ai, B and Liu, X and Wang, Q and Li, C}, title = {SEdb 2.0: a comprehensive super-enhancer database of human and mouse.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D280-D290}, pmid = {36318264}, issn = {1362-4962}, mesh = {Animals ; Humans ; Mice ; Chromatin/genetics ; *Databases, Genetic ; *Enhancer Elements, Genetic ; Gene Expression Regulation ; Transcription Factors/genetics/metabolism ; }, abstract = {Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.licpathway.net/sedb) aims to provide a comprehensive SE resource and annotate their potential roles in gene transcriptions. Compared with SEdb 1.0, we have made the following improvements: (i) Newly added the mouse SEs and expanded the scale of human SEs. SEdb 2.0 contained 1 167 518 SEs from 1739 human H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) samples and 550 226 SEs from 931 mouse H3K27ac ChIP-seq samples, which was five times that of SEdb 1.0. (ii) Newly added transcription factor binding sites (TFBSs) in SEs identified by TF motifs and TF ChIP-seq data. (iii) Added comprehensive (epi)genetic annotations of SEs, including chromatin accessibility regions, methylation sites, chromatin interaction regions and topologically associating domains (TADs). (iv) Newly embedded and updated search and analysis tools, including 'Search SE by TF-based', 'Differential-Overlapping-SE analysis' and 'SE-based TF-Gene analysis'. (v) Newly provided quality control (QC) metrics for ChIP-seq processing. In summary, SEdb 2.0 is a comprehensive update of SEdb 1.0, which curates more SEs and annotation information than SEdb 1.0. SEdb 2.0 provides a friendly platform for researchers to more comprehensively clarify the important role of SEs in the biological process.}, }
@article {pmid36316347, year = {2022}, author = {Telonis, AG and Yang, Q and Huang, HT and Figueroa, ME}, title = {MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6524}, pmid = {36316347}, issn = {2041-1723}, mesh = {Mice ; Animals ; *Epigenome ; Retroelements/genetics ; Transcriptome/genetics ; Mutation ; *Leukemia, Myeloid, Acute/genetics/metabolism ; DNA Methylation/genetics ; }, abstract = {DNMT3A and IDH1/2 mutations combinatorically regulate the transcriptome and the epigenome in acute myeloid leukemia; yet the mechanisms of this interplay are unknown. Using a systems approach within topologically associating domains, we find that genes with significant expression-methylation correlations are enriched in signaling and metabolic pathways. The common denominator across these methylation-regulated genes is the density in MIR retrotransposons of their introns. Moreover, a discrete number of CpGs overlapping enhancers are responsible for regulating most of these genes. Established mouse models recapitulate the dependency of MIR-rich genes on the balanced expression of epigenetic modifiers, while projection of leukemic profiles onto normal hematopoiesis ones further consolidates the dependencies of methylation-regulated genes on MIRs. Collectively, MIR elements on genes and enhancers are susceptible to changes in DNA methylation activity and explain the cooperativity of proteins in this pathway in normal and malignant hematopoiesis.}, }
@article {pmid36309531, year = {2022}, author = {Schöpflin, R and Melo, US and Moeinzadeh, H and Heller, D and Laupert, V and Hertzberg, J and Holtgrewe, M and Alavi, N and Klever, MK and Jungnitsch, J and Comak, E and Türkmen, S and Horn, D and Duffourd, Y and Faivre, L and Callier, P and Sanlaville, D and Zuffardi, O and Tenconi, R and Kurtas, NE and Giglio, S and Prager, B and Latos-Bielenska, A and Vogel, I and Bugge, M and Tommerup, N and Spielmann, M and Vitobello, A and Kalscheuer, VM and Vingron, M and Mundlos, S}, title = {Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6470}, pmid = {36309531}, issn = {2041-1723}, mesh = {Humans ; *Genome/genetics ; Base Sequence ; *Chromatin ; Chromosome Mapping ; Germ Cells ; }, abstract = {Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.}, }
@article {pmid36289338, year = {2022}, author = {Xu, J and Song, F and Lyu, H and Kobayashi, M and Zhang, B and Zhao, Z and Hou, Y and Wang, X and Luan, Y and Jia, B and Stasiak, L and Wong, JH and Wang, Q and Jin, Q and Jin, Q and Fu, Y and Yang, H and Hardison, RC and Dovat, S and Platanias, LC and Diao, Y and Yang, Y and Yamada, T and Viny, AD and Levine, RL and Claxton, D and Broach, JR and Zheng, H and Yue, F}, title = {Subtype-specific 3D genome alteration in acute myeloid leukaemia.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {387-398}, pmid = {36289338}, issn = {1476-4687}, support = {R35 GM124820/GM/NIGMS NIH HHS/United States ; R01 HG009906/HG/NHGRI NIH HHS/United States ; R01 HG011207/HG/NHGRI NIH HHS/United States ; U01 CA200060/CA/NCI NIH HHS/United States ; R24 DK106766/DK/NIDDK NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 CA216421/CA/NCI NIH HHS/United States ; K08 CA215317/CA/NCI NIH HHS/United States ; U01 DA053691/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; Chromatin/genetics ; DNA Methylation ; *Leukemia, Myeloid, Acute/genetics ; *Genome, Human/genetics ; Promoter Regions, Genetic ; Enhancer Elements, Genetic ; Gene Silencing ; Reproducibility of Results ; CRISPR-Cas Systems ; Sequence Analysis ; DNA (Cytosine-5-)-Methyltransferases ; Gene Expression Regulation, Leukemic ; }, abstract = {Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases[1-5]. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&amp;Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.}, }
@article {pmid36283406, year = {2022}, author = {Mohajeri, K and Yadav, R and D'haene, E and Boone, PM and Erdin, S and Gao, D and Moyses-Oliveira, M and Bhavsar, R and Currall, BB and O'Keefe, K and Burt, ND and Lowther, C and Lucente, D and Salani, M and Larson, M and Redin, C and Dudchenko, O and Aiden, EL and Menten, B and Tai, DJC and Gusella, JF and Vergult, S and Talkowski, ME}, title = {Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models.}, journal = {American journal of human genetics}, volume = {109}, number = {11}, pages = {2049-2067}, pmid = {36283406}, issn = {1537-6605}, support = {R01 MH123155/MH/NIMH NIH HHS/United States ; R01 MH115957/MH/NIMH NIH HHS/United States ; R03 HD099547/HD/NICHD NIH HHS/United States ; U01 HG011755/HG/NHGRI NIH HHS/United States ; R01 NS093200/NS/NINDS NIH HHS/United States ; R01 HD096326/HD/NICHD NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; K08 NS117891/NS/NINDS NIH HHS/United States ; P01 GM061354/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Genome ; Haploinsufficiency ; *Induced Pluripotent Stem Cells ; MEF2 Transcription Factors/genetics ; *Neural Stem Cells ; Neurons ; Transcription, Genetic ; }, abstract = {Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.}, }
@article {pmid36201625, year = {2022}, author = {Torosin, NS and Golla, TR and Lawlor, MA and Cao, W and Ellison, CE}, title = {Mode and Tempo of 3D Genome Evolution in Drosophila.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36201625}, issn = {1537-1719}, support = {R01 GM130698/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; *Genome ; Chromatin/genetics ; Evolution, Molecular ; }, abstract = {Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer-promoter contacts. The deleterious nature of gene misexpression implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels of TAD conservation; however, more recent studies have questioned these results. Furthermore, recent work suggests that TAD reorganization is not associated with extensive changes in gene expression. Here, we investigate the evolutionary conservation of TADs among 11 species of Drosophila. We use Hi-C data to identify TADs in each species and employ a comparative phylogenetic approach to derive empirical estimates of the rate of TAD evolution. Surprisingly, we find that TADs evolve rapidly. However, we also find that the rate of evolution depends on the chromatin state of the TAD, with TADs enriched for developmentally regulated chromatin evolving significantly slower than TADs enriched for broadly expressed, active chromatin. We also find that, after controlling for differences in chromatin state, highly conserved TADs do not exhibit higher levels of gene expression constraint. These results suggest that, in general, most TADs evolve rapidly and their divergence is not associated with widespread changes in gene expression. However, higher levels of evolutionary conservation and gene expression constraints in TADs enriched for developmentally regulated chromatin suggest that these TAD subtypes may be more important for regulating gene expression, likely due to the larger number of long-distance enhancer-promoter contacts associated with developmental genes.}, }
@article {pmid36197938, year = {2022}, author = {Simmons, JR and An, R and Amankwaa, B and Zayac, S and Kemp, J and Labrador, M}, title = {Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila.}, journal = {PLoS genetics}, volume = {18}, number = {10}, pages = {e1010396}, pmid = {36197938}, issn = {1553-7404}, support = {P40 OD010949/OD/NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; R21 MH108956/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Chromatin/genetics/metabolism ; DNA/metabolism ; *Drosophila/genetics ; *Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/genetics/metabolism ; Histones/genetics/metabolism ; Insulator Elements/genetics ; Microtubule-Associated Proteins/genetics ; Nuclear Proteins/genetics ; Phosphoric Monoester Hydrolases/genetics ; Polytene Chromosomes/genetics ; }, abstract = {Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.}, }
@article {pmid36196855, year = {2023}, author = {Jouret, G and Egloff, M and Landais, E and Tassy, O and Giuliano, F and Karmous-Benailly, H and Coutton, C and Satre, V and Devillard, F and Dieterich, K and Vieville, G and Kuentz, P and le Caignec, C and Beneteau, C and Isidor, B and Nizon, M and Callier, P and Marquet, V and Bieth, E and Lévy, J and Tabet, AC and Lyonnet, S and Baujat, G and Rio, M and Cartault, F and Scheidecker, S and Gouronc, A and Schalk, A and Jacquin, C and Spodenkiewicz, M and Angélini, C and Pennamen, P and Rooryck, C and Doco-Fenzy, M and Poirsier, C}, title = {Clinical and genomic delineation of the new proximal 19p13.3 microduplication syndrome.}, journal = {American journal of medical genetics. Part A}, volume = {191}, number = {1}, pages = {52-63}, doi = {10.1002/ajmg.a.62983}, pmid = {36196855}, issn = {1552-4833}, mesh = {Humans ; Comparative Genomic Hybridization ; *Abnormalities, Multiple/genetics ; *Microcephaly/genetics ; Syndrome ; Genetic Association Studies ; }, abstract = {A small but growing body of scientific literature is emerging about clinical findings in patients with 19p13.3 microdeletion or duplication. Recently, a proximal 19p13.3 microduplication syndrome was described, associated with growth delay, microcephaly, psychomotor delay and dysmorphic features. The aim of our study was to better characterize the syndrome associated with duplications in the proximal 19p13.3 region (prox 19p13.3 dup), and to propose a comprehensive analysis of the underlying genomic mechanism. We report the largest cohort of patients with prox 19p13.3 dup through a collaborative study. We collected 24 new patients with terminal or interstitial 19p13.3 duplication characterized by array-based Comparative Genomic Hybridization (aCGH). We performed mapping, phenotype-genotype correlations analysis, critical region delineation and explored three-dimensional chromatin interactions by analyzing Topologically Associating Domains (TADs). We define a new 377 kb critical region (CR 1) in chr19: 3,116,922-3,494,377, GRCh37, different from the previously described critical region (CR 2). The new 377 kb CR 1 includes a TAD boundary and two enhancers whose common target is PIAS4. We hypothesize that duplications of CR 1 are responsible for tridimensional structural abnormalities by TAD disruption and misregulation of genes essentials for the control of head circumference during development, by breaking down the interactions between enhancers and the corresponding targeted gene.}, }
@article {pmid36179666, year = {2022}, author = {Ringel, AR and Szabo, Q and Chiariello, AM and Chudzik, K and Schöpflin, R and Rothe, P and Mattei, AL and Zehnder, T and Harnett, D and Laupert, V and Bianco, S and Hetzel, S and Glaser, J and Phan, MHQ and Schindler, M and Ibrahim, DM and Paliou, C and Esposito, A and Prada-Medina, CA and Haas, SA and Giere, P and Vingron, M and Wittler, L and Meissner, A and Nicodemi, M and Cavalli, G and Bantignies, F and Mundlos, S and Robson, MI}, title = {Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.}, journal = {Cell}, volume = {185}, number = {20}, pages = {3689-3704.e21}, pmid = {36179666}, issn = {1097-4172}, support = {ALTF1554-2016/WT_/Wellcome Trust/United Kingdom ; 206475/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; *Chromatin ; Chromatin Assembly and Disassembly ; Enhancer Elements, Genetic ; Evolution, Molecular ; Female ; Genome ; Mammals/metabolism ; *Placenta/metabolism ; Pregnancy ; Promoter Regions, Genetic ; Transcription Factors/genetics/metabolism ; }, abstract = {Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.}, }
@article {pmid36163358, year = {2022}, author = {Martinez-Fundichely, A and Dixon, A and Khurana, E}, title = {Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5640}, pmid = {36163358}, issn = {2041-1723}, support = {R01 CA218668/CA/NCI NIH HHS/United States ; }, mesh = {*Chromatin ; Genome ; Genomics ; Humans ; *Neoplasms/genetics ; }, abstract = {Structural variations (SVs) in cancer cells often impact large genomic regions with functional consequences. However, identification of SVs under positive selection is a challenging task because little is known about the genomic features related to the background breakpoint distribution in different cancers. We report a method that uses a generalized additive model to investigate the breakpoint proximity curves from 2,382 whole-genomes of 32 cancer types. We find that a multivariate model, which includes linear and nonlinear partial contributions of various tissue-specific features and their interaction terms, can explain up to 57% of the observed deviance of breakpoint proximity. In particular, three-dimensional genomic features such as topologically associating domains (TADs), TAD-boundaries and their interaction with other features show significant contributions. The model is validated by identification of known cancer genes and revealed putative drivers in cancers different than those with previous evidence of positive selection.}, }
@article {pmid36161960, year = {2022}, author = {Damas, J and Corbo, M and Kim, J and Turner-Maier, J and Farré, M and Larkin, DM and Ryder, OA and Steiner, C and Houck, ML and Hall, S and Shiue, L and Thomas, S and Swale, T and Daly, M and Korlach, J and Uliano-Silva, M and Mazzoni, CJ and Birren, BW and Genereux, DP and Johnson, J and Lindblad-Toh, K and Karlsson, EK and Nweeia, MT and Johnson, RN and ,  and Lewin, HA}, title = {Evolution of the ancestral mammalian karyotype and syntenic regions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2209139119}, pmid = {36161960}, issn = {1091-6490}, mesh = {Animals ; Cattle/genetics ; Chromosomes, Mammalian/genetics ; Eutheria/genetics ; *Evolution, Molecular ; Humans ; *Karyotype ; *Mammals/genetics ; Phylogeny ; Sloths/genetics ; *Synteny/genetics ; }, abstract = {Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.}, }
@article {pmid36147678, year = {2022}, author = {Chow, CN and Tseng, KC and Hou, PF and Wu, NY and Lee, TY and Chang, WC}, title = {Mysteries of gene regulation: Promoters are not the sole triggers of gene expression.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {4910-4920}, pmid = {36147678}, issn = {2001-0370}, abstract = {Cis-regulatory elements of promoters are essential for gene regulation by transcription factors (TFs). However, the regulatory roles of nonpromoter regions, TFs, and epigenetic marks remain poorly understood in plants. In this study, we characterized the cis-regulatory regions of 53 TFs and 19 histone marks in 328 chromatin immunoprecipitation (ChIP-seq) datasets from Arabidopsis. The genome-wide maps indicated that both promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs. The maps also revealed a diverse of histone combinations. The analysis suggested that exons play critical roles in the regulation of non-coding genes. Additionally, comparative analysis between heat-stress-responsive and nonresponsive genes indicated that the genes with distinct functions also exhibited substantial differences in cis-regulatory regions, histone regulation, and topologically associating domain (TAD) boundary organization. By integrating multiple high-throughput sequencing datasets, this study generated regulatory models for protein-coding genes, non-coding genes, and TAD boundaries to explain the complexity of transcriptional regulation.}, }
@article {pmid36105358, year = {2022}, author = {Doyle, EJ and Morey, L and Conway, E}, title = {Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {986319}, pmid = {36105358}, issn = {2296-634X}, support = {P30 CA240139/CA/NCI NIH HHS/United States ; R01 GM141349/GM/NIGMS NIH HHS/United States ; }, abstract = {Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.}, }
@article {pmid36104317, year = {2022}, author = {Götz, M and Messina, O and Espinola, S and Fiche, JB and Nollmann, M}, title = {Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5375}, pmid = {36104317}, issn = {2041-1723}, mesh = {Animals ; *Chromatin/genetics ; Chromatin Assembly and Disassembly ; DNA ; *Drosophila/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {The spatial organization of chromatin at the scale of topologically associating domains (TADs) and below displays large cell-to-cell variations. Up until now, how this heterogeneity in chromatin conformation is shaped by chromatin condensation, TAD insulation, and transcription has remained mostly elusive. Here, we used Hi-M, a multiplexed DNA-FISH imaging technique providing developmental timing and transcriptional status, to show that the emergence of TADs at the ensemble level partially segregates the conformational space explored by single nuclei during the early development of Drosophila embryos. Surprisingly, a substantial fraction of nuclei display strong insulation even before TADs emerge. Moreover, active transcription within a TAD leads to minor changes to the local inter- and intra-TAD chromatin conformation in single nuclei and only weakly affects insulation to the neighboring TAD. Overall, our results indicate that multiple parameters contribute to shaping the chromatin architecture of single nuclei at the TAD scale.}, }
@article {pmid36097291, year = {2022}, author = {Kane, L and Williamson, I and Flyamer, IM and Kumar, Y and Hill, RE and Lettice, LA and Bickmore, WA}, title = {Cohesin is required for long-range enhancer action at the Shh locus.}, journal = {Nature structural &amp; molecular biology}, volume = {29}, number = {9}, pages = {891-897}, pmid = {36097291}, issn = {1545-9985}, support = {MC_UU_00007/2/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; CCCTC-Binding Factor/genetics/metabolism ; *Cell Cycle Proteins/genetics/metabolism ; Chromatin/genetics ; *Chromosomal Proteins, Non-Histone/genetics/metabolism ; Enhancer Elements, Genetic/genetics ; Hedgehog Proteins/genetics/metabolism ; Mammals/genetics ; Mice ; Transcription Factors/metabolism ; }, abstract = {The regulatory landscapes of developmental genes in mammals can be complex, with enhancers spread over many hundreds of kilobases. It has been suggested that three-dimensional genome organization, particularly topologically associating domains formed by cohesin-mediated loop extrusion, is important for enhancers to act over such large genomic distances. By coupling acute protein degradation with synthetic activation by targeted transcription factor recruitment, here we show that cohesin, but not CTCF, is required for activation of the target gene Shh by distant enhancers in mouse embryonic stem cells. Cohesin is not required for activation directly at the promoter or by an enhancer located closer to the Shh gene. Our findings support the hypothesis that chromatin compaction via cohesin-mediated loop extrusion allows for genes to be activated by enhancers that are located many hundreds of kilobases away in the linear genome and suggests that cohesin is dispensable for enhancers located more proximally.}, }
@article {pmid36075900, year = {2022}, author = {Zheng, L and Wang, W}, title = {Regulation associated modules reflect 3D genome modularity associated with chromatin activity.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5281}, pmid = {36075900}, issn = {2041-1723}, support = {R01 HG009626/HG/NHGRI NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; Chromosomes ; *Genome ; Promoter Regions, Genetic/genetics ; }, abstract = {The 3D genome has been shown to be organized into modules including topologically associating domains (TADs) and compartments that are primarily defined by spatial contacts from Hi-C. There exists a gap to investigate whether and how the spatial modularity of the chromatin is related to the functional modularity resulting from chromatin activity. Despite histone modifications reflecting chromatin activity, inferring spatial modularity of the genome directly from the histone modification patterns has not been well explored. Here, we report that histone modifications show a modular pattern (referred to as regulation associated modules, RAMs) that reflects spatial chromatin modularity. Enhancer-promoter interactions, loop anchors, super-enhancer clusters and extrachromosomal DNAs (ecDNAs) are found to occur more often within the same RAMs than within the same TADs. Consistently, compared to the TAD boundaries, deletions of RAM boundaries perturb the chromatin structure more severely (may even cause cell death) and somatic variants in cancer samples are more enriched in RAM boundaries. These observations suggest that RAMs reflect a modular organization of the 3D genome at a scale better aligned with chromatin activity, providing a bridge connecting the structural and functional modularity of the genome.}, }
@article {pmid36043052, year = {2022}, author = {Sun, Y and Dotson, GA and Muir, LA and Ronquist, S and Oravecz-Wilson, K and Peltier, D and Seike, K and Li, L and Meixner, W and Rajapakse, I and Reddy, P}, title = {Rearrangement of T Cell genome architecture regulates GVHD.}, journal = {iScience}, volume = {25}, number = {9}, pages = {104846}, pmid = {36043052}, issn = {2589-0042}, abstract = {WAPL, cohesin's DNA release factor, regulates three-dimensional (3D) chromatin architecture. The 3D chromatin structure and its relevance to mature T cell functions is not well understood. We show that in vivo lymphopenic expansion, and alloantigen-driven proliferation, alters the 3D structure and function of the genome in mature T cells. Conditional deletion of WAPL, cohesin's DNA release factor, in T cells reduced long-range genomic interactions and altered chromatin A/B compartments and interactions within topologically associating domains (TADs) of the chromatin in T cells at baseline. WAPL deficiency in T cells reduced loop extensions, changed expression of cell cycling genes and reduced proliferation following in vitro and in vivo stimulation, and reduced severity of graft-versus-host disease (GVHD) following experimental allogeneic hematopoietic stem cell transplantation. These data collectively characterize 3D genomic architecture of T cells in vivo and demonstrate biological and clinical implications for its disruption by cohesin release factor WAPL.}, }
@article {pmid36039936, year = {2022}, author = {Che, Y and Yang, X and Jia, P and Wang, T and Xu, D and Guo, T and Ye, K}, title = {D[2] Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {30}, pages = {e2202149}, pmid = {36039936}, issn = {2198-3844}, mesh = {*Histones/genetics ; *Chromatin/genetics ; Genome/genetics ; DNA/genetics ; Genomics ; }, abstract = {The execution of biological activities inside space-limited cell nuclei requires sophisticated organization. Current studies on the 3D genome focus on chromatin interactions and local structures, e.g., topologically associating domains (TADs). In this study, two global physical properties: DNA density and distance to nuclear periphery (DisTP), are introduced and a 2D matrix, D[2] plot, is constructed for mapping genetic and epigenetic markers. Distinct patterns of functional markers on the D[2] plot, indicating its ability to compartmentalize functional genome regions, are observed. Furthermore, enrichments of transcription-related markers are concatenated into a cross-species transcriptional activation model, where the nucleus is divided into four areas: active, intermediate, repress and histone, and repress and repeat. Based on the trajectories of the genomic regions on D[2] plot, the constantly active and newly activated genes are successfully identified during olfactory sensory neuron maturation. The analysis reveals that the D[2] plot effectively categorizes functional regions and provides a universal and transcription-related measurement for the 3D genome.}, }
@article {pmid36036457, year = {2022}, author = {Schwartz, M}, title = {Can abnormal chromatin folding cause high-penetrance cancer predisposition?.}, journal = {Physiological genomics}, volume = {54}, number = {10}, pages = {380-388}, doi = {10.1152/physiolgenomics.00052.2022}, pmid = {36036457}, issn = {1531-2267}, mesh = {*Chromatin/genetics ; Genome ; Humans ; *Neoplasms/genetics ; Penetrance ; Promoter Regions, Genetic ; }, abstract = {Sequencing cancer predisposing genes (CPGs) in evocative patients (i.e., patients with personal and family history of multiple/early-onset/unusual cancers) allows follow-up in their relatives to be adapted when a causative pathogenic variant is identified. Unfortunately, many evocative families remain unexplained. Part of this "missing heritability" could be due to CPG dysregulations caused by remote noncoding genomic alterations. Transcription levels are regulated through the ability of promoters to physically interact with their distant cis-regulatory elements. Three-dimensional chromatin contacts, mediated by a dynamic loop extrusion process, are uncovered by chromosome conformation capture (3C) and 3C-derived techniques, which have enabled the discovery of new pathological mechanisms in developmental diseases and cancers. High-penetrance cancer predisposition is caused by germline hereditary alterations otherwise found at the somatic level in sporadic cancers. Thus, data from both developmental diseases and cancers provide information about possible unknown cancer predisposition mechanisms. This mini-review aims to deduce from these data whether abnormal chromatin folding can cause high-penetrance cancer predisposition.}, }
@article {pmid36031655, year = {2022}, author = {Kulikova, T and Maslova, A and Starshova, P and Rodriguez Ramos, JS and Krasikova, A}, title = {Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes.}, journal = {Chromosoma}, volume = {131}, number = {4}, pages = {207-223}, pmid = {36031655}, issn = {1432-0886}, mesh = {Animals ; Chick Embryo ; *Meiotic Prophase I ; *Oocytes ; Oogenesis/genetics ; Genomics ; Chickens/genetics ; Chromatin/genetics ; Mammals ; }, abstract = {In diplotene oocyte nuclei of all vertebrate species, except mammals, chromosomes lack interchromosomal contacts and chromatin is linearly compartmentalized into distinct chromomere-loop complexes forming lampbrush chromosomes. However, the mechanisms underlying the formation of chromomere-loop complexes remain unexplored. Here we aimed to compare somatic topologically associating domains (TADs), recently identified in chicken embryonic fibroblasts, with chromomere-loop complexes in lampbrush meiotic chromosomes. By measuring 3D-distances and colocalization between linear equidistantly located genomic loci, positioned within one TAD or separated by a TAD border, we confirmed the presence of predicted TADs in chicken embryonic fibroblast nuclei. Using three-colored FISH with BAC probes, we mapped equidistant genomic regions included in several sequential somatic TADs on isolated chicken lampbrush chromosomes. Eight genomic regions, each comprising two or three somatic TADs, were mapped to non-overlapping neighboring lampbrush chromatin domains - lateral loops, chromomeres, or chromomere-loop complexes. Genomic loci from the neighboring somatic TADs could localize in one lampbrush chromomere-loop complex, while genomic loci belonging to the same somatic TAD could be localized in neighboring lampbrush chromomere-loop domains. In addition, FISH-mapping of BAC probes to the nascent transcripts on the lateral loops indicates transcription of at least 17 protein-coding genes and 2 non-coding RNA genes during the lampbrush stage of chicken oogenesis, including genes involved in oocyte maturation and early embryo development.}, }
@article {pmid36003143, year = {2022}, author = {Wang, X and Yan, J and Ye, Z and Zhang, Z and Wang, S and Hao, S and Shen, B and Wei, G}, title = {Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {974750}, pmid = {36003143}, issn = {2296-634X}, abstract = {Background: Doxorubicin resistance remains a major therapeutic challenge leading to poor survival prognosis and treatment failure in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape are well known, potential diagnostic or therapeutic targets associated with the reorganization of three-dimensional (3D) chromatin architecture have not yet been systematically investigated. Methods: Here we performed in situ high-throughput chromosome conformation capture (Hi-C) on parental and doxorubicin-resistant MCF7 (MCF7-DR) human breast cancer cells, followed by integrative analysis of HiC, ATAC-seq, RNA-seq and TCGA data. Results: It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression. The genome of MCF7-DR cells was spatially reorganized into smaller topologically associating domains (TADs) and chromatin loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF, AP-1 and bHLH, to gained TADs or loops. Intriguingly, we observed two condensed genomic regions (∼20 kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Finally, combining data from TCGA, we identified a number of gained and lost enhancer-promoter interactions and their corresponding differentially expressed genes involved in chromatin organization and breast cancer signaling pathways, including FA2H, FOXA1 and JRKL, which might serve as potential treatment targets for breast cancer. Conclusion: These data uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription and provide novel insights into the epigenomic mechanisms involving doxorubicin resistance in breast cancer.}, }
@article {pmid35980315, year = {2022}, author = {Chen, M and Jia, L and Zheng, X and Han, M and Li, L and Zhang, L}, title = {Ancient Human Endogenous Retroviruses Contribute to Genetic Evolution and Regulate Cancer Cell Type-Specific Gene Expression.}, journal = {Cancer research}, volume = {82}, number = {19}, pages = {3457-3473}, doi = {10.1158/0008-5472.CAN-22-0290}, pmid = {35980315}, issn = {1538-7445}, mesh = {3' Untranslated Regions/genetics ; 5' Untranslated Regions/genetics ; Chromatin ; DNA Transposable Elements/genetics ; *Endogenous Retroviruses/genetics ; Evolution, Molecular ; Female ; Gene Expression ; Genome-Wide Association Study ; Humans ; *Neoplasms/genetics ; Placenta ; Pregnancy ; }, abstract = {UNLABELLED: Human endogenous retroviruses (HERV), a type of transposable elements (TE), play crucial roles in human placental morphogenesis, immune response, and cancer progression. Emerging evidence suggests that TEs have been a rich source of regulatory elements in the human genome, but little is known about the global impact of HERVs on transcriptional networks in cancer. Using genome-wide approaches, we show that HERVs are composed primarily of three ancient superfamilies: ERVL-MaLR, ERVL, and ERV1. This analysis suggests that the integration of exonic, intronic, and intergenic HERVs, as well as human or Hominidae gene-specific HERVs, contributes to human genomic innovation. HERVs exonized in genes are located mainly in the 3' untranslated region (UTR) or 3' end and participate in basic biological processes. Active HERVs are located mainly in intronic and intergenic regions and tend to function as enhancers and contribute to cancer cell type-specific gene expression. More importantly, HERVs may also define chromatin topologically associating domain (TAD) and loop boundaries in a cell type-specific manner. Taken together, these findings reveal that ancient HERV elements are a source of diverse regulatory sequences, including 3' UTRs, 5' UTRs, promoters, and enhancers, and they contribute to genetic innovation and cancer cell type-specific gene expression, highlighting the previously underestimated importance of these elements.<br><br>SIGNIFICANCE: Genome-wide analyses show that human endogenous retroviruses mediate cancer cell type-specific gene expression, epigenetic modification, and 3D chromatin architecture, elucidating the relationship between HERVs and diverse cancers.}, }
@article {pmid35969760, year = {2022}, author = {Kurotaki, D and Kikuchi, K and Cui, K and Kawase, W and Saeki, K and Fukumoto, J and Nishiyama, A and Nagamune, K and Zhao, K and Ozato, K and Rocha, PP and Tamura, T}, title = {Chromatin structure undergoes global and local reorganization during murine dendritic cell development and activation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {34}, pages = {e2207009119}, pmid = {35969760}, issn = {1091-6490}, mesh = {Animals ; Cell Differentiation/genetics ; Chromatin/genetics/metabolism ; *Chromatin Assembly and Disassembly ; *Dendritic Cells/cytology ; Gene Expression Regulation ; *Hematopoietic Stem Cells ; Mice ; }, abstract = {Classical dendritic cells (cDCs) are essential for immune responses and differentiate from hematopoietic stem cells via intermediate progenitors, such as monocyte-DC progenitors (MDPs) and common DC progenitors (CDPs). Upon infection, cDCs are activated and rapidly express host defense-related genes, such as those encoding cytokines and chemokines. Chromatin structures, including nuclear compartments and topologically associating domains (TADs), have been implicated in gene regulation. However, the extent and dynamics of their reorganization during cDC development and activation remain unknown. In this study, we comprehensively determined higher-order chromatin structures by Hi-C in DC progenitors and cDC subpopulations. During cDC differentiation, chromatin activation was initially induced at the MDP stage. Subsequently, a shift from inactive to active nuclear compartments occurred at the cDC gene loci in CDPs, which was followed by increased intra-TAD interactions and loop formation. Mechanistically, the transcription factor IRF8, indispensable for cDC differentiation, mediated chromatin activation and changes into the active compartments in DC progenitors, thereby possibly leading to cDC-specific gene induction. Using an infection model, we found that the chromatin structures of host defense-related gene loci were preestablished in unstimulated cDCs, indicating that the formation of higher-order chromatin structures prior to infection may contribute to the rapid responses to pathogens. Overall, these results suggest that chromatin structure reorganization is closely related to the establishment of cDC-specific gene expression and immune functions. This study advances the fundamental understanding of chromatin reorganization in cDC differentiation and activation.}, }
@article {pmid35966880, year = {2022}, author = {Zhou, T and Feng, Q}, title = {Androgen receptor signaling and spatial chromatin organization in castration-resistant prostate cancer.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {924087}, pmid = {35966880}, issn = {2296-858X}, abstract = {Prostate cancer is one of the leading causes of cancer death and affects millions of men in the world. The American Cancer Society estimated about 34,500 deaths from prostate cancer in the United States in year 2022. The Androgen receptor (AR) signaling is a major pathway that sustains local and metastatic prostate tumor growth. Androgen-deprivation therapy (ADT) is the standard of care for metastatic prostate cancer patient and can suppress the tumor growth for a median of 2-3 years. Unfortunately, the malignancy inevitably progresses to castration-resistant prostate cancer (CRPC) which is more aggressive and no longer responsive to ADT. Surprisingly, for most of the CPRC patients, cancer growth still depends on androgen receptor signaling. Accumulating evidence suggests that CRPC cells have rewired their transcriptional program to retain AR signaling in the absence of androgens. Besides AR, other transcription factors also contribute to the resistance mechanism through multiple pathways including enhancing AR signaling pathway and activating other complementary signaling pathways for the favor of AR downstream genes expression. More recent studies have shown the role of transcription factors in reconfiguring chromatin 3D structure and regulating topologically associating domains (TADs). Pioneer factors, transcription factors and coactivators form liquid-liquid phase separation compartment that can modulate transcriptional events along with configuring TADs. The role of AR and other transcription factors on chromatin structure change and formation of condensate compartment in prostate cancer cells has only been recently investigated and appreciated. This review intends to provide an overview of transcription factors that contribute to AR signaling through activation of gene expression, governing 3D chromatin structure and establishing phase to phase separation. A more detailed understanding of the spatial role of transcription factors in CRPC might provide novel therapeutic targets for the treatment of CRPC.}, }
@article {pmid35961952, year = {2022}, author = {Giaimo, BD and Borggrefe, T}, title = {Enhancer-promoter communication: unraveling enhancer strength and positioning within a given topologically associating domain (TAD).}, journal = {Signal transduction and targeted therapy}, volume = {7}, number = {1}, pages = {281}, pmid = {35961952}, issn = {2059-3635}, mesh = {*Chromatin ; *Promoter Regions, Genetic/genetics ; }, }
@article {pmid35950186, year = {2022}, author = {Fang, K and Wang, J and Liu, L and Jin, VX}, title = {Mapping nucleosome and chromatin architectures: A survey of computational methods.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {3955-3962}, pmid = {35950186}, issn = {2001-0370}, support = {R01 GM114142/GM/NIGMS NIH HHS/United States ; U54 CA217297/CA/NCI NIH HHS/United States ; }, abstract = {With ever-growing genomic sequencing data, the data variabilities and the underlying biases of the sequencing technologies pose significant computational challenges ranging from the need for accurately detecting the nucleosome positioning or chromatin interaction to the need for developing normalization methods to eliminate systematic biases. This review mainly surveys the computational methods for mapping the higher-resolution nucleosome and higher-order chromatin architectures. While a detailed discussion of the underlying algorithms is beyond the scope of our survey, we have discussed the methods and tools that can detect the nucleosomes in the genome, then demonstrated the computational methods for identifying 3D chromatin domains and interactions. We further illustrated computational approaches for integrating multi-omics data with Hi-C data and the advance of single-cell (sc)Hi-C data analysis. Our survey provides a comprehensive and valuable resource for biomedical scientists interested in studying nucleosome organization and chromatin structures as well as for computational scientists who are interested in improving upon them.}, }
@article {pmid35938007, year = {2022}, author = {Ahn, J and Lee, J and Kim, DH and Hwang, IS and Park, MR and Cho, IC and Hwang, S and Lee, K}, title = {Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {920641}, pmid = {35938007}, issn = {1664-8021}, abstract = {In mammals, genomic imprinting operates via gene silencing mechanisms. Although conservation of the imprinting mechanism at the H19/IGF2 locus has been generally described in pigs, tissue-specific imprinting at the transcript level, monoallelic-to-biallelic conversion, and spatio-temporal chromatin reorganization remain largely uninvestigated. Here, we delineate spatially regulated imprinting of IGF2 transcripts, age-dependent hepatic mono- to biallelic conversion, and reorganization of topologically associating domains at the porcine H19/IGF2 locus for better translation to human and animal research. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of normal and parthenogenetic porcine embryos revealed the paternally hypermethylated H19 differentially methylated region and paternal expression of IGF2. Using a polymorphism-based approach and omics datasets from chromatin immunoprecipitation sequencing (ChIP-seq), whole-genome sequencing (WGS), RNA-seq, and Hi-C, regulation of IGF2 during development was analyzed. Regulatory elements in the liver were distinguished from those in the muscle where the porcine IGF2 transcript was monoallelically expressed. The IGF2 transcript from the liver was biallelically expressed at later developmental stages in both pigs and humans. Chromatin interaction was less frequent in the adult liver compared to the fetal liver and skeletal muscle. The duration of genomic imprinting effects within the H19/IGF2 locus might be reduced in the liver with biallelic conversion through alternative promoter usage and chromatin remodeling. Our integrative omics analyses of genome, epigenome, and transcriptome provided a comprehensive view of imprinting status at the H19/IGF2 cluster.}, }
@article {pmid35933090, year = {2022}, author = {Sun, Z and Wang, Y and Song, Z and Zhang, H and Wang, Y and Liu, K and Ma, M and Wang, P and Fang, Y and Cai, D and Li, G and Fang, Y}, title = {DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.}, journal = {Journal of advanced research}, volume = {42}, number = {}, pages = {41-53}, pmid = {35933090}, issn = {2090-1224}, mesh = {*DNA Transposable Elements/genetics ; *Oryza/genetics ; DNA Methylation ; Gene Duplication ; Chromatin/genetics ; Transcription, Genetic/genetics ; }, abstract = {INTRODUCTION: Polyploidy is a major force in plant evolution and the domestication of cultivated crops.<br><br>OBJECTIVES: The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.<br><br>METHODS: The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.<br><br>RESULTS: We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.<br><br>CONCLUSION: The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.}, }
@article {pmid35932041, year = {2022}, author = {Li, D and Strong, A and Hou, C and Downes, H and Pritchard, AB and Mazzeo, P and Zackai, EH and Conlin, LK and Hakonarson, H}, title = {Interstitial deletion 4p15.32p16.1 and complex chromoplexy in a female proband with severe neurodevelopmental delay, growth failure and dysmorphism.}, journal = {Molecular cytogenetics}, volume = {15}, number = {1}, pages = {33}, pmid = {35932041}, issn = {1755-8166}, abstract = {Complex chromosomal rearrangements involve the restructuring of genetic material within a single chromosome or across multiple chromosomes. These events can cause serious human disease by disrupting coding DNA and gene regulatory elements via deletions, duplications, and structural rearrangements. Here we describe a 5-year-old female with severe developmental delay, dysmorphic features, multi-suture craniosynostosis, and growth failure found to have a complex series of balanced intra- and inter-chromosomal rearrangements involving chromosomes 4, 11, 13, and X. Initial clinical studies were performed by karyotype, chromosomal microarray, and FISH with research-based short-read genome sequencing coupled with sanger sequencing to precisely map her breakpoints to the base pair resolution to understand the molecular basis of her phenotype. Genome analysis revealed two pathogenic deletions at 4p16.1-p15.32 and 4q31.1, accounting for her developmental delay and dysmorphism. We identified over 60 breakpoints, many with blunt ends and limited homology, supporting a role for non-homologous end joining in restructuring and resolution of the seminal chromoplexy event. We propose that the complexity of our patient's genomic rearrangements with a high number of breakpoints causes dysregulation of gene expression by three-dimensional chromatin interactions or topologically associating domains leading to growth failure and craniosynostosis. Our work supports an important role for genome sequencing in understanding the molecular basis of complex chromosomal rearrangements in human disease.}, }
@article {pmid35867573, year = {2022}, author = {Campbell, M and Chantarasrivong, C and Yanagihashi, Y and Inagaki, T and Davis, RR and Nakano, K and Kumar, A and Tepper, CG and Izumiya, Y}, title = {KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin.}, journal = {Journal of virology}, volume = {96}, number = {14}, pages = {e0056522}, pmid = {35867573}, issn = {1098-5514}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; Gene Expression Regulation, Viral ; Genome, Viral ; *Herpesvirus 8, Human/genetics ; Humans ; Trans-Activators/genetics ; Virus Latency/genetics ; }, abstract = {Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a 3D KSHV genomic structural model with 2 kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by structural maintenance of chromosomes (SMC1) cohesin complex and CCCTC-binding factor (CTCF), and the KSHV transactivator was recruited to those sites during reactivation. Triggering KSHV gene expression decreased prewired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible noncoding RNA regions moved toward the inner space of the structure, resembling the configuration of a "bird cage" during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help facilitate viral gene transcription. IMPORTANCE The 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposi's sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 bp resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral life cycle.}, }
@article {pmid35867254, year = {2022}, author = {Sabaté, T and Zimmer, C and Bertrand, E}, title = {Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2532}, number = {}, pages = {275-290}, pmid = {35867254}, issn = {1940-6029}, mesh = {*Chromatin/genetics ; Chromatin Assembly and Disassembly ; *Chromosomes ; DNA ; Genome, Human ; Humans ; }, abstract = {Hi-C and related sequencing-based techniques have brought a detailed understanding of the 3D genome architecture and the discovery of novel structures such as topologically associating domains (TADs) and chromatin loops, which emerge from cohesin-mediated DNA extrusion. However, these techniques require cell fixation, which precludes assessment of chromatin structure dynamics, and are generally restricted to population averages, thus masking cell-to-cell heterogeneity. By contrast, live-cell imaging allows to characterize and quantify the temporal dynamics of chromatin, potentially including TADs and loops in single cells. Specific chromatin loci can be visualized at high temporal and spatial resolution by inserting a repeat array from bacterial operator sequences bound by fluorescent tags. Using two different types of repeats allows to tag both anchors of a loop in different colors, thus enabling to track them separately even when they are in close vicinity. Here, we describe a versatile cloning method for generating many repeat array repair cassettes in parallel and inserting them by CRISPR-Cas9 into the human genome. This method should be instrumental to studying chromatin loop dynamics in single human cells.}, }
@article {pmid35867243, year = {2022}, author = {Miranda, M and Noordermeer, D and Moindrot, B}, title = {Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2532}, number = {}, pages = {15-33}, pmid = {35867243}, issn = {1940-6029}, mesh = {Alleles ; Animals ; *Chromatin/genetics ; *Chromosomes ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Mammals/genetics ; }, abstract = {Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.}, }
@article {pmid35860407, year = {2022}, author = {Sengupta, K and Denkiewicz, M and Chiliński, M and Szczepińska, T and Mollah, AF and Korsak, S and D'Souza, R and Ruan, Y and Plewczynski, D}, title = {Multi-scale phase separation by explosive percolation with single-chromatin loop resolution.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {3591-3603}, pmid = {35860407}, issn = {2001-0370}, abstract = {The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.}, }
@article {pmid35832633, year = {2022}, author = {Lamberti, WF and Zang, C}, title = {Extracting physical characteristics of higher-order chromatin structures from 3D image data.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {3387-3398}, pmid = {35832633}, issn = {2001-0370}, abstract = {Higher-order chromatin structures have functional impacts on gene regulation and cell identity determination. Using high-throughput sequencing (HTS)-based methods like Hi-C, active or inactive compartments and open or closed topologically associating domain (TAD) structures can be identified on a cell population level. Recently developed high-resolution three-dimensional (3D) molecular imaging techniques such as 3D electron microscopy with in situ hybridization (3D-EMSIH) and 3D structured illumination microscopy (3D-SIM) enable direct detection of physical representations of chromatin structures in a single cell. However, computational analysis of 3D image data with explainability and interpretability on functional characteristics of chromatin structures is still challenging. We developed Extracting Physical-Characteristics from Images of Chromatin Structures (EPICS), a machine-learning based computational method for processing high-resolution chromatin 3D image data. Using EPICS on images produced by 3D-EMISH or 3D-SIM techniques, we generated more direct 3D representations of higher-order chromatin structures, identified major chromatin domains, and determined the open or closed status of each domain. We identified several high-contributing features from the model as the major physical characteristics that define the open or closed chromatin domains, demonstrating the explainability and interpretability of EPICS. EPICS can be applied to the analysis of other high-resolution 3D molecular imaging data for spatial genomics studies. The R and Python codes of EPICS are available at https://github.com/zang-lab/epics.}, }
@article {pmid35821502, year = {2022}, author = {Ballarino, R and Bouwman, BAM and Agostini, F and Harbers, L and Diekmann, C and Wernersson, E and Bienko, M and Crosetto, N}, title = {An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {400}, pmid = {35821502}, issn = {2052-4463}, mesh = {Cell Line, Tumor ; DNA/metabolism ; *DNA Breaks, Double-Stranded ; Genomics ; Humans ; *Neurogenesis ; }, abstract = {Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.}, }
@article {pmid35817979, year = {2022}, author = {Anania, C and Acemel, RD and Jedamzick, J and Bolondi, A and Cova, G and Brieske, N and Kühn, R and Wittler, L and Real, FM and Lupiáñez, DG}, title = {In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.}, journal = {Nature genetics}, volume = {54}, number = {7}, pages = {1026-1036}, pmid = {35817979}, issn = {1546-1718}, mesh = {Animals ; Binding Sites/genetics ; CCCTC-Binding Factor/genetics/metabolism ; *Chromatin/genetics ; Chromosomes/metabolism ; Genome/genetics ; *Genome-Wide Association Study ; Mice ; }, abstract = {Vertebrate genomes organize into topologically associating domains, delimited by boundaries that insulate regulatory elements from nontarget genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding site (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors such as CBS number and orientation. Combined deletions demonstrated that CBSs cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by nonconvergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.}, }
@article {pmid35812944, year = {2022}, author = {Wu, H and Song, X and Lyu, S and Ren, Y and Liu, T and Hou, X and Li, Y and Zhang, C}, title = {Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis).}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {905202}, pmid = {35812944}, issn = {1664-462X}, abstract = {Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.}, }
@article {pmid35777365, year = {2022}, author = {Fujita, Y and Pather, SR and Ming, GL and Song, H}, title = {3D spatial genome organization in the nervous system: From development and plasticity to disease.}, journal = {Neuron}, volume = {110}, number = {18}, pages = {2902-2915}, pmid = {35777365}, issn = {1097-4199}, support = {R01 AG057497/AG/NIA NIH HHS/United States ; R35 NS097370/NS/NINDS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R01 MH125528/MH/NIMH NIH HHS/United States ; R35 NS116843/NS/NINDS NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; *Genome ; Nervous System ; }, abstract = {Chromatin is organized into multiscale three-dimensional structures, including chromosome territories, A/B compartments, topologically associating domains, and chromatin loops. This hierarchically organized genomic architecture regulates gene transcription, which, in turn, is essential for various biological processes during brain development and adult plasticity. Here, we review different aspects of spatial genome organization and their functions in regulating gene expression in the nervous system, as well as their dysregulation in brain disorders. We also highlight new technologies to probe and manipulate chromatin architecture and discuss how investigating spatial genome organization can lead to a better understanding of the nervous system and associated disorders.}, }
@article {pmid35768498, year = {2022}, author = {Wei, C and Jia, L and Huang, X and Tan, J and Wang, M and Niu, J and Hou, Y and Sun, J and Zeng, P and Wang, J and Qing, L and Ma, L and Liu, X and Tang, X and Li, F and Jiang, S and Liu, J and Li, T and Fan, L and Sun, Y and Gao, J and Li, C and Ding, J}, title = {CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation.}, journal = {Cell research}, volume = {32}, number = {8}, pages = {744-760}, pmid = {35768498}, issn = {1748-7838}, mesh = {CCCTC-Binding Factor/metabolism ; Cell Differentiation ; *Chromatin ; Chromatin Assembly and Disassembly ; Embryonic Stem Cells/metabolism ; *Neural Stem Cells/metabolism ; }, abstract = {Chromatin is spatially organized into three-dimensional structures at different levels including A/B compartments, topologically associating domains and loops. The canonical CTCF-mediated loop extrusion model can explain the formation of loops. However, the organization mechanisms underlying long-range chromatin interactions such as interactions between A-A compartments are still poorly understood. Here we show that different from the canonical loop extrusion model, RYBP-mediated phase separation of CTCF organizes inter-A compartment interactions. Based on this model, we designed and verified an induced CTCF phase separation system in embryonic stem cells (ESCs), which facilitated inter-A compartment interactions, improved self-renewal of ESCs and inhibited their differentiation toward neural progenitor cells. These findings support a novel and non-canonical role of CTCF in organizing long-range chromatin interactions via phase separation.}, }
@article {pmid35759905, year = {2022}, author = {Sawh, AN and Mango, SE}, title = {Chromosome organization in 4D: insights from C. elegans development.}, journal = {Current opinion in genetics &amp; development}, volume = {75}, number = {}, pages = {101939}, doi = {10.1016/j.gde.2022.101939}, pmid = {35759905}, issn = {1879-0380}, mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Chromatin/genetics ; Genome/genetics ; Nucleosomes/genetics ; Promoter Regions, Genetic ; }, abstract = {Eukaryotic genome organization is ordered and multilayered, from the nucleosome to chromosomal scales. These layers are not static during development, but are remodeled over time and between tissues. Thus, animal model studies with high spatiotemporal resolution are necessary to understand the various forms and functions of genome organization in vivo. In C. elegans, sequencing- and imaging-based advances have provided insight on how histone modifications, regulatory elements, and large-scale chromosome conformations are established and changed. Recent observations include unexpected physiological roles for topologically associating domains, different roles for the nuclear lamina at different chromatin scales, cell-type-specific enhancer and promoter regulatory grammars, and prevalent compartment variability in early development. Here, we summarize these and other recent findings in C. elegans, and suggest future avenues of research to enrich our in vivo knowledge of the forms and functions of nuclear organization.}, }
@article {pmid35741810, year = {2022}, author = {Liu, T and Wang, Z}, title = {scHiCEmbed: Bin-Specific Embeddings of Single-Cell Hi-C Data Using Graph Auto-Encoders.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741810}, issn = {2073-4425}, support = {R35 GM137974/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromatin ; Cluster Analysis ; *Genome ; Software ; }, abstract = {Most publicly accessible single-cell Hi-C data are sparse and cannot reach a higher resolution. Therefore, learning latent representations (bin-specific embeddings) of sparse single-cell Hi-C matrices would provide us with a novel way of mining valuable information hidden in the limited number of single-cell Hi-C contacts. We present scHiCEmbed, an unsupervised computational method for learning bin-specific embeddings of single-cell Hi-C data, and the computational system is applied to the tasks of 3D structure reconstruction of whole genomes and detection of topologically associating domains (TAD). The only input of scHiCEmbed is a raw or scHiCluster-imputed single-cell Hi-C matrix. The main process of scHiCEmbed is to embed each node/bin in a higher dimensional space using graph auto-encoders. The learned n-by-3 bin-specific embedding/latent matrix is considered the final reconstructed 3D genome structure. For TAD detection, we use constrained hierarchical clustering on the latent matrix to classify bins: S_Dbw is used to determine the optimal number of clusters, and each cluster is considered as one potential TAD. Our reconstructed 3D structures for individual chromatins at different cell stages reveal the expanding process of chromatins during the cell cycle. We observe that the TADs called from single-cell Hi-C data are not shared across individual cells and that the TAD boundaries called from raw or imputed single-cell Hi-C are significantly different from those called from bulk Hi-C, confirming the cell-to-cell variability in terms of TAD definitions. The source code for scHiCEmbed is publicly available, and the URL can be found in the conclusion section.}, }
@article {pmid35730671, year = {2022}, author = {Tian, GG and Hou, C and Li, J and Wu, J}, title = {Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development.}, journal = {Clinical and translational medicine}, volume = {12}, number = {6}, pages = {e927}, pmid = {35730671}, issn = {2001-1326}, mesh = {Animals ; *Chromatin/genetics ; Chromosomes ; Genome/genetics ; Male ; Mammals/genetics ; Mice ; *Oogonial Stem Cells ; Recombination, Genetic ; }, abstract = {BACKGROUND: During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three-dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.<br><br>METHODS: The high-throughput chromosome conformation capture technique was used to probe the 3D structure of chromatin in mouse germ cells at each stage of FGSC development.<br><br>RESULTS: The global 3D genome was dramatically reorganized during FGSC development. In topologically associating domains, the chromatin structure was weakened in germinal vesicle stage oocytes and still present in meiosis I stage oocytes but had vanished in meiosis II oocytes. This switch between topologically associating domains was related to the biological process of FGSC development. Moreover, we constructed a landscape of chromosome X organization, which showed that the X chromosome occupied a smaller proportion of the active (A) compartment than the autosome during FGSC development. By comparing the high-order chromatin structure between female and male germline development, we found that 3D genome organization was remodelled by two different potential mechanisms during gamete development, in which interchromosomal interactions, compartments, and topologically associating domain were decreased during FGSC development but reorganized and recovered during spermatogenesis. Finally, we identified conserved chromatin structures between FGSC development and early embryonic development.<br><br>CONCLUSIONS: These results provide a valuable resource to characterize chromatin organization and for further studies of FGSC development.}, }
@article {pmid35726060, year = {2022}, author = {Wang, W and Chandra, A and Goldman, N and Yoon, S and Ferrari, EK and Nguyen, SC and Joyce, EF and Vahedi, G}, title = {TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.}, journal = {Nature immunology}, volume = {23}, number = {7}, pages = {1052-1062}, pmid = {35726060}, issn = {1529-2916}, support = {U01 DK127768/DK/NIDDK NIH HHS/United States ; UC4 DK112217/DK/NIDDK NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; U01 DK112217/DK/NIDDK NIH HHS/United States ; R01 HL145754/HL/NHLBI NIH HHS/United States ; }, mesh = {CCCTC-Binding Factor/genetics/metabolism ; Cell Cycle Proteins/metabolism ; *Chromatin ; *Enhancer Elements, Genetic/genetics ; Gene Expression Regulation ; T-Lymphocytes/metabolism ; }, abstract = {The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.}, }
@article {pmid35725901, year = {2022}, author = {Liu, E and Lyu, H and Peng, Q and Liu, Y and Wang, T and Han, J}, title = {TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {608}, pmid = {35725901}, issn = {2399-3642}, mesh = {*Chromatin/genetics ; *Chromosomes ; Genome ; Linear Models ; Reproducibility of Results ; }, abstract = {Topologically associating domains (TADs) are fundamental building blocks of three dimensional genome, and organized into complex hierarchies. Identifying hierarchical TADs on Hi-C data helps to understand the relationship between genome architectures and gene regulation. Herein we propose TADfit, a multivariate linear regression model for profiling hierarchical chromatin domains, which tries to fit the interaction frequencies in Hi-C contact matrix with and without replicates using all-possible hierarchical TADs, and the significant ones can be determined by the regression coefficients obtained with the help of an online learning solver called Follow-The-Regularized-Leader (FTRL). Beyond the existing methods, TADfit has an ability to handle multiple contact matrix replicates and find partially overlapping TADs on them, which helps to find the comprehensive underlying TADs across replicates from different experiments. The comparative results tell that TADfit has better accuracy and reproducibility, and the hierarchical TADs called by it exhibit a reasonable biological relevance.}, }
@article {pmid35715427, year = {2022}, author = {Bolt, CC and Lopez-Delisle, L and Hintermann, A and Mascrez, B and Rauseo, A and Andrey, G and Duboule, D}, title = {Context-dependent enhancer function revealed by targeted inter-TAD relocation.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3488}, pmid = {35715427}, issn = {2041-1723}, support = {F32 HD093555/HD/NICHD NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; Chromosomes ; *Enhancer Elements, Genetic/genetics ; Extremities ; Transcription Factors/genetics ; }, abstract = {The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.}, }
@article {pmid35714583, year = {2022}, author = {Michieletto, D and Bickmore, WA}, title = {TADs do not stay in the loop.}, journal = {Molecular cell}, volume = {82}, number = {12}, pages = {2188-2189}, doi = {10.1016/j.molcel.2022.05.033}, pmid = {35714583}, issn = {1097-4164}, support = {MC_UU_00007/2/MRC_/Medical Research Council/United Kingdom ; 212203/WT_/Wellcome Trust/United Kingdom ; }, mesh = {CCCTC-Binding Factor/genetics ; *Chromatin ; }, abstract = {In a recent issue of Science, Gabriele et al. have, for the first time, quantified the dynamics of a topologically associating domain (TAD) in live cells by coupling super-resolution imaging and computational modelling, concluding that a TAD spends most of its life in a "partially extruded state" and that CTCF-CTCF loops are rare.}, }
@article {pmid35710139, year = {2022}, author = {Sudarshan, D and Avvakumov, N and Lalonde, ME and Alerasool, N and Joly-Beauparlant, C and Jacquet, K and Mameri, A and Lambert, JP and Rousseau, J and Lachance, C and Paquet, E and Herrmann, L and Thonta Setty, S and Loehr, J and Bernardini, MQ and Rouzbahman, M and Gingras, AC and Coulombe, B and Droit, A and Taipale, M and Doyon, Y and Côté, J}, title = {Recurrent chromosomal translocations in sarcomas create a megacomplex that mislocalizes NuA4/TIP60 to Polycomb target loci.}, journal = {Genes &amp; development}, volume = {36}, number = {11-12}, pages = {664-683}, pmid = {35710139}, issn = {1549-5477}, support = {FDN-143314//CIHR/Canada ; }, mesh = {Chromatin ; DNA-Binding Proteins/metabolism ; *Endometrial Neoplasms/genetics/metabolism/pathology ; Female ; Histones/metabolism ; Humans ; Polycomb Repressive Complex 2/genetics/metabolism ; Polycomb-Group Proteins/genetics/metabolism ; *Sarcoma/genetics ; *Sarcoma, Endometrial Stromal/genetics/metabolism/pathology ; Translocation, Genetic/genetics ; }, abstract = {Chromosomal translocations frequently promote carcinogenesis by producing gain-of-function fusion proteins. Recent studies have identified highly recurrent chromosomal translocations in patients with endometrial stromal sarcomas (ESSs) and ossifying fibromyxoid tumors (OFMTs), leading to an in-frame fusion of PHF1 (PCL1) to six different subunits of the NuA4/TIP60 complex. While NuA4/TIP60 is a coactivator that acetylates chromatin and loads the H2A.Z histone variant, PHF1 is part of the Polycomb repressive complex 2 (PRC2) linked to transcriptional repression of key developmental genes through methylation of histone H3 on lysine 27. In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation. The chimeric protein assembles a megacomplex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically associating domain including part of the HOXD cluster. This is linked to aberrant gene expression-most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1-implicated with a PRC2 component in the most frequent translocation in ESSs, JAZF1-SUZ12-is a potent transcription activator that physically associates with NuA4/TIP60, its fusion creating outcomes similar to those of EPC1-PHF1 Importantly, the specific increased expression of PRC2 targets/HOX genes was also confirmed with ESS patient samples. Altogether, these results indicate that most chromosomal translocations linked to these sarcomas use the same molecular oncogenic mechanism through a physical merge of NuA4/TIP60 and PRC2 complexes, leading to mislocalization of histone marks and aberrant Polycomb target gene expression.}, }
@article {pmid35710138, year = {2022}, author = {Taylor, T and Sikorska, N and Shchuka, VM and Chahar, S and Ji, C and Macpherson, NN and Moorthy, SD and de Kort, MAC and Mullany, S and Khader, N and Gillespie, ZE and Langroudi, L and Tobias, IC and Lenstra, TL and Mitchell, JA and Sexton, T}, title = {Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.}, journal = {Genes &amp; development}, volume = {36}, number = {11-12}, pages = {699-717}, pmid = {35710138}, issn = {1549-5477}, support = {R01 HG010045/HG/NHGRI NIH HHS/United States ; FRN 153186//CIHR/Canada ; }, mesh = {Animals ; Chromatin ; *Enhancer Elements, Genetic ; Gene Expression Regulation, Developmental ; Mice ; *Promoter Regions, Genetic ; SOXB1 Transcription Factors/*genetics ; Transcription Factors/metabolism ; }, abstract = {How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream from the Sox2 enhancer, is widely distributed over multiple transcription factor-bound regions and maintained in a CTCF-independent manner. Furthermore, partial disruption of promoter-enhancer interactions by ectopic chromatin loop formation has no effect on Sox2 transcription. These findings indicate that many transcription factors are involved in modulating chromatin architecture independently of CTCF.}, }
@article {pmid35688654, year = {2022}, author = {Shukla, V and Cetnarowska, A and Hyldahl, M and Mandrup, S}, title = {Interplay between regulatory elements and chromatin topology in cellular lineage determination.}, journal = {Trends in genetics : TIG}, volume = {38}, number = {10}, pages = {1048-1061}, doi = {10.1016/j.tig.2022.05.011}, pmid = {35688654}, issn = {0168-9525}, mesh = {Cell Lineage/genetics ; *Chromatin/genetics ; DNA ; *Enhancer Elements, Genetic ; Transcription Factors/genetics/metabolism ; }, abstract = {Cellular lineage determination is controlled by combinations of lineage-selective transcription factors (TFs) and associated coregulators that bind to cis-regulatory elements in DNA and regulate gene expression. The ability of these factors to regulate transcription is determined not only by their cooperativity, but also by biochemical and structural properties of the chromatin, sculpting higher-order genome organization. Here, we review recent advances in the understanding of the interplay between chromatin topology and transcription. Studies from many different fields, including adipocyte lineage determination, indicate that lineage determination and differentiation are dependent on elaborate crosstalk between cis-regulatory elements, leading to the formation of transcriptional hubs. Chromatin topology appears to provide a dynamic and supportive, rather than a deterministic, scaffold for this crosstalk.}, }
@article {pmid35687908, year = {2022}, author = {Tsujikawa, LM and Kharenko, OA and Stotz, SC and Rakai, BD and Sarsons, CD and Gilham, D and Wasiak, S and Fu, L and Sweeney, M and Johansson, JO and Wong, NCW and Kulikowski, E}, title = {Breaking boundaries: Pan BETi disrupt 3D chromatin structure, BD2-selective BETi are strictly epigenetic transcriptional regulators.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {152}, number = {}, pages = {113230}, doi = {10.1016/j.biopha.2022.113230}, pmid = {35687908}, issn = {1950-6007}, mesh = {*COVID-19 ; Cell Cycle Proteins/metabolism ; Chromatin ; Endothelial Cells/metabolism ; Epigenesis, Genetic ; Humans ; Nuclear Proteins/genetics/metabolism ; *Transcription Factors/metabolism ; }, abstract = {BACKGROUND: Bromodomain and extraterminal proteins (BETs) are more than just epigenetic regulators of transcription. Here we highlight a new role for the BET protein BRD4 in the maintenance of higher order chromatin structure at Topologically Associating Domain Boundaries (TADBs). BD2-selective and pan (non-selective) BET inhibitors (BETi) differentially support chromatin structure, selectively affecting transcription and cell viability.<br><br>METHODS: Using RNA-seq and BRD4 ChIP-seq, the differential effect of BETi treatment on the transcriptome and BRD4 chromatin occupancy of human aortic endothelial cells from diabetic patients (dHAECs) stimulated with TNF&#x3b1; was evaluated. Chromatin decondensation and DNA fragmentation was assessed by immunofluorescence imaging and quantification. Key dHAEC findings were verified in proliferating monocyte-like THP-1 cells using real time-PCR, BRD4 co-immunoprecipitation studies, western blots, proliferation and apoptosis assays.<br><br>FINDINGS: We discovered that 1) BRD4 co-localizes with Ying-Yang 1 (YY1) at TADBs, critical chromatin structure complexes proximal to many DNA repair genes. 2) BD2-selective BETi enrich BRD4/YY1 associations, while pan-BETi do not. 3) Failure to support chromatin structures through BRD4/YY1 enrichment inhibits DNA repair gene transcription, which induces DNA damage responses, and causes widespread chromatin decondensation, DNA fragmentation, and apoptosis. 4) BD2-selective BETi maintain high order chromatin structure and cell viability, while reducing deleterious pro-inflammatory transcription.<br><br>INTERPRETATION: BRD4 plays a previously unrecognized role at TADBs. BETi differentially impact TADB stability. Our results provide translational insight for the development of BETi as therapeutics for a range of diseases including CVD, chronic kidney disease, cancer, and COVID-19.}, }
@article {pmid35685367, year = {2022}, author = {Segueni, J and Noordermeer, D}, title = {CTCF: A misguided jack-of-all-trades in cancer cells.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {2685-2698}, pmid = {35685367}, issn = {2001-0370}, abstract = {The emergence and progression of cancers is accompanied by a dysregulation of transcriptional programs. The three-dimensional (3D) organization of the human genome has emerged as an important multi-level mediator of gene transcription and regulation. In cancer cells, this organization can be restructured, providing a framework for the deregulation of gene activity. The CTCF protein, initially identified as the product from a tumor suppressor gene, is a jack-of-all-trades for the formation of 3D genome organization in normal cells. Here, we summarize how CTCF is involved in the multi-level organization of the human genome and we discuss emerging insights into how perturbed CTCF function and DNA binding causes the activation of oncogenes in cancer cells, mostly through a process of enhancer hijacking. Moreover, we highlight non-canonical functions of CTCF that can be relevant for the emergence of cancers as well. Finally, we provide guidelines for the computational identification of perturbed CTCF binding and reorganized 3D genome structure in cancer cells.}, }
@article {pmid35676475, year = {2022}, author = {Emerson, DJ and Zhao, PA and Cook, AL and Barnett, RJ and Klein, KN and Saulebekova, D and Ge, C and Zhou, L and Simandi, Z and Minsk, MK and Titus, KR and Wang, W and Gong, W and Zhang, D and Yang, L and Venev, SV and Gibcus, JH and Yang, H and Sasaki, T and Kanemaki, MT and Yue, F and Dekker, J and Chen, CL and Gilbert, DM and Phillips-Cremins, JE}, title = {Cohesin-mediated loop anchors confine the locations of human replication origins.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {812-819}, pmid = {35676475}, issn = {1476-4687}, support = {R01 MH120269/MH/NIMH NIH HHS/United States ; UM1 HG011536/HG/NHGRI NIH HHS/United States ; R01 HG010658/HG/NHGRI NIH HHS/United States ; DP1 MH129957/MH/NIMH NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; U54 DK107965/DK/NIDDK NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; U01 HL129998/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DK107980/DK/NIDDK NIH HHS/United States ; }, mesh = {*Cell Cycle Proteins/metabolism ; *Chromatin/genetics ; *Chromosomal Proteins, Non-Histone/metabolism ; DNA Replication ; Humans ; *Replication Origin/genetics ; S Phase ; }, abstract = {DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability[1,2]. At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)[3-6], subTADs[7] and loops[8] in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.}, }
@article {pmid35664233, year = {2022}, author = {Zhang, S and Tao, W and Han, JJ}, title = {3D chromatin structure changes during spermatogenesis and oogenesis.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {2434-2441}, pmid = {35664233}, issn = {2001-0370}, abstract = {Gametogenesis, including spermatogenesis and oogenesis, are unique differentiation processes involving extraordinarily complex and precise regulatory mechanisms that require the interactions of multiple cell types, hormones, paracrine factors, genes and epigenetic regulators, and extensive chromatin 3D structure re-organization. In recent years, the development of 3D genome technology represented by Hi-C, enabled mapping of the 3D re-organization of chromosomes during zygogenesis at an unprecedented resolution. The 3D remodeling is achieved by folding chromatin into loops, topologically associating domains (TADs), and compartments (A and B), which ultimately affect transcriptional activity. In this review, we summarize the research progresses and findings on chromatin 3D structure changes during spermatogenesis and oogenesis.}, }
@article {pmid35633286, year = {2022}, author = {Zhang, Y and Tian, GG and Wang, X and Hou, C and Hu, X and Wu, J}, title = {Retinoic acid induced meiosis initiation in female germline stem cells by remodelling three-dimensional chromatin structure.}, journal = {Cell proliferation}, volume = {55}, number = {7}, pages = {e13242}, pmid = {35633286}, issn = {1365-2184}, mesh = {Adaptor Proteins, Signal Transducing/genetics/metabolism ; Chromatin ; Meiosis ; *Oogonial Stem Cells/metabolism ; *Tretinoin/pharmacology ; }, abstract = {OBJECTIVES: This study aimed to clarify the regulation and mechanism of meiotic initiation in FGSC development.<br><br>MATERIALS AND METHODS: FGSCs were induced to differentiate into meiosis in differentiation medium. RNA sequencing was performed to analysis the difference of transcription level. High-through chromosome conformation capture sequencing (Hi-C) was performed to analysis changes of three-dimensional chromatin structure. Chromosome conformation capture further confirmed a spatial chromatin loop. ChIP-qPCR and dual luciferase reporter were used to test the interaction between Stimulated by retinoic acid gene 8 (STRA8) protein and Trip13 promoter.<br><br>RESULTS: Compared with FGSCs, the average diameter of STRA8-positive germ cells increased from 13&#x2009;&#x3bc;m to 16.8&#xa0;&#x3bc;m. Furthermore, there were 4788 differentially expressed genes between the two cell stages; Meiosis and chromatin structure-associated terms were significantly enriched. Additionally, Hi-C results showed that FGSCs underwent A/B compartment switching (switch rate was 29.81%), the number of topologically associating domains (TADs) increasing, the average size of TADs decreasing, and chromatin loop changes at genome region of Trip13 from undifferentiated stage to meiosis-initiation stage. Furthermore, we validated that Trip13 promoter contacted distal enhancer to form spatial chromatin loop and STRA8 could bind Trip13 promoter to promote gene expression.<br><br>CONCLUSION: FGSCs underwent chromatin structure remodelling from undifferentiated stage to meiosis-initiation stage, which facilitated STRA8 binding to Trip13 promoter and promoting its expression.}, }
@article {pmid35588541, year = {2022}, author = {Bin Akhtar, G and Buist, M and Rastegar, M}, title = {MeCP2 and transcriptional control of eukaryotic gene expression.}, journal = {European journal of cell biology}, volume = {101}, number = {3}, pages = {151237}, doi = {10.1016/j.ejcb.2022.151237}, pmid = {35588541}, issn = {1618-1298}, mesh = {DNA Methylation ; *Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Gene Expression ; Gene Expression Regulation ; *Methyl-CpG-Binding Protein 2/genetics/metabolism ; RNA/metabolism ; }, abstract = {Eukaryotic gene expression is controlled at multiple steps that work in harmony to ensure proper maintenance of cellular morphology and function. Such regulatory mechanisms would include transcriptional gene regulation, which is in turn controlled by chromatin remodeling, distinct topologically associating domains of the chromatin structure, cis-regulatory elements such as enhancers and promoters, action of trans-acting factors, DNA methylation, RNA modifications, and post-translational modification of histones. These guiding mechanisms of gene expression play critical roles in the epigenetic setting of individual cells within the eukaryotic systems. Some epigenetic factors may play multiple functional roles in guarding the accurate gene expression program of the eukaryotic cells, especially within the central nervous system. A well-studied example of such multi-functional factors is the methyl-CpG-binding protein 2 (MeCP2), a nuclear protein that is encoded by the X-linked MECP2 gene. Here, we aim to provide an overview of eukaryotic gene regulation, the three-dimensional chromatin organization, standard techniques to study newly synthesized RNA transcripts, and the role of MeCP2 as an important transcriptional regulator in eukaryotes.}, }
@article {pmid35585235, year = {2022}, author = {Dequeker, BJH and Scherr, MJ and Brandão, HB and Gassler, J and Powell, S and Gaspar, I and Flyamer, IM and Lalic, A and Tang, W and Stocsits, R and Davidson, IF and Peters, JM and Duderstadt, KE and Mirny, LA and Tachibana, K}, title = {MCM complexes are barriers that restrict cohesin-mediated loop extrusion.}, journal = {Nature}, volume = {606}, number = {7912}, pages = {197-203}, pmid = {35585235}, issn = {1476-4687}, support = {DK107980/NH/NIH HHS/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; *Cell Cycle Proteins/metabolism ; Chromatids/chemistry/metabolism ; *Chromosomal Proteins, Non-Histone/metabolism ; *DNA/chemistry/metabolism ; G1 Phase ; HCT116 Cells ; Humans ; Mice ; Minichromosome Maintenance Complex Component 3/chemistry/metabolism ; *Minichromosome Maintenance Proteins/chemistry/metabolism ; Multienzyme Complexes/chemistry/metabolism ; Nucleic Acid Conformation ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism ; }, abstract = {Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)[1-3], which contribute to transcription, recombination and genomic stability[4,5]. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered[6-12]. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.}, }
@article {pmid35551512, year = {2022}, author = {Lei, Z and Meng, H and Liu, L and Zhao, H and Rao, X and Yan, Y and Wu, H and Liu, M and He, A and Yi, C}, title = {Mitochondrial base editor induces substantial nuclear off-target mutations.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {804-811}, pmid = {35551512}, issn = {1476-4687}, mesh = {*Cell Nucleus/genetics ; *Cytosine/metabolism ; DNA, Mitochondrial/genetics ; *Gene Editing ; *Mitochondria/genetics/metabolism ; *Mutation ; }, abstract = {DddA-derived cytosine base editors (DdCBEs)-which are fusions of split DddA halves and transcription activator-like effector (TALE) array proteins from bacteria-enable targeted C•G-to-T•A conversions in mitochondrial DNA[1]. However, their genome-wide specificity is poorly understood. Here we show that the mitochondrial base editor induces extensive off-target editing in the nuclear genome. Genome-wide, unbiased analysis of its editome reveals hundreds of off-target sites that are TALE array sequence (TAS)-dependent or TAS-independent. TAS-dependent off-target sites in the nuclear DNA are often specified by only one of the two TALE repeats, challenging the principle that DdCBEs are guided by paired TALE proteins positioned in close proximity. TAS-independent off-target sites on nuclear DNA are frequently shared among DdCBEs with distinct TALE arrays. Notably, they co-localize strongly with binding sites for the transcription factor CTCF and are enriched in topologically associating domain boundaries. We engineered DdCBE to alleviate such off-target effects. Collectively, our results have implications for the use of DdCBEs in basic research and therapeutic applications, and suggest the need to thoroughly define and evaluate the off-target effects of base-editing tools.}, }
@article {pmid35551308, year = {2022}, author = {Zhou, J}, title = {Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale.}, journal = {Nature genetics}, volume = {54}, number = {5}, pages = {725-734}, pmid = {35551308}, issn = {1546-1718}, support = {DP2 GM146336/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; *Chromosomes/genetics ; Genome/genetics ; Polycomb-Group Proteins/genetics ; Promoter Regions, Genetic/genetics ; Transcription Factors/genetics ; }, abstract = {To learn how genomic sequence influences multiscale three-dimensional (3D) genome architecture, this manuscript presents a sequence-based deep-learning approach, Orca, that predicts directly from sequence the 3D genome architecture from kilobase to whole-chromosome scale. Orca captures the sequence dependencies of structures including chromatin compartments and topologically associating domains, as well as diverse types of interactions from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions with cell-type specificity. Orca enables various applications including predicting structural variant effects on multiscale genome organization and it recapitulated effects of experimentally studied variants at varying sizes (300 bp to 90 Mb). Moreover, Orca enables in silico virtual screens to probe the sequence basis of 3D genome organization at different scales. At the submegabase scale, it predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, virtual screens of sequence activities suggest a model for the sequence basis of chromatin compartments with a prominent role of transcription start sites.}, }
@article {pmid35530130, year = {2022}, author = {Fan, Z and Wu, C and Chen, M and Jiang, Y and Wu, Y and Mao, R and Fan, Y}, title = {The generation of PD-L1 and PD-L2 in cancer cells: From nuclear chromatin reorganization to extracellular presentation.}, journal = {Acta pharmaceutica Sinica. B}, volume = {12}, number = {3}, pages = {1041-1053}, pmid = {35530130}, issn = {2211-3835}, abstract = {The immune checkpoint blockade (ICB) targeting on PD-1/PD-L1 has shown remarkable promise in treating cancers. However, the low response rate and frequently observed severe side effects limit its broad benefits. It is partially due to less understanding of the biological regulation of PD-L1. Here, we systematically and comprehensively summarized the regulation of PD-L1 from nuclear chromatin reorganization to extracellular presentation. In PD-L1 and PD-L2 highly expressed cancer cells, a new TAD (topologically associating domain) (chr9: 5,400,000-5,600,000) around CD274 and CD273 was discovered, which includes a reported super-enhancer to drive synchronous transcription of PD-L1 and PD-L2. The re-shaped TAD allows transcription factors such as STAT3 and IRF1 recruit to PD-L1 locus in order to guide the expression of PD-L1. After transcription, the PD-L1 is tightly regulated by miRNAs and RNA-binding proteins via the long 3'UTR. At translational level, PD-L1 protein and its membrane presentation are tightly regulated by post-translational modification such as glycosylation and ubiquitination. In addition, PD-L1 can be secreted via exosome to systematically inhibit immune response. Therefore, fully dissecting the regulation of PD-L1/PD-L2 and thoroughly detecting PD-L1/PD-L2 as well as their regulatory networks will bring more insights in ICB and ICB-based combinational therapy.}, }
@article {pmid35524567, year = {2022}, author = {Poszewiecka, B and Pienkowski, VM and Nowosad, K and Robin, JD and Gogolewski, K and Gambin, A}, title = {TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W744-52}, pmid = {35524567}, issn = {1362-4962}, abstract = {In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement's breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.}, }
@article {pmid35524220, year = {2022}, author = {Li, D and He, M and Tang, Q and Tian, S and Zhang, J and Li, Y and Wang, D and Jin, L and Ning, C and Zhu, W and Hu, S and Long, K and Ma, J and Liu, J and Zhang, Z and Li, M}, title = {Comparative 3D genome architecture in vertebrates.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {99}, pmid = {35524220}, issn = {1741-7007}, mesh = {Animals ; Chickens/genetics ; *Chromatin ; DNA Transposable Elements ; Euchromatin/genetics ; *Heterochromatin/genetics ; Mammals/genetics ; Vertebrates/genetics ; }, abstract = {BACKGROUND: The three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species.<br><br>RESULTS: This analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture.<br><br>CONCLUSIONS: Our analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.}, }
@article {pmid35509102, year = {2022}, author = {Deng, S and Feng, Y and Pauklin, S}, title = {3D chromatin architecture and transcription regulation in cancer.}, journal = {Journal of hematology &amp; oncology}, volume = {15}, number = {1}, pages = {49}, pmid = {35509102}, issn = {1756-8722}, mesh = {*Chromatin ; DNA-Binding Proteins ; Gene Expression Regulation ; Humans ; *Neoplasms/genetics ; Promoter Regions, Genetic ; }, abstract = {Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.}, }
@article {pmid35508135, year = {2022}, author = {Gilbertson, SE and Walter, HC and Gardner, K and Wren, SN and Vahedi, G and Weinmann, AS}, title = {Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans.}, journal = {Cell reports}, volume = {39}, number = {5}, pages = {110769}, pmid = {35508135}, issn = {2211-1247}, support = {R01 AI061061/AI/NIAID NIH HHS/United States ; R01 HL145754/HL/NHLBI NIH HHS/United States ; R56 AI061061/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Chromatin ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; Gene Rearrangement/genetics ; *Genome, Human ; Genomics ; Humans ; Mice ; }, abstract = {Distinguishing between conserved and divergent regulatory mechanisms is essential for translating preclinical research from mice to humans, yet there is a lack of information about how evolutionary genome rearrangements affect the regulation of the immune response, a rapidly evolving system. The current model is topologically associating domains (TADs) are conserved between species, buffering evolutionary rearrangements and conserving long-range interactions within a TAD. However, we find that TADs frequently span evolutionary translocation and inversion breakpoints near genes with species-specific expression in immune cells, creating unique enhancer-promoter interactions exclusive to the mouse or human genomes. This includes TADs encompassing immune-related transcription factors, cytokines, and receptors. For example, we uncover an evolutionary rearrangement that created a shared LPS-inducible regulatory module between OASL and P2RX7 in human macrophages that is absent in mice. Therefore, evolutionary genome rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer elements from divergent genomic locations between species to create unique regulatory modules.}, }
@article {pmid35502750, year = {2022}, author = {Galupa, R and Picard, C and Servant, N and Nora, EP and Zhan, Y and van Bemmel, JG and El Marjou, F and Johanneau, C and Borensztein, M and Ancelin, K and Giorgetti, L and Heard, E}, title = {Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication.}, journal = {Development (Cambridge, England)}, volume = {149}, number = {9}, pages = {}, pmid = {35502750}, issn = {1477-9129}, mesh = {Animals ; CCCTC-Binding Factor/genetics/metabolism ; Chromatin ; Communication ; Gene Expression ; Genome ; Mice ; *RNA, Long Noncoding/genetics ; *X Chromosome Inactivation/genetics ; }, abstract = {The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterations in gene expression, whereas genomic rearrangements involving TAD boundaries disrupt normal gene expression and can lead to pathological phenotypes. Here, we targeted the TAD neighboring that of the noncoding transcript Xist, which controls X-chromosome inactivation. Inverting 245 kb within the TAD led to expected rearrangement of CTCF-based contacts but revealed heterogeneity in the 'contact' potential of different CTCF sites. Expression of most genes therein remained unaffected in mouse embryonic stem cells and during differentiation. Interestingly, expression of Xist was ectopically upregulated. The same inversion in mouse embryos led to biased Xist expression. Smaller inversions and deletions of CTCF clusters led to similar results: rearrangement of contacts and limited changes in local gene expression, but significant changes in Xist expression in embryos. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighboring TADs, highlighting the existence of mechanisms of inter-TAD communication.}, }
@article {pmid35476527, year = {2022}, author = {Panarotto, M and Davidson, IF and Litos, G and Schleiffer, A and Peters, JM}, title = {Cornelia de Lange syndrome mutations in NIPBL can impair cohesin-mediated DNA loop extrusion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {18}, pages = {e2201029119}, pmid = {35476527}, issn = {1091-6490}, mesh = {Cell Cycle Proteins/genetics ; Chromosomal Proteins, Non-Histone/genetics ; DNA/genetics ; *De Lange Syndrome/genetics ; Humans ; Mutation ; }, abstract = {Cornelia de Lange syndrome (CdLS) is a developmental multisystem disorder frequently associated with mutations in NIPBL. CdLS is thought to arise from developmental gene regulation defects, but how NIPBL mutations cause these is unknown. Here we show that several NIPBL mutations impair the DNA loop extrusion activity of cohesin. Because this activity is required for the formation of chromatin loops and topologically associating domains, which have important roles in gene regulation, our results suggest that defects in cohesin-mediated loop extrusion contribute to the etiology of CdLS by altering interactions between developmental genes and their enhancers.}, }
@article {pmid35470444, year = {2022}, author = {Jouret, G and Heide, S and Sorlin, A and Faivre, L and Chantot-Bastaraud, S and Beneteau, C and Denis-Musquer, M and Turnpenny, PD and Coutton, C and Vieville, G and Thevenon, J and Larson, A and Petit, F and Boudry, E and Smol, T and Delobel, B and Duban-Bedu, B and Fallerini, C and Mari, F and Lo Rizzo, C and Renieri, A and Caberg, JH and Denommé-Pichon, AS and Tran Mau-Them, F and Maystadt, I and Courtin, T and Keren, B and Mouthon, L and Charles, P and Cuinat, S and Isidor, B and Theis, P and Müller, C and Kulisic, M and Türkmen, S and Stieber, D and Bourgeois, D and Scalais, E and Klink, B}, title = {Understanding the new BRD4-related syndrome: Clinical and genomic delineation with an international cohort study.}, journal = {Clinical genetics}, volume = {102}, number = {2}, pages = {117-122}, doi = {10.1111/cge.14141}, pmid = {35470444}, issn = {1399-0004}, mesh = {Cell Cycle Proteins/genetics ; Child ; *De Lange Syndrome/diagnosis/genetics/pathology ; Female ; Genomics ; Humans ; Mutation ; *Nuclear Proteins/genetics ; Phenotype ; Pregnancy ; Transcription Factors/genetics ; }, abstract = {BRD4 is part of a multiprotein complex involved in loading the cohesin complex onto DNA, a fundamental process required for cohesin-mediated loop extrusion and formation of Topologically Associating Domains. Pathogenic variations in this complex have been associated with a growing number of syndromes, collectively known as cohesinopathies, the most classic being Cornelia de Lange syndrome. However, no cohort study has been conducted to delineate the clinical and molecular spectrum of BRD4-related disorder. We formed an international collaborative study, and collected 14 new patients, including two fetuses. We performed phenotype and genotype analysis, integrated prenatal findings from fetopathological examinations, phenotypes of pediatric patients and adults. We report the first cohort of patients with BRD4-related disorder and delineate the dysmorphic features at different ages. This work extends the phenotypic spectrum of cohesinopathies and characterize a new clinically relevant and recognizable pattern, distinguishable from the other cohesinopathies.}, }
@article {pmid35462859, year = {2022}, author = {Habash, NW and Sehrawat, TS and Shah, VH and Cao, S}, title = {Epigenetics of alcohol-related liver diseases.}, journal = {JHEP reports : innovation in hepatology}, volume = {4}, number = {5}, pages = {100466}, pmid = {35462859}, issn = {2589-5559}, support = {R01 AA021171/AA/NIAAA NIH HHS/United States ; R01 DK059615/DK/NIDDK NIH HHS/United States ; R37 AA021171/AA/NIAAA NIH HHS/United States ; }, abstract = {Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.}, }
@article {pmid35456393, year = {2022}, author = {Liu, W and Zhong, W and Chen, J and Huang, B and Hu, M and Li, Y}, title = {Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization.}, journal = {Genes}, volume = {13}, number = {4}, pages = {}, pmid = {35456393}, issn = {2073-4425}, support = {R35HG011922/NH/NIH HHS/United States ; R01NR019245/NH/NIH HHS/United States ; U01DA052713/NH/NIH HHS/United States ; U01 DK127421/DK/NIDDK NIH HHS/United States ; R01MH123724/NH/NIH HHS/United States ; P50HD103573/NH/NIH HHS/United States ; }, mesh = {Brain ; *Chromatin ; *Chromosomes ; Gene Expression Regulation ; Genome, Human ; Humans ; }, abstract = {The human genome has a complex and dynamic three-dimensional (3D) organization, which plays a critical role for gene regulation and genome function. The importance of 3D genome organization in brain development and function has been well characterized in a region- and cell-type-specific fashion. Recent technological advances in chromosome conformation capture (3C)-based techniques, imaging approaches, and ligation-free methods, along with computational methods to analyze the data generated, have revealed 3D genome features at different scales in the brain that contribute to our understanding of genetic mechanisms underlying neuropsychiatric diseases and other brain-related traits. In this review, we discuss how these advances aid in the genetic dissection of brain-related traits.}, }
@article {pmid35440598, year = {2022}, author = {Aljahani, A and Hua, P and Karpinska, MA and Quililan, K and Davies, JOJ and Oudelaar, AM}, title = {Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2139}, pmid = {35440598}, issn = {2041-1723}, support = {MR/R008108/MRC_/Medical Research Council/United Kingdom ; }, mesh = {CCCTC-Binding Factor/genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; *Chromatin/genetics ; *Chromosomal Proteins, Non-Histone/genetics/metabolism ; Chromosomes/metabolism ; }, abstract = {Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date (20 bp resolution) and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.}, }
@article {pmid35420890, year = {2022}, author = {Gabriele, M and Brandão, HB and Grosse-Holz, S and Jha, A and Dailey, GM and Cattoglio, C and Hsieh, TS and Mirny, L and Zechner, C and Hansen, AS}, title = {Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6592}, pages = {496-501}, pmid = {35420890}, issn = {1095-9203}, support = {DP2 GM140938/GM/NIGMS NIH HHS/United States ; R33 CA257878/CA/NCI NIH HHS/United States ; UM1 HG011536/HG/NHGRI NIH HHS/United States ; R00 GM130896/GM/NIGMS NIH HHS/United States ; R01 GM114190/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; CCCTC-Binding Factor ; Cell Cycle Proteins/metabolism ; *Chromatin ; *Chromosomal Proteins, Non-Histone/metabolism ; Mice ; }, abstract = {Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability remain unknown. Here, we directly visualized chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantified looping dynamics by Bayesian inference. Unexpectedly, the Fbn2 loop was both rare and dynamic, with a looped fraction of approximately 3 to 6.5% and a median loop lifetime of approximately 10 to 30 minutes. Our results establish that the Fbn2 TAD is highly dynamic, and about 92% of the time, cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries. This suggests that single CTCF boundaries, rather than the fully CTCF-CTCF looped state, may be the primary regulators of functional interactions.}, }
@article {pmid35418676, year = {2022}, author = {Zuin, J and Roth, G and Zhan, Y and Cramard, J and Redolfi, J and Piskadlo, E and Mach, P and Kryzhanovska, M and Tihanyi, G and Kohler, H and Eder, M and Leemans, C and van Steensel, B and Meister, P and Smallwood, S and Giorgetti, L}, title = {Nonlinear control of transcription through enhancer-promoter interactions.}, journal = {Nature}, volume = {604}, number = {7906}, pages = {571-577}, pmid = {35418676}, issn = {1476-4687}, support = {759366/ERC_/European Research Council/International ; }, mesh = {Animals ; Chromatin/genetics ; *Chromosomes ; *Enhancer Elements, Genetic/genetics ; Gene Expression Regulation ; Genomics ; Mammals/genetics ; Promoter Regions, Genetic/genetics ; }, abstract = {Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)[1-4]. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.}, }
@article {pmid35413815, year = {2022}, author = {Sefer, E}, title = {A comparison of topologically associating domain callers over mammals at high resolution.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {127}, pmid = {35413815}, issn = {1471-2105}, mesh = {Animals ; *Chromatin/genetics ; *Mammals/genetics ; }, abstract = {BACKGROUND: Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over High-throughput Chromosome Conformation Capture (Hi-C) interaction dataset. Substantial degree of efforts have been devoted to develop techniques for inferring TADs from Hi-C interaction dataset. Many TAD-calling methods have been developed which differ in their criteria and assumptions in TAD inference. Correspondingly, TADs inferred via these callers vary in terms of both similarities and biological features they are enriched in.<br><br>RESULT: We have carried out a systematic comparison of 27 TAD-calling methods over mammals. We use Micro-C, a recent high-resolution variant of Hi-C, to compare TADs at a very high resolution, and classify the methods into 3 categories: feature-based methods, Clustering methods, Graph-partitioning methods. We have evaluated TAD boundaries, gaps between adjacent TADs, and quality of TADs across various criteria. We also found particularly CTCF and Cohesin proteins to be effective in formation of TADs with corner dots. We have also assessed the callers performance on simulated datasets since a gold standard for TADs is missing. TAD sizes and numbers change remarkably between TAD callers and dataset resolutions, indicating that TADs are hierarchically-organized domains, instead of disjoint regions. A core subset of feature-based TAD callers regularly perform the best while inferring reproducible domains, which are also enriched for TAD related biological properties.<br><br>CONCLUSION: We have analyzed the fundamental principles of TAD-calling methods, and identified the existing situation in TAD inference across high resolution Micro-C interaction datasets over mammals. We come up with a systematic, comprehensive, and concise framework to evaluate the TAD-calling methods performance across Micro-C datasets. Our research will be useful in selecting appropriate methods for TAD inference and evaluation based on available data, experimental design, and biological question of interest. We also introduce our analysis as a benchmarking tool with publicly available source code.}, }
@article {pmid35410381, year = {2022}, author = {Xie, L and Dong, P and Qi, Y and Hsieh, TS and English, BP and Jung, S and Chen, X and De Marzio, M and Casellas, R and Chang, HY and Zhang, B and Tjian, R and Liu, Z}, title = {BRD2 compartmentalizes the accessible genome.}, journal = {Nature genetics}, volume = {54}, number = {4}, pages = {481-491}, pmid = {35410381}, issn = {1546-1718}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Cell Cycle Proteins/genetics/metabolism ; Chromatin/genetics ; Chromosomes/genetics/metabolism ; Mammals/genetics ; *Nuclear Proteins/genetics/metabolism ; Protein Binding ; Protein Domains ; *Transcription Factors/genetics/metabolism ; }, abstract = {Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions.}, }
@article {pmid35400201, year = {2022}, author = {Feng, Y and Cai, L and Hong, W and Zhang, C and Tan, N and Wang, M and Wang, C and Liu, F and Wang, X and Ma, J and Gao, C and Kumar, M and Mo, Y and Geng, Q and Luo, C and Lin, Y and Chen, H and Wang, SY and Watson, MJ and Jegga, AG and Pedersen, RA and Fu, JD and Wang, ZV and Fan, GC and Sadayappan, S and Wang, Y and Pauklin, S and Huang, F and Huang, W and Jiang, L}, title = {Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy.}, journal = {Circulation}, volume = {145}, number = {22}, pages = {1663-1683}, pmid = {35400201}, issn = {1524-4539}, support = {R01 HL160811/HL/NHLBI NIH HHS/United States ; R01 HL157456/HL/NHLBI NIH HHS/United States ; R01 GM132149/GM/NIGMS NIH HHS/United States ; R01 AR078001/AR/NIAMS NIH HHS/United States ; R01 HL143490/HL/NHLBI NIH HHS/United States ; R38 HL155775/HL/NHLBI NIH HHS/United States ; R01 HL139006/HL/NHLBI NIH HHS/United States ; R01 HL130356/HL/NHLBI NIH HHS/United States ; R01 HL105826/HL/NHLBI NIH HHS/United States ; C59392/A25064/CRUK_/Cancer Research UK/United Kingdom ; R01 HL136025/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Cardiomyopathy, Dilated/metabolism ; Chromatin/genetics/metabolism ; Histones/metabolism ; Humans ; *Induced Pluripotent Stem Cells/metabolism ; Mice ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Transcriptional reconfiguration is central to heart failure, the most common cause of which is dilated cardiomyopathy (DCM). The effect of 3-dimensional chromatin topology on transcriptional dysregulation and pathogenesis in human DCM remains elusive.<br><br>METHODS: We generated a compendium of 3-dimensional epigenome and transcriptome maps from 101 biobanked human DCM and nonfailing heart tissues through highly integrative chromatin immunoprecipitation (H3K27ac [acetylation of lysine 27 on histone H3]), in situ high-throughput chromosome conformation capture, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and RNA sequencing. We used human induced pluripotent stem cell-derived cardiomyocytes and mouse models to interrogate the key transcription factor implicated in 3-dimensional chromatin organization and transcriptional regulation in DCM pathogenesis.<br><br>RESULTS: We discovered that the active regulatory elements (H3K27ac peaks) and their connectome (H3K27ac loops) were extensively reprogrammed in DCM hearts and contributed to transcriptional dysregulation implicated in DCM development. For example, we identified that nontranscribing NPPA-AS1 (natriuretic peptide A antisense RNA 1) promoter functions as an enhancer and physically interacts with the NPPA (natriuretic peptide A) and NPPB (natriuretic peptide B) promoters, leading to the cotranscription of NPPA and NPPB in DCM hearts. We revealed that DCM-enriched H3K27ac loops largely resided in conserved high-order chromatin architectures (compartments, topologically associating domains) and their anchors unexpectedly had equivalent chromatin accessibility. We discovered that the DCM-enriched H3K27ac loop anchors exhibited a strong enrichment for HAND1 (heart and neural crest derivatives expressed 1), a key transcription factor involved in early cardiogenesis. In line with this, its protein expression was upregulated in human DCM and mouse failing hearts. To further validate whether HAND1 is a causal driver for the reprogramming of enhancer-promoter connectome in DCM hearts, we performed comprehensive 3-dimensional epigenome mappings in human induced pluripotent stem cell-derived cardiomyocytes. We found that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced a distinct gain of enhancer-promoter connectivity and correspondingly increased the expression of their connected genes implicated in DCM pathogenesis, thus recapitulating the transcriptional signature in human DCM hearts. Electrophysiology analysis demonstrated that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced abnormal calcium handling. Furthermore, cardiomyocyte-specific overexpression of Hand1 in the mouse hearts resulted in dilated cardiac remodeling with impaired contractility/Ca[2+] handling in cardiomyocytes, increased ratio of heart weight/body weight, and compromised cardiac function, which were ascribed to recapitulation of transcriptional reprogramming in DCM.<br><br>CONCLUSIONS: This study provided novel chromatin topology insights into DCM pathogenesis and illustrated a model whereby a single transcription factor (HAND1) reprograms the genome-wide enhancer-promoter connectome to drive DCM pathogenesis.}, }
@article {pmid35388001, year = {2022}, author = {Chu, Z and Gu, L and Hu, Y and Zhang, X and Li, M and Chen, J and Teng, D and Huang, M and Shen, CH and Cai, L and Yoshida, T and Qi, Y and Niu, Z and Feng, A and Geng, S and Frederick, DT and Specht, E and Piris, A and Sullivan, RJ and Flaherty, KT and Boland, GM and Georgopoulos, K and Liu, D and Shi, Y and Zheng, B}, title = {STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1859}, pmid = {35388001}, issn = {2041-1723}, support = {R01 CA219814/CA/NCI NIH HHS/United States ; R01 HL140622/HL/NHLBI NIH HHS/United States ; R35 CA210104/CA/NCI NIH HHS/United States ; }, mesh = {Cell Cycle Proteins/genetics/metabolism ; *Chromosomal Proteins, Non-Histone/genetics/metabolism ; Genome ; Humans ; Interferons/genetics ; *Melanoma/genetics ; }, abstract = {The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization, especially the long-range enhancer-promoter contacts and subsequent gene expression control in cancer, remains poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of acetylated histone H3 lysine 27 (H3K27ac)-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-seq, STAG2 ChIP-seq and H3K27ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may enhance the immune evasion potential in STAG2-mutant cancer.}, }
@article {pmid35380694, year = {2022}, author = {Serna-Pujol, N and Salinas-Pena, M and Mugianesi, F and Le Dily, F and Marti-Renom, MA and Jordan, A}, title = {Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion.}, journal = {Nucleic acids research}, volume = {50}, number = {7}, pages = {3892-3910}, pmid = {35380694}, issn = {1362-4962}, mesh = {Base Composition ; *Chromatin/genetics ; Chromatin Assembly and Disassembly ; Gene Expression ; *Histones/genetics/metabolism ; Humans ; }, abstract = {Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.}, }
@article {pmid35379945, year = {2022}, author = {Brown, JM and De Ornellas, S and Parisi, E and Schermelleh, L and Buckle, VJ}, title = {RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure.}, journal = {Nature protocols}, volume = {17}, number = {5}, pages = {1306-1331}, pmid = {35379945}, issn = {1750-2799}, support = {MC_UU_00016/1/MRC_/Medical Research Council/United Kingdom ; MR/N00969X/1/MRC_/Medical Research Council/United Kingdom ; MR/K015777X/1/MRC_/Medical Research Council/United Kingdom ; BB/L01811X/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 104924/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 091911/WT_/Wellcome Trust/United Kingdom ; 107457/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Cell Nucleus/genetics/metabolism ; *Chromatin/metabolism ; DNA/genetics/metabolism ; Exonucleases/metabolism ; In Situ Hybridization, Fluorescence/methods ; Interphase ; Mammals ; }, abstract = {DNA fluorescence in situ hybridization (FISH) has been a central technique in advancing our understanding of how chromatin is organized within the nucleus. With the increasing resolution offered by super-resolution microscopy, the optimal maintenance of chromatin structure within the nucleus is essential for accuracy in measurements and interpretation of data. However, standard 3D-FISH requires potentially destructive heat denaturation in the presence of chaotropic agents such as formamide to allow access to the DNA strands for labeled FISH probes. To avoid the need to heat-denature, we developed Resolution After Single-strand Exonuclease Resection (RASER)-FISH, which uses exonuclease digestion to generate single-stranded target DNA for efficient probe binding over a 2 d process. Furthermore, RASER-FISH is easily combined with immunostaining of nuclear proteins or the detection of RNAs. Here, we provide detailed procedures for RASER-FISH in mammalian cultured cells to detect single loci, chromatin tracks and topologically associating domains with conventional and super-resolution 3D structured illumination microscopy. Moreover, we provide a validation and characterization of our method, demonstrating excellent preservation of chromatin structure and nuclear integrity, together with improved hybridization efficiency, compared with classic 3D-FISH protocols.}, }
@article {pmid35354608, year = {2022}, author = {Chathoth, KT and Mikheeva, LA and Crevel, G and Wolfe, JC and Hunter, I and Beckett-Doyle, S and Cotterill, S and Dai, H and Harrison, A and Zabet, NR}, title = {The role of insulators and transcription in 3D chromatin organization of flies.}, journal = {Genome research}, volume = {32}, number = {4}, pages = {682-698}, pmid = {35354608}, issn = {1549-5469}, support = {/WT_/Wellcome Trust/United Kingdom ; 202012/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Chromatin/genetics ; Chromosomes/metabolism ; DNA-Binding Proteins/genetics ; Drosophila/genetics/metabolism ; *Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/genetics/metabolism ; Eye Proteins/genetics ; Microtubule-Associated Proteins/genetics ; Nuclear Proteins/genetics ; Transcription Factors/metabolism ; }, abstract = {The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.}, }
@article {pmid35346781, year = {2022}, author = {Yin, S and NandyMazumdar, M and Paranjapye, A and Harris, A}, title = {Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene.}, journal = {Genomics}, volume = {114}, number = {3}, pages = {110350}, pmid = {35346781}, issn = {1089-8646}, support = {R01 HD068901/HD/NICHD NIH HHS/United States ; R01 HL094585/HL/NHLBI NIH HHS/United States ; T32 GM008056/GM/NIGMS NIH HHS/United States ; }, mesh = {*Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Enhancer Elements, Genetic ; Chromatin ; Gene Expression Regulation ; Activating Transcription Factors/genetics/metabolism ; }, abstract = {Robust protocols to examine 3D chromatin structure have greatly advanced knowledge of gene regulatory mechanisms. Here we focus on the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which provides a paradigm for validating models of gene regulation built upon genome-wide analysis. We examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR gene coordinate its expression in intestinal epithelial cells. Using CRISPR/Cas9 to remove CREs, individually and in tandem, followed by assays of gene expression and higher-order chromatin structure (4C-seq), we reveal the cross-talk and dependency of two cell-specific intronic enhancers. The results suggest a mechanism whereby the locus responds when CREs are lost, which may involve activating transcription factors such as FOXA2. Also, by removing the 5' topologically-associating domain (TAD) boundary, we illustrate its impact on CFTR gene expression and architecture. These data suggest a multi-layered regulatory hierarchy that is highly sensitive to perturbations.}, }
@article {pmid35341742, year = {2022}, author = {Paranjapye, A and NandyMazumdar, M and Harris, A}, title = {Krüppel-Like Factor 5 Regulates CFTR Expression Through Repression by Maintaining Chromatin Architecture Coupled with Direct Enhancer Activation.}, journal = {Journal of molecular biology}, volume = {434}, number = {10}, pages = {167561}, pmid = {35341742}, issn = {1089-8638}, support = {R01 HD068901/HD/NICHD NIH HHS/United States ; R01 HL094585/HL/NHLBI NIH HHS/United States ; R01 HL117843/HL/NHLBI NIH HHS/United States ; }, mesh = {*Chromatin/metabolism ; *Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Enhancer Elements, Genetic ; Epithelial Cells/metabolism ; Humans ; *Kruppel-Like Transcription Factors/genetics/metabolism ; *Transcriptional Activation ; }, abstract = {Single cell RNA-sequencing has accurately identified cell types within the human airway that express the Cystic Fibrosis Transmembrane Conductance regulator (CFTR) gene. Low abundance CFTR transcripts are seen in many secretory cells, while high levels are restricted to rare pulmonary ionocytes. Here we focus on the mechanisms coordinating basal CFTR expression in the secretory compartment. Cell-selective regulation of CFTR is achieved within its invariant topologically associating domain by the recruitment of cis-regulatory elements (CREs). CRE activity is coordinated by cell-type-selective transcription factors. One such factor, Krüppel-Like Factor 5 (KLF5), profoundly represses CFTR transcript and protein in primary human airway epithelial cells and airway cell lines. Here we reveal the mechanism of action of KLF5 upon the CFTR gene. We find that depletion or ablation of KLF5 from airway epithelial cells changes higher order chromatin structure at the CFTR locus. Critical looping interactions that are required for normal gene expression are altered, the H3K27ac active chromatin mark is redistributed, and CTCF occupancy is modified. However, mutation of a single KLF5 binding site within a pivotal airway cell CRE abolishes CFTR expression. Hence, KLF5 has both direct activating and indirect repressive effects, which together coordinate CFTR expression in the airway.}, }
@article {pmid35332326, year = {2022}, author = {Girdhar, K and Hoffman, GE and Bendl, J and Rahman, S and Dong, P and Liao, W and Hauberg, ME and Sloofman, L and Brown, L and Devillers, O and Kassim, BS and Wiseman, JR and Park, R and Zharovsky, E and Jacobov, R and Flatow, E and Kozlenkov, A and Gilgenast, T and Johnson, JS and Couto, L and Peters, MA and Phillips-Cremins, JE and Hahn, CG and Gur, RE and Tamminga, CA and Lewis, DA and Haroutunian, V and ,  and Dracheva, S and Lipska, BK and Marenco, S and Kundakovic, M and Fullard, JF and Jiang, Y and Roussos, P and Akbarian, S}, title = {Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains.}, journal = {Nature neuroscience}, volume = {25}, number = {4}, pages = {474-483}, pmid = {35332326}, issn = {1546-1726}, support = {R01 MH094714/MH/NIMH NIH HHS/United States ; R21 MH103877/MH/NIMH NIH HHS/United States ; U01 MH103365/MH/NIMH NIH HHS/United States ; U01 MH103392/MH/NIMH NIH HHS/United States ; DP1 MH129957/MH/NIMH NIH HHS/United States ; U01 MH103346/MH/NIMH NIH HHS/United States ; U01 MH103340/MH/NIMH NIH HHS/United States ; U01 MH103339/MH/NIMH NIH HHS/United States ; U01 DA048279/DA/NIDA NIH HHS/United States ; P50 MH096890/MH/NIMH NIH HHS/United States ; R21 MH105881/MH/NIMH NIH HHS/United States ; R01 NS114226/NS/NINDS NIH HHS/United States ; P50 MH106934/MH/NIMH NIH HHS/United States ; R01 MH105472/MH/NIMH NIH HHS/United States ; R01 MH106056/MH/NIMH NIH HHS/United States ; ZIC MH002903/ImNIH/Intramural NIH HHS/United States ; R21 MH102791/MH/NIMH NIH HHS/United States ; R01 MH105898/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; *Bipolar Disorder/genetics ; Brain ; Chromatin ; Humans ; Lysine/genetics ; *Schizophrenia/genetics ; }, abstract = {Chromosomal organization, scaling from the 147-base pair (bp) nucleosome to megabase-ranging domains encompassing multiple transcriptional units, including heritability loci for psychiatric traits, remains largely unexplored in the human brain. In this study, we constructed promoter- and enhancer-enriched nucleosomal histone modification landscapes for adult prefrontal cortex from H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from 388 controls and 351 individuals diagnosed with schizophrenia (SCZ) or bipolar disorder (BD) (n = 739). We mapped thousands of cis-regulatory domains (CRDs), revealing fine-grained, 10[4]-10[6]-bp chromosomal organization, firmly integrated into Hi-C topologically associating domain stratification by open/repressive chromosomal environments and nuclear topography. Large clusters of hyper-acetylated CRDs were enriched for SCZ heritability, with prominent representation of regulatory sequences governing fetal development and glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated dysregulation of risk-associated regulatory sequences assembled into kilobase- to megabase-scaling chromosomal domains.}, }
@article {pmid35328034, year = {2022}, author = {Zhao, C and Liu, T and Wang, Z}, title = {Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions.}, journal = {Genes}, volume = {13}, number = {3}, pages = {}, pmid = {35328034}, issn = {2073-4425}, support = {R35 GM137974/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome/genetics ; *Genomics ; }, abstract = {Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same TAD and between different TADs, and also in the same gap region (the region between two consecutive TADs) and between different gap regions. We found that the protein-coding genes from the same TAD or gap region are more likely to share similar protein functions, and this trend is more obvious with TADs than the gap regions. We further created two types of gene-gene spatial interaction networks: the first type is based on Hi-C contacts, whereas the second type is based on both Hi-C contacts and the relationship of being in the same TAD. A graph auto-encoder was applied to learn the network topology, reconstruct the two types of networks, and predict the functions of the central genes/nodes based on the functions of the neighboring genes/nodes. It was found that better performance was achieved with the second type of network. Furthermore, we detected long-range spatially-interactive regions based on Hi-C contacts and calculated the functional similarities of the gene pairs from these regions.}, }
@article {pmid35309301, year = {2022}, author = {Xia, Y and Liu, X and Mu, W and Ma, C and Wang, L and Jiao, Y and Cui, B and Hu, S and Gao, Y and Liu, T and Sun, H and Zong, S and Liu, X and Zhao, Y}, title = {Capturing 3D Chromatin Maps of Human Primary Monocytes: Insights From High-Resolution Hi-C.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {837336}, pmid = {35309301}, issn = {1664-3224}, mesh = {*Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Chromosomes ; Epigenesis, Genetic ; Humans ; *Monocytes ; }, abstract = {Although the variation in chromatin architecture during adaptive immune responses has been thoroughly investigated, the 3D landscape of innate immunity is still unknown. Herein, chromatin regulation and heterogeneity among human primary monocytes were investigated. Peripheral blood was collected from two healthy persons and two patients with systemic lupus erythematosus (SLE), and CD14[+] monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq analyses. Raw data from the THP1 cell line Hi-C library were used for comparison. For each sample, we constructed three Hi-C libraries and obtained approximately 3 billion paired-end reads in total. Resolution analysis showed that more than 80% of bins presented depths greater than 1000 at a 5 kb resolution. The constructed high-resolution chromatin interaction maps presented similar landscapes in the four individuals, which showed significant divergence from the THP1 cell line chromatin structure. The variability in chromatin interactions around HLA-D genes in the HLA complex region was notable within individuals. We further found that the CD16-encoding gene (FCGR3A) is located at a variable topologically associating domain (TAD) boundary and that chromatin loop dynamics might modulate CD16 expression. Our results indicate both the stability and variability of high-resolution chromatin interaction maps among human primary monocytes. This work sheds light on the potential mechanisms by which the complex interplay of epigenetics and spatial 3D architecture regulates chromatin in innate immunity.}, }
@article {pmid35304523, year = {2022}, author = {Sanders, JT and Golloshi, R and Das, P and Xu, Y and Terry, PH and Nash, DG and Dekker, J and McCord, RP}, title = {Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4721}, pmid = {35304523}, issn = {2045-2322}, support = {F32 GM100617/GM/NIGMS NIH HHS/United States ; R01 HG003143/HG/NHGRI NIH HHS/United States ; R35 GM133557/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Cell Nucleus/metabolism ; *Chromatin/metabolism ; Chromatin Assembly and Disassembly ; *Chromosomes ; Genome ; }, abstract = {Layers of genome organization are becoming increasingly better characterized, but less is known about how these structures respond to perturbation or shape changes. Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin. But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence. We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories. Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress. From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.}, }
@article {pmid35277200, year = {2022}, author = {Zhang, J and Liu, P and He, M and Wang, Y and Kui, H and Jin, L and Li, D and Li, M}, title = {Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues.}, journal = {Journal of animal science and biotechnology}, volume = {13}, number = {1}, pages = {32}, pmid = {35277200}, issn = {1674-9782}, abstract = {BACKGROUND: A growing body of evidence has revealed that the mammalian genome is organized into hierarchical layers that are closely correlated with and may even be causally linked with variations in gene expression. Recent studies have characterized chromatin organization in various porcine tissues and cell types and compared them among species and during the early development of pigs. However, how chromatin organization differs among pig breeds is poorly understood.<br><br>RESULTS: In this study, we investigated the 3D genome organization and performed transcriptome characterization of two adipose depots (upper layer of backfat [ULB] and greater omentum [GOM]) in wild boars and Bama pigs; the latter is a typical indigenous pig in China. We found that over 95% of the A/B compartments and topologically associating domains (TADs) are stable between wild boars and Bama pigs. In contrast, more than 70% of promoter-enhancer interactions (PEIs) are dynamic and widespread, involving over a thousand genes. Alterations in chromatin structure are associated with changes in the expression of genes that are involved in widespread biological functions such as basic cellular functions, endocrine function, energy metabolism and the immune response. Approximately 95% and 97% of the genes associated with reorganized A/B compartments and PEIs in the two pig breeds differed between GOM and ULB, respectively.<br><br>CONCLUSIONS: We reported 3D genome organization in adipose depots from different pig breeds. In a comparison of Bama pigs and wild boar, large-scale compartments and TADs were mostly conserved, while fine-scale PEIs were extensively reorganized. The chromatin architecture in these two pig breeds was reorganized in an adipose depot-specific manner. These results contribute to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar.}, }
@article {pmid35274679, year = {2022}, author = {Hicks, P and Oluwadare, O}, title = {HiCARN: resolution enhancement of Hi-C data using cascading residual networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {9}, pages = {2414-2421}, pmid = {35274679}, issn = {1367-4811}, mesh = {Humans ; Mice ; Animals ; Reproducibility of Results ; *Software ; *Chromatin ; Chromosomes ; Molecular Conformation ; }, abstract = {MOTIVATION: High throughput chromosome conformation capture (Hi-C) contact matrices are used to predict 3D chromatin structures in eukaryotic cells. High-resolution Hi-C data are less available than low-resolution Hi-C data due to sequencing costs but provide greater insight into the intricate details of 3D chromatin structures such as enhancer-promoter interactions and sub-domains. To provide a cost-effective solution to high-resolution Hi-C data collection, deep learning models are used to predict high-resolution Hi-C matrices from existing low-resolution matrices across multiple cell types.<br><br>RESULTS: Here, we present two Cascading Residual Networks called HiCARN-1 and HiCARN-2, a convolutional neural network and a generative adversarial network, that use a novel framework of cascading connections throughout the network for Hi-C contact matrix prediction from low-resolution data. Shown by image evaluation and Hi-C reproducibility metrics, both HiCARN models, overall, outperform state-of-the-art Hi-C resolution enhancement algorithms in predictive accuracy for both human and mouse 1/16, 1/32, 1/64 and 1/100 downsampled high-resolution Hi-C data. Also, validation by extracting topologically associating domains, chromosome 3D structure and chromatin loop predictions from the enhanced data shows that HiCARN can proficiently reconstruct biologically significant regions.<br><br>HiCARN can be accessed and utilized as an open-sourced software at: https://github.com/OluwadareLab/HiCARN and is also available as a containerized application that can be run on any platform.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid35274099, year = {2022}, author = {Galan, S and Serra, F and Marti-Renom, MA}, title = {Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {1}, pages = {lqac021}, pmid = {35274099}, issn = {2631-9268}, support = {609989/ERC_/European Research Council/International ; }, abstract = {Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored. Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using self-organizing feature maps and their functionality characterized by their epigenetic states. The resulting clusters were then input to a convolutional neural network aiming at the de novo detecting chromatin loops from Hi-C interaction matrices. Our new method, called LOOPbit, is able to automatically detect significant interactions with a higher proportion of enhancer-promoter loops compared to other callers. Our highly specific loop caller adds a new layer of detail to the link between chromatin structure and function.}, }
@article {pmid35236295, year = {2022}, author = {Mourad, R}, title = {TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {82}, pmid = {35236295}, issn = {1471-2105}, mesh = {Chromatin ; *Genome ; *Transcription Factors/genetics ; }, abstract = {BACKGROUND/AIM: In higher eukaryotes, the three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression, DNA repair and DNA replication regulations. Alteration of 3D organization, in particular topologically associating domains (TADs), is detrimental to the organism and can give rise to a broad range of diseases such as cancers.<br><br>METHODS: Here, we propose a versatile regression framework which not only identifies TADs in a fast and accurate manner, but also detects differential TAD borders across conditions for which few methods exist, and predicts 3D genome reorganization after chromosomal rearrangement. Moreover, the framework is biologically meaningful, has an intuitive interpretation and is easy to visualize.<br><br>RESULT AND CONCLUSION: The novel regression ranks among top TAD callers. Moreover, it identifies new features of the genome we called TAD facilitators, and that are enriched with specific transcription factors. It also unveils the importance of cell-type specific transcription factors in establishing novel TAD borders during neuronal differentiation. Lastly, it compares favorably with the state-of-the-art method for predicting rearranged 3D genome.}, }
@article {pmid35228717, year = {2022}, author = {Pommier, Y and Nussenzweig, A and Takeda, S and Austin, C}, title = {Human topoisomerases and their roles in genome stability and organization.}, journal = {Nature reviews. Molecular cell biology}, volume = {23}, number = {6}, pages = {407-427}, pmid = {35228717}, issn = {1471-0080}, support = {Z01 BC006150/ImNIH/Intramural NIH HHS/United States ; Z01 BC006161/ImNIH/Intramural NIH HHS/United States ; }, mesh = {DNA Damage/genetics ; DNA Replication/genetics ; *Genomic Instability ; Humans ; Mitochondria/genetics ; *Neoplasms/genetics ; }, abstract = {Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA-protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer.}, }
@article {pmid35202564, year = {2022}, author = {Franke, M and Daly, AF and Palmeira, L and Tirosh, A and Stigliano, A and Trifan, E and Faucz, FR and Abboud, D and Petrossians, P and Tena, JJ and Vitali, E and Lania, AG and Gómez-Skarmeta, JL and Beckers, A and Stratakis, CA and Trivellin, G}, title = {Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism.}, journal = {American journal of human genetics}, volume = {109}, number = {4}, pages = {553-570}, pmid = {35202564}, issn = {1537-6605}, support = {Z01 HD008720/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Acromegaly/complications/genetics/pathology ; Child, Preschool ; Chromatin/genetics ; Communication ; DNA-Binding Proteins/genetics ; *Genetic Diseases, X-Linked/genetics ; *Gigantism/complications/genetics/pathology ; Humans ; *Pituitary Neoplasms/genetics ; Receptors, G-Protein-Coupled/genetics ; Transcription Factors/genetics ; }, abstract = {X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)-secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes VGLL1, CD40LG, ARHGEF6, RBMX, and GPR101) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. The mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone was previously unclear. Using Hi-C and 4C-seq, we characterized the normal chromatin structure at the X-LAG locus. We showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Next, using 4C-seq with GPR101, RBMX, and VGLL1 viewpoints, we showed that the duplications in multiple X-LAG-affected individuals led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG. We then identified several pituitary active cis-regulatory elements (CREs) within the neo-TAD and demonstrated in vitro that one of them significantly enhanced reporter gene expression. At the same time, we showed that the GPR101 promoter permits the incorporation of new regulatory information. Our results indicate that X-LAG is a TADopathy of the endocrine system in which Xq26.3 duplications disrupt the local chromatin architecture forming a neo-TAD. Rewiring GPR101-enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in pituitary tumors caused by X-LAG.}, }
@article {pmid35181793, year = {2022}, author = {Wu, H and Zhang, P and Ai, Z and Wei, L and Zhang, H and Yang, F and Cui, L}, title = {StackTADB: a stacking-based ensemble learning model for predicting the boundaries of topologically associating domains (TADs) accurately in fruit flies.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {2}, pages = {}, doi = {10.1093/bib/bbac023}, pmid = {35181793}, issn = {1477-4054}, mesh = {Animals ; *Chromatin ; Chromosomes ; DNA-Binding Proteins/genetics ; Drosophila/genetics ; *Drosophila Proteins/genetics ; Eye Proteins/genetics ; Machine Learning ; Software ; }, abstract = {Chromosome is composed of many distinct chromatin domains, referred to variably as topological domains or topologically associating domains (TADs). The domains are stable across different cell types and highly conserved across species, thus these chromatin domains have been considered as the basic units of chromosome folding and regarded as an important secondary structure in chromosome organization. However, the identification of TAD boundaries is still a great challenge due to the high cost and low resolution of Hi-C data or experiments. In this study, we propose a novel ensemble learning framework, termed as StackTADB, for predicting the boundaries of TADs. StackTADB integrates four base classifiers including Random Forest, Logistic Regression, K-NearestNeighbor and Support Vector Machine. From the analysis of a series of examinations on the data set in the previous study, it is concluded that StackTADB has optimal performance in six metrics, AUC, Accuracy, MCC, Precision, Recall and F1 score, and it is superior to the existing methods. In addition, the comparison of the performance of multiple features shows that Kmers-based features play an essential role in predicting TADs boundaries of fruit flies, and we also apply the SHapley Additive exPlanations (SHAP) framework to interpret the predictions of StackTADB to identify the reason why Kmers-based features are vital. The experimental results show that the subsequences matching the BEAF-32 motif play a crucial role in predicting the boundaries of TADs. The source code is freely available at https://github.com/HaoWuLab-Bioinformatics/StackTADB and the webserver of StackTADB is freely available at http://hwtad.sdu.edu.cn:8002/StackTADB.}, }
@article {pmid35176995, year = {2022}, author = {Osman, N and Shawky, AE and Brylinski, M}, title = {Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.}, journal = {BMC genomic data}, volume = {23}, number = {1}, pages = {13}, pmid = {35176995}, issn = {2730-6844}, support = {R35 GM119524/GM/NIGMS NIH HHS/United States ; }, mesh = {*Breast Neoplasms/genetics ; Chromatin/genetics ; Female ; Gene Expression Regulation, Neoplastic ; Genome, Human ; *Genome-Wide Association Study ; Humans ; Male ; Polymorphism, Single Nucleotide ; *Prostatic Neoplasms/genetics ; }, abstract = {BACKGROUND: Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging.<br><br>RESULTS: In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants.<br><br>CONCLUSIONS: Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.}, }
@article {pmid35166842, year = {2022}, author = {Ilyin, AA and Kononkova, AD and Golova, AV and Shloma, VV and Olenkina, OM and Nenasheva, VV and Abramov, YA and Kotov, AA and Maksimov, DA and Laktionov, PP and Pindyurin, AV and Galitsyna, AA and Ulianov, SV and Khrameeva, EE and Gelfand, MS and Belyakin, SN and Razin, SV and Shevelyov, YY}, title = {Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila.}, journal = {Nucleic acids research}, volume = {50}, number = {6}, pages = {3203-3225}, pmid = {35166842}, issn = {1362-4962}, mesh = {Animals ; Cell Differentiation/genetics ; *Chromatin/genetics ; Dosage Compensation, Genetic ; *Drosophila/genetics ; Germ Cells ; Male ; }, abstract = {Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis - in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters' detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.}, }
@article {pmid35145304, year = {2022}, author = {Ortabozkoyun, H and Huang, PY and Cho, H and Narendra, V and LeRoy, G and Gonzalez-Buendia, E and Skok, JA and Tsirigos, A and Mazzoni, EO and Reinberg, D}, title = {CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters.}, journal = {Nature genetics}, volume = {54}, number = {2}, pages = {202-212}, pmid = {35145304}, issn = {1546-1718}, support = {P01 CA229086/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; F31 HD090892/HD/NICHD NIH HHS/United States ; R01 NS100897/NS/NINDS NIH HHS/United States ; R01 CA229235/CA/NCI NIH HHS/United States ; R35 GM122515/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/chemistry/genetics/*metabolism ; CRISPR-Cas Systems ; Cell Cycle Proteins/metabolism ; Cell Differentiation ; Cell Line ; Chromatin/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Embryonic Stem Cells/cytology/*metabolism ; Gene Editing ; Gene Expression ; Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Homeodomain Proteins/*genetics ; Mice ; Transcription Factors/chemistry/genetics/*metabolism ; }, abstract = {CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.}, }
@article {pmid35144531, year = {2022}, author = {Chang, JM and Weng, YF and Chang, WT and Lin, FA and Cavalli, G}, title = {HiCmapTools: a tool to access HiC contact maps.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {64}, pmid = {35144531}, issn = {1471-2105}, support = {Advanced Grant 3DEpi/ERC_/European Research Council/International ; 788972/ERC_/European Research Council/International ; }, mesh = {*Chromatin ; *Genomics ; }, abstract = {BACKGROUND: With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets.<br><br>RESULTS: We present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density.<br><br>CONCLUSIONS: HiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++&#x2009;and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/ .}, }
@article {pmid35140205, year = {2022}, author = {Owens, DDG and Anselmi, G and Oudelaar, AM and Downes, DJ and Cavallo, A and Harman, JR and Schwessinger, R and Bucakci, A and Greder, L and de Ornellas, S and Jeziorska, D and Telenius, J and Hughes, JR and de Bruijn, MFTR}, title = {Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {773}, pmid = {35140205}, issn = {2041-1723}, support = {G0902418/MRC_/Medical Research Council/United Kingdom ; 105281/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_00016/2/MRC_/Medical Research Council/United Kingdom ; 108870/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 106130/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00016/14/MRC_/Medical Research Council/United Kingdom ; 203728/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12009/2/MRC_/Medical Research Council/United Kingdom ; MR/N00969X/1/MRC_/Medical Research Council/United Kingdom ; MR/K015777X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cell Cycle Proteins/metabolism ; Cell Differentiation ; Chromatin/*metabolism ; Core Binding Factor Alpha 2 Subunit/*genetics/*metabolism ; DNA/chemistry ; *Gene Expression ; Gene Expression Regulation, Developmental ; Hematopoietic Stem Cells/metabolism ; Mesoderm/metabolism ; Mice ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; }, abstract = {The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.}, }
@article {pmid35115029, year = {2022}, author = {Pei, L and Huang, X and Liu, Z and Tian, X and You, J and Li, J and Fang, DD and Lindsey, K and Zhu, L and Zhang, X and Wang, M}, title = {Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {45}, pmid = {35115029}, issn = {1474-760X}, mesh = {Cell Differentiation ; *Chromatin ; *Cotton Fiber ; Genome ; }, abstract = {BACKGROUND: Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process.<br><br>RESULTS: To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes.<br><br>CONCLUSIONS: This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.}, }
@article {pmid35113722, year = {2022}, author = {Batut, PJ and Bing, XY and Sisco, Z and Raimundo, J and Levo, M and Levine, MS}, title = {Genome organization controls transcriptional dynamics during development.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6580}, pages = {566-570}, doi = {10.1126/science.abi7178}, pmid = {35113722}, issn = {1095-9203}, support = {R35 GM118147/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromatin/chemistry/genetics ; Chromosomes, Insect/chemistry/genetics ; Drosophila/embryology/*genetics ; Enhancer Elements, Genetic ; *Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Genes, Insect ; *Genome, Insect ; Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Single-Cell Analysis ; *Transcription, Genetic ; }, abstract = {Past studies offer contradictory claims for the role of genome organization in the regulation of gene activity. Here, we show through high-resolution chromosome conformation analysis that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. Quantitative live imaging and targeted genome editing demonstrate that this two-tiered organization is critical for the precise temporal dynamics of Hox gene transcription during development. Tethering elements mediate long-range enhancer-promoter interactions and foster fast activation kinetics. Conversely, the boundaries of topologically associating domains (TADs) prevent spurious interactions with enhancers and silencers located in neighboring TADs. These two levels of genome organization operate independently of one another to ensure precision of transcriptional dynamics and the reliability of complex patterning processes.}, }
@article {pmid35104223, year = {2022}, author = {Liu, K and Li, H and Li, Y and Wang, J and Wang, J}, title = {A comparison of topologically associating domain callers based on Hi-C data.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/TCBB.2022.3147805}, pmid = {35104223}, issn = {1557-9964}, abstract = {Topologically associating domains (TADs) are local chromatin interaction domains, which have been shown to play an important role in gene expression regulation. TADs were originally discovered in the investigation of 3D genome organization based on High-throughput Chromosome Conformation Capture (Hi-C) data. Continuous considerable efforts have been dedicated to developing methods for detecting TADs from Hi-C data. Different computational methods for TADs identification vary in their assumptions and criteria in calling TADs. As a consequence, the TADs called by these methods differ in their similarities and biological features they are enriched in. In this work, we performed a systematic comparison of twenty-four TAD callers. We first compared the TADs and gaps between adjacent TADs across different methods, resolutions, and sequencing depths. We then assessed the quality of TADs and TAD boundaries according to three criteria: the decay of contact frequencies over the genomic distance, enrichment and depletion of regulatory elements around TAD boundaries, and reproducibility of TADs and TAD boundaries in replicate samples. Last, due to the lack of a gold standard for TADs, we also evaluated the performance of the methods on synthetic datasets.}, }
@article {pmid35098228, year = {2022}, author = {Chu, X and Wang, J}, title = {Dynamics and Pathways of Chromosome Structural Organizations during Cell Transdifferentiation.}, journal = {JACS Au}, volume = {2}, number = {1}, pages = {116-127}, pmid = {35098228}, issn = {2691-3704}, abstract = {Direct conversion of one differentiated cell type into another is defined as cell transdifferentiation. In avoidance of forming pluripotency, cell transdifferentiation can reduce the potential risk of tumorigenicity, thus offering significant advantages over cell reprogramming in clinical applications. Until now, the mechanism of cell transdifferentiation is still largely unknown. It has been well recognized that cell transdifferentiation is determined by the underlying gene expression regulation, which relies on the accurate adaptation of the chromosome structure. To dissect the transdifferentiation at the molecular level, we develop a nonequilibrium landscape-switching model to investigate the chromosome structural dynamics during the state transitions between the human fibroblast and neuron cells. We uncover the high irreversibility of the transdifferentiation at the local chromosome structural ranges, where the topologically associating domains form. In contrast, the pathways in the two opposite directions of the transdifferentiation projected onto the chromosome compartment profiles are highly overlapped, indicating that the reversibility vanishes at the long-range chromosome structures. By calculating the contact strengths in the chromosome at the states along the paths, we observe strengthening contacts in compartment A concomitant with weakening contacts in compartment B at the early stages of the transdifferentiation. This further leads to adapting contacts toward the ones at the embryonic stem cell. In light of the intimate structure-function relationship at the chromosomal level, we suggest an increase of "stemness" during the transdifferentiation. In addition, we find that the neuron progenitor cell (NPC), a cell developmental state, is located on the transdifferentiation pathways projected onto the long-range chromosome contacts. The findings are consistent with the previous single-cell RNA sequencing experiment, where the NPC-like cell states were observed during the direct conversion of the fibroblast to neuron cells. Thus, we offer a promising microscopic and physical approach to study the cell transdifferentiation mechanism from the chromosome structural perspective.}, }
@article {pmid35090532, year = {2022}, author = {Long, HS and Greenaway, S and Powell, G and Mallon, AM and Lindgren, CM and Simon, MM}, title = {Making sense of the linear genome, gene function and TADs.}, journal = {Epigenetics &amp; chromatin}, volume = {15}, number = {1}, pages = {4}, pmid = {35090532}, issn = {1756-8935}, support = {UM1 HG006370/HG/NHGRI NIH HHS/United States ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_U142684171/MRC_/Medical Research Council/United Kingdom ; }, mesh = {CCCTC-Binding Factor/genetics/metabolism ; *Chromatin/genetics ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation Sequencing ; *Genome ; }, abstract = {BACKGROUND: Topologically associating domains (TADs) are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching between active and inactive compartments. This has led to the speculation that genes which are required for similar processes may fall within the same TADs, allowing them to share regulatory programs and efficiently switch between chromatin compartments. However, evidence to link genes within TADs to the same regulatory program is limited.<br><br>RESULTS: We investigated the functional similarity of genes which fall within the same TAD. To do this we developed a TAD randomisation algorithm to generate sets of "random TADs" to act as null distributions. We found that while pairs of paralogous genes are enriched in TADs overall, they are largely depleted in TADs with CCCTC-binding factor (CTCF) ChIP-seq peaks at both boundaries. By assessing gene constraint as a proxy for functional importance we found that genes which singly occupy a TAD have greater functional importance than genes which share a TAD, and these genes are enriched for developmental processes. We found little evidence that pairs of genes in CTCF bound TADs are more likely to be co-expressed or share functional annotations than can be explained by their linear proximity alone.<br><br>CONCLUSIONS: These results suggest that algorithmically defined TADs consist of two functionally different groups, those which are bound by CTCF and those which are not. We detected no association between genes sharing the same CTCF TADs and increased co-expression or functional similarity, other than that explained by linear genome proximity. We do, however, find that functionally important genes are more likely to fall within a TAD on their own suggesting that TADs play an important role in the insulation of these genes.}, }
@article {pmid35088940, year = {2022}, author = {Lybaek, H and Robson, M and de Leeuw, N and Hehir-Kwa, JY and Jeffries, A and Haukanes, BI and Berland, S and de Bruijn, D and Mundlos, S and Spielmann, M and Houge, G}, title = {LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions.}, journal = {Autism research : official journal of the International Society for Autism Research}, volume = {15}, number = {3}, pages = {421-433}, pmid = {35088940}, issn = {1939-3806}, mesh = {Animals ; *Autism Spectrum Disorder/genetics ; *Autistic Disorder/genetics ; Cell Adhesion Molecules, Neuronal/*genetics ; Female ; Haplotypes ; Humans ; Male ; Mammals ; Polymorphism, Genetic ; }, abstract = {LRFN5 is a regulator of synaptic development and the only gene in a 5.4 Mb mammalian-specific conserved topologically associating domain (TAD); the LRFN5 locus. An association between locus structural changes and developmental delay (DD) and/or autism was suggested by several cases in DECIPHER and own records. More significantly, we found that maternal inheritance of a specific LRFN5 locus haplotype segregated with an identical type of autism in distantly related males. This autism-susceptibility haplotype had a specific TAD pattern. We also found a male/female quantitative difference in the amount histone-3-lysine-9-associated chromatin around the LRFN5 gene itself (p < 0.01), possibly related to the male-restricted autism susceptibility. To better understand locus behavior, the prevalence of a 60 kb deletion polymorphism was investigated. Surprisingly, in three cohorts of individuals with DD (n = 8757), the number of deletion heterozygotes was 20%-26% lower than expected from Hardy-Weinberg equilibrium. This suggests allelic interaction, also because the conversions from heterozygosity to wild-type or deletion homozygosity were of equal magnitudes. Remarkably, in a control group of medical students (n = 1416), such conversions were three times more common (p = 0.00001), suggesting a regulatory role of this allelic interaction. Taken together, LRFN5 regulation appears unusually complex, and LRFN5 dysregulation could be an epigenetic cause of autism. LAY SUMMARY: LRFN5 is involved with communication between brain cells. The gene sits alone in a huge genomic niche, called the LRFN5 locus, of complex structure and high mammalian conservation. We have found that a specific locus structure increases autism susceptibility in males, but we do not yet know how common this epigenetic cause of autism is. It is, however, a cause that potentially could explain why higher-functioning autism is more common in males than females.}, }
@article {pmid35087776, year = {2021}, author = {Wang, H and Cui, B and Sun, H and Zhang, F and Rao, J and Wang, R and Zhao, S and Shen, S and Liu, Y}, title = {Aberrant GATA2 Activation in Pediatric B-Cell Acute Lymphoblastic Leukemia.}, journal = {Frontiers in pediatrics}, volume = {9}, number = {}, pages = {795529}, pmid = {35087776}, issn = {2296-2360}, abstract = {GATA2 is a transcription factor that is critical for the generation and survival of hematopoietic stem cells (HSCs). It also plays an important role in the regulation of myeloid differentiation. Accordingly, GATA2 expression is restricted to HSCs and hematopoietic progenitors as well as early erythroid cells and megakaryocytic cells. Here we identified aberrant GATA2 expression in B-cell acute lymphoblastic leukemia (B-ALL) by analyzing transcriptome sequencing data obtained from St. Jude Cloud. Differentially expressed genes upon GATA2 activation showed significantly myeloid-like transcription signature. Further analysis identified several tumor-associated genes as targets of GATA2 activation including BAG3 and EPOR. In addition, the correlation between KMT2A-USP2 fusion and GATA2 activation not only indicates a potential trans-activating mechanism of GATA2 but also suggests that GATA2 is a target of KMT2A-USP2. Furthermore, by integrating whole-genome and transcriptome sequencing data, we showed that GATA2 is also cis activated. A somatic focal deletion located in the GATA2 neighborhood that disrupts the boundaries of topologically associating domains was identified in one B-ALL patient with GATA2 activation. These evidences support the hypothesis that GATA2 could be involved in leukemogenesis of B-ALL and can be transcriptionally activated through multiple mechanisms. The findings of aberrant activation of GATA2 and its molecular function extend our understanding of transcriptional factor dysregulation in B-ALL.}, }
@article {pmid35065445, year = {2022}, author = {Ing-Simmons, E and Rigau, M and Vaquerizas, JM}, title = {Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation.}, journal = {Current opinion in cell biology}, volume = {74}, number = {}, pages = {37-46}, doi = {10.1016/j.ceb.2021.12.004}, pmid = {35065445}, issn = {1879-0410}, support = {MC_UP_1605/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Chromatin/genetics ; Drosophila/metabolism ; *Drosophila Proteins/metabolism ; Gene Expression Regulation, Developmental ; Genome ; Mice ; Zebrafish ; *Zygote/metabolism ; }, abstract = {The genome of an early embryo undergoes significant remodelling at the epigenetic, transcriptional, and structural levels. New technological developments have made it possible to study 3D genome organisation in the zygote and early embryo of many different species. Recent studies in human embryos, zebrafish, medaka, and Xenopus have revealed that, similar to previous results in mouse and Drosophila, the zygotic genome is unstructured prior to zygotic genome activation. While these studies show that topologically associating domains are established coincident with zygotic genome activation across species, other 3D genome structures have more varied timing. Here, we review recent studies examining the timing and mechanisms of establishment of 3D genome organisation in the early embryo, and discuss similarities and differences between species. Investigating the establishment of 3D chromatin conformation in early embryos has the potential to reveal novel mechanisms of 3D genome organisation.}, }
@article {pmid35047813, year = {2022}, author = {Tsagiopoulou, M and Pechlivanis, N and Maniou, MC and Psomopoulos, F}, title = {InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {1}, pages = {lqab121}, pmid = {35047813}, issn = {2631-9268}, abstract = {The integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs.}, }
@article {pmid35039499, year = {2022}, author = {Li, CC and Zhang, G and Du, J and Liu, D and Li, Z and Ni, Y and Zhou, J and Li, Y and Hou, S and Zheng, X and Lan, Y and Liu, B and He, A}, title = {Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {346}, pmid = {35039499}, issn = {2041-1723}, mesh = {Animals ; Chromatin/*chemistry ; Cluster Analysis ; Core Binding Factor Alpha 2 Subunit/metabolism ; Embryo, Mammalian/*cytology ; Enhancer Elements, Genetic/genetics ; Genome ; Hematopoietic Stem Cells/*cytology ; *Histone Code ; Mice, Inbred C57BL ; Molecular Sequence Annotation ; Promoter Regions, Genetic/genetics ; Transcription Factors/metabolism ; }, abstract = {The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.}, }
@article {pmid35026526, year = {2022}, author = {Miura, H and Hiratani, I}, title = {Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales.}, journal = {Current opinion in genetics &amp; development}, volume = {73}, number = {}, pages = {101898}, doi = {10.1016/j.gde.2021.101898}, pmid = {35026526}, issn = {1879-0380}, mesh = {Animals ; Cell Cycle/genetics ; Cell Nucleus/genetics ; Chromatin/genetics ; *Chromosomes/genetics ; *Genome/genetics ; Interphase/genetics ; Mammals/genetics ; }, abstract = {In the mammalian cell nucleus, chromosomes are folded differently in interphase and mitosis. Interphase chromosomes are relatively decondensed and display at least two unique layers of higher-order organization: topologically associating domains (TADs) and cell-type-specific A/B compartments, which correlate well with early/late DNA replication timing (RT). In mitosis, these structures rapidly disappear but are gradually reconstructed during G1 phase, coincident with the establishment of the RT program. However, these structures also change dynamically during cell differentiation and reprogramming, and yet we are surprisingly ignorant about the relationship between their cell cycle dynamics and developmental dynamics. In this review, we summarize the recent findings on this topic, discuss how these two processes might be coordinated with each other and its potential significance.}, }
@article {pmid35016721, year = {2022}, author = {Jablonski, KP and Carron, L and Mozziconacci, J and Forné, T and Hütt, MT and Lesne, A}, title = {Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study.}, journal = {Human genomics}, volume = {16}, number = {1}, pages = {2}, pmid = {35016721}, issn = {1479-7364}, mesh = {Gene Expression Regulation ; Genome ; *Genome-Wide Association Study ; Humans ; *Neoplasms/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {BACKGROUND: Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in three-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically associating domains (TADs) and their borders.<br><br>RESULTS: For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e., the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases displays such a preferential localization of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that localization of risk loci in TAD borders differs between cancers and non-cancer diseases. Furthermore, different TAD border enrichments are observed in embryonic stem cells and differentiated cells, consistent with changes in topological domains along embryogenesis and delineating their contribution to disease risk.<br><br>CONCLUSIONS: Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with an effect on an individual gene, the other acting in interplay with 3D genome organization.}, }
@article {pmid35013308, year = {2022}, author = {Li, D and Ning, C and Zhang, J and Wang, Y and Tang, Q and Kui, H and Wang, T and He, M and Jin, L and Li, J and Lin, Y and Zeng, B and Yin, H and Zhao, X and Zhang, Y and Xu, H and Zhu, Q and Li, M}, title = {Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {131}, pmid = {35013308}, issn = {2041-1723}, mesh = {Animals ; Avian Proteins/classification/*genetics/metabolism ; Chickens/*genetics/growth &amp; development/metabolism ; Chromatin/chemistry/*ultrastructure ; Enhancer Elements, Genetic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Ontology ; Granulosa Cells/cytology/*metabolism ; Molecular Sequence Annotation ; Oocytes/cytology/metabolism ; Oogenesis/*genetics ; Promoter Regions, Genetic ; *Transcriptome ; }, abstract = {Folliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells.}, }
@article {pmid34981210, year = {2022}, author = {Tian, GG and Zhao, X and Hou, C and Xie, W and Li, X and Wang, Y and Wang, L and Li, H and Zhao, X and Li, J and Wu, J}, title = {Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {79}, number = {1}, pages = {22}, pmid = {34981210}, issn = {1420-9071}, mesh = {Adult Stem Cells/metabolism ; Animals ; Base Sequence ; CCCTC-Binding Factor/*metabolism ; Cell Shape ; Chromatin/metabolism ; Chromosomes, Mammalian/metabolism ; Female ; *Genome ; *Imaging, Three-Dimensional ; Induced Pluripotent Stem Cells/metabolism ; Male ; Mice, Inbred C57BL ; Oogonial Stem Cells/cytology/*metabolism ; }, abstract = {The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female germline stem cells (FGSCs) and identify its regulating key factor based on the data-driven of multiple omics data. By comparison with pluripotent stem cells (PSCs), adult stem cells (ASCs), and somatic cells at three major levels of chromatin architecture, A/B compartments, topologically associating domains, and chromatin loops, the chromatin architecture of FGSCs was most similar to that of other ASCs and largely different from that of PSCs and somatic cells. After integrative analysis of the three-dimensional chromatin structure, active compartment-associating loops (aCALs) were identified as a signature of high-order chromatin organization in FGSCs, which revealed that CCCTC-binding factor was a major factor to maintain the properties of FGSCs through regulation of aCALs. We found FGSCs belong to ASCs at chromatin structure level and characterized aCALs as the high-order chromatin structure signature of FGSCs. Furthermore, CTCF was identified to play a key role in regulating aCALS to maintain the biological functions of FGSCs. These data provide a valuable resource for future studies of the features of chromatin organization in mammalian stem cells and further understanding of the fundamental characteristics of FGSCs.}, }
@article {pmid34979097, year = {2022}, author = {Zheng, Y and Zhang, L and Jin, L and Zhang, P and Li, F and Guo, M and Gao, Q and Zeng, Y and Li, M and Zeng, W}, title = {Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {2}, pages = {101559}, pmid = {34979097}, issn = {1083-351X}, mesh = {*Adult Germline Stem Cells/cytology/metabolism ; Animals ; Cell Differentiation/physiology ; *Chromatin/metabolism ; Male ; *Spermatogenesis/physiology ; *Spermatogonia/cytology ; Swine ; }, abstract = {Spermatogonial stem cells (SSCs) are able to undergo both self-renewal and differentiation. Unlike self-renewal, which replenishes the SSC and progenitor pool, differentiation is an irreversible process committing cells to meiosis. Although the preparations for meiotic events in differentiating spermatogonia (Di-SG) are likely to be accompanied by alterations in chromatin structure, the three-dimensional chromatin architectural differences between SSCs and Di-SG, and the higher-order chromatin dynamics during spermatogonial differentiation, have not been systematically investigated. Here, we performed in situ high-throughput chromosome conformation capture, RNA-seq, and chromatin immunoprecipitation-sequencing analyses on porcine undifferentiated spermatogonia (which consist of SSCs and progenitors) and Di-SG. We identified that Di-SG exhibited less compact chromatin structural organization, weakened compartmentalization, and diminished topologically associating domains in comparison with undifferentiated spermatogonia, suggesting that diminished higher-order chromatin architecture in meiotic cells, as shown by recent reports, might be preprogrammed in Di-SG. Our data also revealed that A/B compartments, representing open or closed chromatin regions respectively, and topologically associating domains were related to dynamic gene expression during spermatogonial differentiation. Furthermore, we unraveled the contribution of promoter-enhancer interactions to premeiotic transcriptional regulation, which has not been accomplished in previous studies due to limited cell input and resolution. Together, our study uncovered the three-dimensional chromatin structure of SSCs/progenitors and Di-SG, as well as the interplay between higher-order chromatin architecture and dynamic gene expression during spermatogonial differentiation. These findings provide novel insights into the mechanisms for SSC self-renewal and differentiation and have implications for diagnosis and treatment of male sub-/infertility.}, }
@article {pmid34963660, year = {2022}, author = {Salari, H and Di Stefano, M and Jost, D}, title = {Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.}, journal = {Genome research}, volume = {32}, number = {1}, pages = {28-43}, pmid = {34963660}, issn = {1549-5469}, mesh = {Cell Nucleus ; *Chromatin/genetics ; Chromatin Assembly and Disassembly ; *Chromosomes/genetics ; }, abstract = {Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the "liquid" or "solid" state of chromatin are in fact two sides of the same coin.}, }
@article {pmid34957106, year = {2021}, author = {Kumar, S and Kaur, S and Seem, K and Kumar, S and Mohapatra, T}, title = {Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {774719}, pmid = {34957106}, issn = {2296-634X}, abstract = {The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.}, }
@article {pmid34942797, year = {2021}, author = {Conte, M and Fiorillo, L and Annunziatella, C and Esposito, A and Musella, F and Abraham, A and Bianco, S and Chiariello, AM}, title = {Dynamic and equilibrium properties of finite-size polymer models of chromosome folding.}, journal = {Physical review. E}, volume = {104}, number = {5-1}, pages = {054402}, doi = {10.1103/PhysRevE.104.054402}, pmid = {34942797}, issn = {2470-0053}, mesh = {Cell Nucleus ; Chromatin ; *Chromosomes ; *Polymers ; }, abstract = {Novel technologies are revealing that chromosomes have a complex three-dimensional organization within the cell nucleus that serves functional purposes. Models from polymer physics have been developed to quantitively understand the molecular principles controlling their structure and folding mechanisms. Here, by using massive molecular-dynamics simulations we show that classical scaling laws combined with finite-size effects of a simple polymer model can effectively explain the scaling behavior that chromatin exhibits at the topologically associating domains level, as revealed by experimental observations. Model results are then validated against recently published high-resolution in situ Hi-C data.}, }
@article {pmid34933938, year = {2022}, author = {Huang, N and Seow, WQ and Appert, A and Dong, Y and Stempor, P and Ahringer, J}, title = {Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation.}, journal = {Genome research}, volume = {32}, number = {2}, pages = {357-366}, pmid = {34933938}, issn = {1549-5469}, support = {092096/WT_/Wellcome Trust/United Kingdom ; MR/S021620/1/MRC_/Medical Research Council/United Kingdom ; C6946/A14492/CRUK_/Cancer Research UK/United Kingdom ; 101863/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Caenorhabditis elegans/genetics/metabolism ; *Chromatin/genetics/metabolism ; Chromosomes/genetics ; Genome ; }, abstract = {Nuclear organization and chromatin interactions are important for genome function, yet determining chromatin connections at high resolution remains a major challenge. To address this, we developed Accessible Region Conformation Capture (ARC-C), which profiles interactions between regulatory elements genome-wide without a capture step. Applied to Caenorhabditis elegans, ARC-C identifies approximately 15,000 significant interactions between regulatory elements at 500-bp resolution. Of 105 TFs or chromatin regulators tested, we find that the binding sites of 60 are enriched for interacting with each other, making them candidates for mediating interactions. These include cohesin and condensin II. Applying ARC-C to a mutant of transcription factor BLMP-1 detected changes in interactions between its targets. ARC-C simultaneously profiles domain-level architecture, and we observe that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) that interact with A/B (active/inactive) compartment-like structure. Furthermore, we discover that inactive compartment interactions are dependent on H3K9 methylation. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.}, }
@article {pmid34912810, year = {2021}, author = {Tian, W and Wang, Z and Wang, D and Zhi, Y and Dong, J and Jiang, R and Han, R and Li, Z and Kang, X and Li, H and Liu, X}, title = {Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {782268}, pmid = {34912810}, issn = {2296-634X}, abstract = {Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.}, }
@article {pmid34889941, year = {2022}, author = {San Martin, R and Das, P and Dos Reis Marques, R and Xu, Y and Roberts, JM and Sanders, JT and Golloshi, R and McCord, RP}, title = {Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression.}, journal = {The Journal of cell biology}, volume = {221}, number = {2}, pages = {}, pmid = {34889941}, issn = {1540-8140}, support = {R35 GM133557/GM/NIGMS NIH HHS/United States ; R35GM133557/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Line, Tumor ; Chromatin/metabolism ; Chromosomes, Human/*metabolism ; Cohort Studies ; *Disease Progression ; Genes, Neoplasm ; Genome, Human ; Humans ; Male ; *Models, Biological ; Neoplasm Metastasis ; Prostatic Neoplasms/genetics/*pathology ; Serine Endopeptidases/metabolism ; Transcriptional Activation/genetics ; }, abstract = {Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression. .}, }
@article {pmid34868269, year = {2021}, author = {Cardozo Gizzi, AM}, title = {A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {780822}, pmid = {34868269}, issn = {1664-8021}, abstract = {The genome tridimensional (3D) organization and its role towards the regulation of key cell processes such as transcription is currently a main question in biology. Interphase chromosomes are spatially segregated into "territories," epigenetically-defined large domains of chromatin that interact to form "compartments" with common transcriptional status, and insulator-flanked domains called "topologically associating domains" (TADs). Moreover, chromatin organizes around nuclear structures such as lamina, speckles, or the nucleolus to acquire a higher-order genome organization. Due to recent technological advances, the different hierarchies are being solved. Particularly, advances in microscopy technologies are shedding light on the genome structure at multiple levels. Intriguingly, more and more reports point to high variability and stochasticity at the single-cell level. However, the functional consequences of such variability in genome conformation are still unsolved. Here, I will discuss the implication of the cell-to-cell heterogeneity at the different scales in the context of newly developed imaging approaches, particularly multiplexed Fluorescence in situ hybridization methods that enabled "chromatin tracing." Extensions of these methods are now combining spatial information of dozens to thousands of genomic loci with the localization of nuclear features such as the nucleolus, nuclear speckles, or even histone modifications, creating the fast-moving field of "spatial genomics." As our view of genome organization shifts the focus from ensemble to single-cell, new insights to fundamental questions begin to emerge.}, }
@article {pmid34821995, year = {2022}, author = {Cinque, L and Micale, L and Manara, E and Esposito, A and Palumbo, O and Chiariello, AM and Bianco, S and Guerri, G and Bertelli, M and Giuffrida, MG and Bernardini, L and Notarangelo, A and Nicodemi, M and Castori, M}, title = {A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.}, journal = {Human genetics}, volume = {141}, number = {2}, pages = {217-227}, pmid = {34821995}, issn = {1432-1203}, mesh = {Adolescent ; Adult ; Chromosome Breakpoints ; Chromosomes, Human, Pair 1/genetics ; Chromosomes, Human, Pair 17/genetics ; Facies ; Female ; Fingers/*abnormalities ; Foot Deformities, Congenital/*genetics ; *Gene Rearrangement ; Hand Deformities, Congenital/*genetics ; Humans ; In Situ Hybridization, Fluorescence ; Male ; Potassium Channels, Inwardly Rectifying/chemistry/*genetics ; *Regulatory Sequences, Nucleic Acid ; Sequence Deletion ; Translocation, Genetic ; Young Adult ; }, abstract = {Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.}, }
@article {pmid34805161, year = {2021}, author = {Maslova, A and Krasikova, A}, title = {FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {753097}, pmid = {34805161}, issn = {2296-634X}, abstract = {The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.}, }
@article {pmid34785659, year = {2021}, author = {Wu, DY and Li, X and Sun, QR and Dou, CL and Xu, T and He, H and Luo, H and Fu, H and Bu, GW and Luo, B and Zhang, X and Ma, BG and Peng, C and Miao, YL}, title = {Defective chromatin architectures in embryonic stem cells derived from somatic cell nuclear transfer impair their differentiation potentials.}, journal = {Cell death &amp; disease}, volume = {12}, number = {12}, pages = {1085}, pmid = {34785659}, issn = {2041-4889}, mesh = {Animals ; Cell Differentiation ; Chromatin/*metabolism ; Embryonic Stem Cells/*metabolism ; Female ; Humans ; Mice ; Nuclear Transfer Techniques/*standards ; }, abstract = {Nuclear transfer embryonic stem cells (ntESCs) hold enormous promise for individual-specific regenerative medicine. However, the chromatin states of ntESCs remain poorly characterized. In this study, we employed ATAC-seq and Hi-C techniques to explore the chromatin accessibility and three-dimensional (3D) genome organization of ntESCs. The results show that the chromatin accessibility and genome structures of somatic cells are re-arranged to ESC-like states overall in ntESCs, including compartments, topologically associating domains (TADs) and chromatin loops. However, compared to fertilized ESCs (fESCs), ntESCs show some abnormal openness and structures that have not been reprogrammed completely, which impair the differentiation potential of ntESCs. The histone modification H3K9me3 may be involved in abnormal structures in ntESCs, including incorrect compartment switches and incomplete TAD rebuilding. Moreover, ntESCs and iPSCs show high similarity in 3D genome structures, while a few differences are detected due to different somatic cell origins and reprogramming mechanisms. Through systematic analyses, our study provides a global view of chromatin accessibility and 3D genome organization in ntESCs, which can further facilitate the understanding of the similarities and differences between ntESCs and fESCs.}, }
@article {pmid34749781, year = {2021}, author = {Cheng, Y and Liu, M and Hu, M and Wang, S}, title = {TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {309}, pmid = {34749781}, issn = {1474-760X}, support = {DP2 GM137414/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromatin/chemistry ; Chromosomes, Human, X/*chemistry ; *Epigenesis, Genetic ; Female ; Humans ; Transcription, Genetic ; }, abstract = {BACKGROUND: Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains.<br><br>RESULTS: Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains.<br><br>CONCLUSIONS: In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.}, }
@article {pmid34747029, year = {2022}, author = {Yildirir, G and Sperschneider, J and Malar C, M and Chen, ECH and Iwasaki, W and Cornell, C and Corradi, N}, title = {Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.}, journal = {The New phytologist}, volume = {233}, number = {3}, pages = {1097-1107}, doi = {10.1111/nph.17842}, pmid = {34747029}, issn = {1469-8137}, mesh = {Fungi ; Genome, Fungal ; *Glomeromycota/genetics/metabolism ; *Mycorrhizae/physiology ; Plants/genetics ; }, abstract = {Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains. In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic diversity in a group of obligate plant symbionts: the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within-species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps reveal a 'checkerboard' pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A-compartment is more gene-dense and contains most core genes, while the B-compartment is more repeat-rich and has higher rates of chromosomal rearrangement. While the B-compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta upregulated candidate effectors, suggesting a possible host-induced change in chromosome conformation. Overall, this study provides a fine-scale view into the genome biology and evolution of model plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.}, }
@article {pmid34741515, year = {2022}, author = {Stilianoudakis, SC and Marshall, MA and Dozmorov, MG}, title = {preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {3}, pages = {621-630}, pmid = {34741515}, issn = {1367-4811}, support = {P50 AA022537/AA/NIAAA NIH HHS/United States ; }, mesh = {*Chromatin ; *Chromosomes ; Genome ; Genomics ; Machine Learning ; }, abstract = {MOTIVATION: Chromosome conformation capture technologies (Hi-C) revealed extensive DNA folding into discrete 3D domains, such as Topologically Associating Domains and chromatin loops. The correct binding of CTCF and cohesin at domain boundaries is integral in maintaining the proper structure and function of these 3D domains. 3D domains have been mapped at the resolutions of 1 kilobase and above. However, it has not been possible to define their boundaries at the resolution of boundary-forming proteins.<br><br>RESULTS: To predict domain boundaries at base-pair resolution, we developed preciseTAD, an optimized transfer learning framework trained on high-resolution genome annotation data. In contrast to current TAD/loop callers, preciseTAD-predicted boundaries are strongly supported by experimental evidence. Importantly, this approach can accurately delineate boundaries in cells without Hi-C data. preciseTAD provides a powerful framework to improve our understanding of how genomic regulators are shaping the 3D structure of the genome at base-pair resolution.<br><br>preciseTAD is an R/Bioconductor package available at https://bioconductor.org/packages/preciseTAD/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34721522, year = {2021}, author = {Liehr, T}, title = {Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {720507}, pmid = {34721522}, issn = {1664-8021}, abstract = {Here the role of molecular cytogenetics in the context of yet available all other cytogenomic approaches is discussed. A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). The latter contains the methodology itself, the types of probe- and target-DNA, as well as probe sets. The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. Overall, molecular cytogenetics is far from being outdated and actively involved in up-to-date diagnostics and research.}, }
@article {pmid34689653, year = {2022}, author = {Awotoye, W and Comnick, C and Pendleton, C and Zeng, E and Alade, A and Mossey, PA and Gowans, LJJ and Eshete, MA and Adeyemo, WL and Naicker, T and Adeleke, C and Busch, T and Li, M and Petrin, A and Olotu, J and Hassan, M and Pape, J and Miller, SE and Donkor, P and Anand, D and Lachke, SA and Marazita, ML and Adeyemo, AA and Murray, JC and Albokhari, D and Sobreira, N and Butali, A}, title = {Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus.}, journal = {Journal of dental research}, volume = {101}, number = {4}, pages = {465-472}, pmid = {34689653}, issn = {1544-0591}, support = {R90 DE024296/DE/NIDCR NIH HHS/United States ; K99 DE022378/DE/NIDCR NIH HHS/United States ; R01 DE028300/DE/NIDCR NIH HHS/United States ; R03 DE024776/DE/NIDCR NIH HHS/United States ; R00 DE022378/DE/NIDCR NIH HHS/United States ; K43 DE029427/DE/NIDCR NIH HHS/United States ; }, mesh = {*Cleft Lip/genetics ; *Cleft Palate/genetics ; Female ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Male ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p2df = 1.16E-08, pGxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.}, }
@article {pmid34675966, year = {2021}, author = {Marti-Marimon, M and Vialaneix, N and Lahbib-Mansais, Y and Zytnicki, M and Camut, S and Robelin, D and Yerle-Bouissou, M and Foissac, S}, title = {Major Reorganization of Chromosome Conformation During Muscle Development in Pig.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {748239}, pmid = {34675966}, issn = {1664-8021}, abstract = {The spatial organization of the genome in the nucleus plays a crucial role in eukaryotic cell functions, yet little is known about chromatin structure variations during late fetal development in mammals. We performed in situ high-throughput chromosome conformation capture (Hi-C) sequencing of DNA from muscle samples of pig fetuses at two late stages of gestation. Comparative analysis of the resulting Hi-C interaction matrices between both groups showed widespread differences of different types. First, we discovered a complex landscape of stable and group-specific Topologically Associating Domains (TADs). Investigating the nuclear partition of the chromatin into transcriptionally active and inactive compartments, we observed a genome-wide fragmentation of these compartments between 90 and 110 days of gestation. Also, we identified and characterized the distribution of differential cis- and trans-pairwise interactions. In particular, trans-interactions at chromosome extremities revealed a mechanism of telomere clustering further confirmed by 3D Fluorescence in situ Hybridization (FISH). Altogether, we report major variations of the three-dimensional genome conformation during muscle development in pig, involving several levels of chromatin remodeling and structural regulation.}, }
@article {pmid34621295, year = {2021}, author = {Servetti, M and Pisciotta, L and Tassano, E and Cerminara, M and Nobili, L and Boeri, S and Rosti, G and Lerone, M and Divizia, MT and Ronchetto, P and Puliti, A}, title = {Neurodevelopmental Disorders in Patients With Complex Phenotypes and Potential Complex Genetic Basis Involving Non-Coding Genes, and Double CNVs.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {732002}, pmid = {34621295}, issn = {1664-8021}, abstract = {Neurodevelopmental disorders (NDDs) are a heterogeneous class of brain diseases, with a complex genetic basis estimated to account for up to 50% of cases. Nevertheless, genetic diagnostic yield is about 20%. Array-comparative genomic hybridization (array-CGH) is an established first-level diagnostic test able to detect pathogenic copy number variants (CNVs), however, most identified variants remain of uncertain significance (VUS). Failure of interpretation of VUSs may depend on various factors, including complexity of clinical phenotypes and inconsistency of genotype-phenotype correlations. Indeed, although most NDD-associated CNVs are de novo, transmission from unaffected parents to affected children of CNVs with high risk for NDDs has been observed. Moreover, variability of genetic components overlapped by CNVs, such as long non-coding genes, genomic regions with long-range effects, and additive effects of multiple CNVs can make CNV interpretation challenging. We report on 12 patients with complex phenotypes possibly explained by complex genetic mechanisms, including involvement of antisense genes and boundaries of topologically associating domains. Eight among the 12 patients carried two CNVs, either de novo or inherited, respectively, by each of their healthy parents, that could additively contribute to the patients' phenotype. CNVs overlapped either known NDD-associated or novel candidate genes (PTPRD, BUD13, GLRA3, MIR4465, ABHD4, and WSCD2). Bioinformatic enrichment analyses showed that genes overlapped by the co-occurring CNVs have synergistic roles in biological processes fundamental in neurodevelopment. Double CNVs could concur in producing deleterious effects, according to a two-hit model, thus explaining the patients' phenotypes and the incomplete penetrance, and variable expressivity, associated with the single variants. Overall, our findings could contribute to the knowledge on clinical and genetic diagnosis of complex forms of NDD.}, }
@article {pmid34605807, year = {2021}, author = {Esquivel-López, A and Arzate-Mejía, R and Pérez-Molina, R and Furlan-Magaril, M}, title = {In-Nucleus Hi-C in Drosophila Cells.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {175}, pages = {}, doi = {10.3791/62106}, pmid = {34605807}, issn = {1940-087X}, mesh = {Animals ; Cell Nucleus ; *Chromatin ; *Drosophila/genetics ; Drosophila melanogaster/genetics ; Genomics ; }, abstract = {The genome is organized into topologically associating domains (TADs) delimited by boundaries that isolate interactions between domains. In Drosophila, the mechanisms underlying TAD formation and boundaries are still under investigation. The application of the in-nucleus Hi-C method described here helped to dissect the function of architectural protein (AP)-binding sites at TAD boundaries isolating the Notch gene. Genetic modification of domain boundaries that cause loss of APs results in TAD fusion, transcriptional defects, and long-range topological alterations. These results provided evidence demonstrating the contribution of genetic elements to domain boundary formation and gene expression control in Drosophila. Here, the in-nucleus Hi-C method has been described in detail, which provides important checkpoints to assess the quality of the experiment along with the protocol. Also shown are the required numbers of sequencing reads and valid Hi-C pairs to analyze genomic interactions at different genomic scales. CRISPR/Cas9-mediated genetic editing of regulatory elements and high-resolution profiling of genomic interactions using this in-nucleus Hi-C protocol could be a powerful combination for the investigation of the structural function of genetic elements.}, }
@article {pmid34603780, year = {2021}, author = {Luo, H and Li, X and Tian, GG and Li, D and Hou, C and Ding, X and Hou, L and Lyu, Q and Yang, Y and Cooney, AJ and Xie, W and Xiong, J and Wang, H and Zhao, X and Wu, J}, title = {Offspring production of ovarian organoids derived from spermatogonial stem cells by defined factors with chromatin reorganization.}, journal = {Journal of advanced research}, volume = {33}, number = {}, pages = {81-98}, pmid = {34603780}, issn = {2090-1224}, mesh = {*Adult Germline Stem Cells ; Animals ; Cell Culture Techniques, Three Dimensional ; Chromatin/genetics ; Female ; Male ; Mice ; Organoids ; *Spermatogonia ; }, abstract = {INTRODUCTION: Fate determination of germline stem cells remains poorly understood at the chromatin structure level.<br><br>OBJECTIVES: Our research hopes to develop successful offspring production of ovarian organoids derived from spermatogonial stem cells (SSCs) by defined factors.<br><br>METHODS: The offspring production from oocytes transdifferentiated from mouse SSCs with tracking of transplanted SSCs in vivo, single cell whole exome sequencing, and in 3D cell culture reconstitution of the process of oogenesis derived from SSCs. The defined factors were screened with ovarian organoids. We uncovered extensive chromatin reorganization during SSC conversion into induced germline stem cells (iGSCs) using high throughput chromosome conformation.<br><br>RESULTS: We demonstrate successful production of offspring from oocytes transdifferentiated from mouse spermatogonial stem cells (SSCs). Furthermore, we demonstrate direct induction of germline stem cells (iGSCs) differentiated into functional oocytes by transduction of H19, Stella, and Zfp57 and inactivation of Plzf in SSCs after screening with ovarian organoids. We uncovered extensive chromatin reorganization during SSC conversion into iGSCs, which was highly similar to female germline stem cells. We observed that although topologically associating domains were stable during SSC conversion, chromatin interactions changed in a striking manner, altering 35% of inactive and active chromosomal compartments throughout the genome.<br><br>CONCLUSION: We demonstrate successful offspring production of ovarian organoids derived from SSCs by defined factors with chromatin reorganization. These findings have important implications in various areas including mammalian gametogenesis, genetic and epigenetic reprogramming, biotechnology, and medicine.}, }
@article {pmid34584207, year = {2021}, author = {Grabowicz, IE and Wilczyński, B and Kamińska, B and Roura, AJ and Wojtaś, B and Dąbrowski, MJ}, title = {Author Correction: The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19628}, doi = {10.1038/s41598-021-99319-4}, pmid = {34584207}, issn = {2045-2322}, }
@article {pmid34534448, year = {2021}, author = {He, L and Ding, Y and Zhao, Y and So, KK and Peng, XL and Li, Y and Yuan, J and He, Z and Chen, X and Sun, H and Wang, H}, title = {CRISPR/Cas9/AAV9-mediated in vivo editing identifies MYC regulation of 3D genome in skeletal muscle stem cell.}, journal = {Stem cell reports}, volume = {16}, number = {10}, pages = {2442-2458}, pmid = {34534448}, issn = {2213-6711}, mesh = {Animals ; CRISPR-Cas Systems ; Chromatin/*metabolism ; Gene Editing/methods ; Gene Expression Regulation ; *Genes, myc ; *Genome ; Mice ; MyoD Protein/genetics/*metabolism ; Nucleic Acid Conformation ; Proto-Oncogene Proteins c-bcl-6/genetics/*metabolism ; RNA, Guide, Kinetoplastida/genetics/*metabolism ; Satellite Cells, Skeletal Muscle/*physiology ; Transcription Factors/genetics/metabolism ; }, abstract = {Skeletal muscle satellite cells (SCs) are stem cells responsible for muscle development and regeneration. Although CRISPR/Cas9 has been widely used, its application in endogenous SCs remains elusive. Here, we generate mice expressing Cas9 in SCs and achieve robust editing in juvenile SCs at the postnatal stage through AAV9-mediated short guide RNA (sgRNA) delivery. Additionally, we reveal that quiescent SCs are resistant to CRISPR/Cas9-mediated editing. As a proof of concept, we demonstrate efficient editing of master transcription factor (TF) Myod1 locus using the CRISPR/Cas9/AAV9-sgRNA system in juvenile SCs. Application on two key TFs, MYC and BCL6, unveils distinct functions in SC activation and muscle regeneration. Particularly, we reveal that MYC orchestrates SC activation through regulating 3D genome architecture. Its depletion results in strengthening of the topologically associating domain boundaries thus may affect gene expression. Altogether, our study establishes a platform for editing endogenous SCs that can be harnessed to elucidate the functionality of key regulators governing SC activities.}, }
@article {pmid34518536, year = {2021}, author = {Franke, M and De la Calle-Mustienes, E and Neto, A and Almuedo-Castillo, M and Irastorza-Azcarate, I and Acemel, RD and Tena, JJ and Santos-Pereira, JM and Gómez-Skarmeta, JL}, title = {CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5415}, pmid = {34518536}, issn = {2041-1723}, mesh = {Animals ; Body Patterning/genetics ; CCCTC-Binding Factor/deficiency/*genetics ; CRISPR-Cas Systems ; Chromatin/genetics/metabolism ; Embryo, Nonmammalian/embryology/*metabolism ; Enhancer Elements, Genetic/genetics ; *Gene Expression Regulation, Developmental ; Gene Knockout Techniques/*methods ; Organogenesis/genetics ; Promoter Regions, Genetic/genetics ; RNA-Seq/methods ; Zebrafish/embryology/*genetics ; Zebrafish Proteins/deficiency/*genetics ; }, abstract = {Coordinated chromatin interactions between enhancers and promoters are critical for gene regulation. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), which are sub-megabase chromatin structures. In vitro CTCF depletion leads to a loss of TADs but has only limited effects over gene expression, challenging the concept that CTCF-mediated chromatin structures are a fundamental requirement for gene regulation. However, how CTCF and a perturbed chromatin structure impacts gene expression during development remains poorly understood. Here we link the loss of CTCF and gene regulation during patterning and organogenesis in a ctcf knockout zebrafish model. CTCF absence leads to loss of chromatin structure and affects the expression of thousands of genes, including many developmental regulators. Our results demonstrate the essential role of CTCF in providing the structural context for enhancer-promoter interactions, thus regulating developmental genes.}, }
@article {pmid34494283, year = {2021}, author = {MacPhillamy, C and Pitchford, WS and Alinejad-Rokny, H and Low, WY}, title = {Opportunity to improve livestock traits using 3D genomics.}, journal = {Animal genetics}, volume = {52}, number = {6}, pages = {785-798}, doi = {10.1111/age.13135}, pmid = {34494283}, issn = {1365-2052}, mesh = {Animals ; Breeding/*methods ; Cattle/genetics ; Chickens/genetics ; Genomics/*methods ; Goats/genetics ; Livestock/*genetics ; Sheep, Domestic/genetics ; Sus scrofa/genetics ; }, abstract = {The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.}, }
@article {pmid34436670, year = {2021}, author = {Melo, US and Piard, J and Fischer-Zirnsak, B and Klever, MK and Schöpflin, R and Mensah, MA and Holtgrewe, M and Arbez-Gindre, F and Martin, A and Guigue, V and Gaillard, D and Landais, E and Roze, V and Kremer, V and Ramanah, R and Cabrol, C and Harms, FL and Kornak, U and Spielmann, M and Mundlos, S and Van Maldergem, L}, title = {Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus.}, journal = {Human genetics}, volume = {140}, number = {10}, pages = {1459-1469}, pmid = {34436670}, issn = {1432-1203}, mesh = {Abnormalities, Multiple/*genetics ; Adult ; Cadaver ; *Evolution, Molecular ; Female ; Fetus ; Genetic Variation ; Genome, Human ; Humans ; Lung/*abnormalities/*growth &amp; development/*ultrastructure ; Lung Diseases/*genetics ; Male ; Organogenesis/*genetics ; Pregnancy ; }, abstract = {During human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease.}, }
@article {pmid34433485, year = {2021}, author = {Ge, X and Frank-Bertoncelj, M and Klein, K and McGovern, A and Kuret, T and Houtman, M and Burja, B and Micheroli, R and Shi, C and Marks, M and Filer, A and Buckley, CD and Orozco, G and Distler, O and Morris, AP and Martin, P and Eyre, S and Ospelt, C}, title = {Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {247}, pmid = {34433485}, issn = {1474-760X}, support = {207491/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 21348/VAC_/Versus Arthritis/United Kingdom ; 21745/VAC_/Versus Arthritis/United Kingdom ; 21754/VAC_/Versus Arthritis/United Kingdom ; }, mesh = {Adult ; Arthritis, Rheumatoid/*genetics/*pathology ; Base Sequence ; Chromatin/metabolism ; Databases, Genetic ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/drug effects ; Female ; Fibroblasts/drug effects/metabolism/*pathology ; Gene Regulatory Networks/drug effects ; Genetic Predisposition to Disease ; *Genomics ; Humans ; Immunoglobulin J Recombination Signal Sequence-Binding Protein/genetics ; Inheritance Patterns/*genetics ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/genetics ; Probability ; Receptor, Interferon alpha-beta/metabolism ; Receptors, Interferon/metabolism ; Reproducibility of Results ; Risk Factors ; Synovial Membrane/*pathology ; Tumor Necrosis Factor alpha-Induced Protein 3/metabolism ; Tumor Necrosis Factor-alpha/pharmacology ; Young Adult ; }, abstract = {BACKGROUND: Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded stromal cells, such as synovial fibroblasts (FLS), despite their crucial involvement in the pathogenesis of RA. Here we integrate DNA architecture, 3D chromatin interactions, DNA accessibility, and gene expression in FLS, B cells, and T cells with genetic fine mapping of RA loci.<br><br>RESULTS: We identify putative causal variants, enhancers, genes, and cell types for 30-60% of RA loci and demonstrate that FLS account for up to 24% of RA heritability. TNF stimulation of FLS alters the organization of topologically associating domains, chromatin state, and the expression of putative causal genes such as TNFAIP3 and IFNAR1. Several putative causal genes constitute RA-relevant functional networks in FLS with roles in cellular proliferation and activation. Finally, we demonstrate that risk variants can have joint-specific effects on target gene expression in RA FLS, which may contribute to the development of the characteristic pattern of joint involvement in RA.<br><br>CONCLUSION: Overall, our research provides the first direct evidence for a causal role of FLS in the genetic susceptibility for RA accounting for up to a quarter of RA heritability.}, }
@article {pmid34432858, year = {2021}, author = {Groves, IJ and Drane, ELA and Michalski, M and Monahan, JM and Scarpini, CG and Smith, SP and Bussotti, G and Várnai, C and Schoenfelder, S and Fraser, P and Enright, AJ and Coleman, N}, title = {Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.}, journal = {PLoS pathogens}, volume = {17}, number = {8}, pages = {e1009875}, pmid = {34432858}, issn = {1553-7374}, support = {13080/CRUK_/Cancer Research UK/United Kingdom ; A13080/CRUK_/Cancer Research UK/United Kingdom ; MR/T016787/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Carcinogenesis/metabolism/*pathology ; Chromatin/genetics/*metabolism ; Epigenesis, Genetic ; Female ; *Genome, Viral ; Human papillomavirus 16/*isolation &amp; purification ; Humans ; Papillomavirus Infections/*complications ; Tumor Cells, Cultured ; Uterine Cervical Neoplasms/genetics/metabolism/*pathology/virology ; *Virus Integration ; }, abstract = {Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art 'HPV integrated site capture' (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a 'looping' mechanism by which flanking host regions become amplified. Furthermore, using our 'HPV16-specific Region Capture Hi-C' technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a 'cancer-causing gene' is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.}, }
@article {pmid34429265, year = {2022}, author = {Chiliński, M and Sengupta, K and Plewczynski, D}, title = {From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect.}, journal = {Seminars in cell &amp; developmental biology}, volume = {121}, number = {}, pages = {171-185}, doi = {10.1016/j.semcdb.2021.08.007}, pmid = {34429265}, issn = {1096-3634}, mesh = {Chromatin/*metabolism ; Genome, Human/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Protein Interaction Maps/*genetics ; }, abstract = {The three-dimensional structure of the human genome has been proven to have a significant functional impact on gene expression. The high-order spatial chromatin is organised first by looping mediated by multiple protein factors, and then it is further formed into larger structures of topologically associated domains (TADs) or chromatin contact domains (CCDs), followed by A/B compartments and finally the chromosomal territories (CTs). The genetic variation observed in human population influences the multi-scale structures, posing a question regarding the functional impact of structural variants reflected by the variability of the genes expression patterns. The current methods of evaluating the functional effect include eQTLs analysis which uses statistical testing of influence of variants on spatially close genes. Rarely, non-coding DNA sequence changes are evaluated by their impact on the biomolecular interaction network (BIN) reflecting the cellular interactome that can be analysed by the classical graph-theoretic algorithms. Therefore, in the second part of the review, we introduce the concept of BIN, i.e. a meta-network model of the complete molecular interactome developed by integrating various biological networks. The BIN meta-network model includes DNA-protein binding by the plethora of protein factors as well as chromatin interactions, therefore allowing connection of genomics with the downstream biomolecular processes present in a cell. As an illustration, we scrutinise the chromatin interactions mediated by the CTCF protein detected in a ChIA-PET experiment in the human lymphoblastoid cell line GM12878. In the corresponding BIN meta-network the DNA spatial proximity is represented as a graph model, combined with the Proteins-Interaction Network (PIN) of human proteome using the Gene Association Network (GAN). Furthermore, we enriched the BIN with the signalling and metabolic pathways and Gene Ontology (GO) terms to assert its functional context. Finally, we mapped the Single Nucleotide Polymorphisms (SNPs) from the GWAS studies and identified the chromatin mutational hot-spots associated with a significant enrichment of SNPs related to autoimmune diseases. Afterwards, we mapped Structural Variants (SVs) from healthy individuals of 1000 Genomes Project and identified an interesting example of the missing protein complex associated with protein Q6GYQ0 due to a deletion on chromosome 14. Such an analysis using the meta-network BIN model is therefore helpful in evaluating the influence of genetic variation on spatial organisation of the genome and its functional effect in a cell.}, }
@article {pmid34426703, year = {2022}, author = {Arrastia, MV and Jachowicz, JW and Ollikainen, N and Curtis, MS and Lai, C and Quinodoz, SA and Selck, DA and Ismagilov, RF and Guttman, M}, title = {Single-cell measurement of higher-order 3D genome organization with scSPRITE.}, journal = {Nature biotechnology}, volume = {40}, number = {1}, pages = {64-73}, pmid = {34426703}, issn = {1546-1696}, support = {U01 HL130007/HL/NHLBI NIH HHS/United States ; U01 DA040612/DA/NIDA NIH HHS/United States ; U01 HG007910/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Cell Nucleus/genetics ; Chromatin ; DNA/genetics ; *Genome/genetics ; Mice ; Mouse Embryonic Stem Cells ; }, abstract = {Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.}, }
@article {pmid34415531, year = {2022}, author = {Nicoletti, C}, title = {Methods for the Differential Analysis of Hi-C Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2301}, number = {}, pages = {61-95}, pmid = {34415531}, issn = {1940-6029}, mesh = {Cell Nucleus/genetics ; Chromatin/genetics ; Chromatin Assembly and Disassembly ; Chromosomes/genetics ; *Genome ; Software ; }, abstract = {The 3D organization of chromatin within the nucleus enables dynamic regulation and cell type-specific transcription of the genome. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories); at the level of individual chromatin fibers, which are organized into compartmentalized domains (e.g., Topologically Associating Domains-TADs), and at the level of short-range chromatin interactions between functional elements of the genome (e.g., enhancer-promoter loops).The widespread availability of Chromosome Conformation Capture (3C)-based high-throughput techniques has been instrumental in advancing our knowledge of chromatin nuclear organization. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D interactions, as it is theoretically able to detect any pair of restriction fragments connected as a result of ligation by proximity.This chapter will illustrate how to compare the chromatin interactome in different experimental conditions, starting from pre-computed Hi-C contact matrices, how to visualize the results, and how to correlate the observed variations in chromatin interaction strength with changes in gene expression.}, }
@article {pmid34415530, year = {2022}, author = {Zufferey, M and Tavernari, D and Ciriello, G}, title = {Methods for the Analysis of Topologically Associating Domains (TADs).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2301}, number = {}, pages = {39-59}, pmid = {34415530}, issn = {1940-6029}, mesh = {Cell Nucleus ; Chromatin/genetics ; Chromosomes/genetics ; Genome ; *Genomics ; }, abstract = {Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus, allow building genome-scale maps of intra- and inter-chromosomal contacts (contact maps). Statistical and algorithmic analyses of Hi-C data consist in extracting information from these contact maps. One of the most striking patterns observed in intra-chromosomal Hi-C contact maps emerged from genomic regions that exhibit dense intra-region but sparse inter-region contacts. These have been termed topologically associating domains (TADs). The identification of TADs from Hi-C contact maps is of great interest as they have been shown to act as unit of chromosome organization and, potentially, functional activity. Several approaches have been developed to identify TADs (TAD callers). However, results from these methods are often dependent on data resolution and poorly concordant. In this chapter, we present four TAD callers and we provide detailed protocols for their use. In addition, we show how to compare TADs identified by different callers and how to assess the enrichment for TAD-associated biological features. TAD calling has become a key step in the study of chromatin 3D organization in different cellular contexts. Here we provide guidelines to improve the robustness and quality of these analyses.}, }
@article {pmid34399301, year = {2021}, author = {Liang, J and Perez-Rathke, A}, title = {Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.}, journal = {Current opinion in structural biology}, volume = {71}, number = {}, pages = {200-214}, pmid = {34399301}, issn = {1879-033X}, support = {R35 GM127084/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromatin ; Chromatin Assembly and Disassembly ; *Chromosomes ; Genome ; Molecular Conformation ; }, abstract = {Computational three-dimensional chromatin modeling has helped uncover principles of genome organization. Here, we discuss methods for modeling three-dimensional chromatin structures, with focus on a minimalistic polymer model which inverts population Hi-C into single-cell conformations. Utilizing only basic physical properties, this model reveals that a few specific Hi-C interactions can fold chromatin into conformations consistent with single-cell imaging, Dip-C, and FISH measurements. Aggregated single-cell chromatin conformations also reproduce Hi-C frequencies. This approach allows quantification of structural heterogeneity and discovery of many-body interaction units and has revealed additional insights, including (1) topologically associating domains as a byproduct of folding driven by specific interactions, (2) cell subpopulations with different structural scaffolds are developmental stage dependent, and (3) the functional landscape of many-body units within enhancer-rich regions. We also discuss these findings in relation to the genome structure-function relationship.}, }
@article {pmid34382189, year = {2021}, author = {Boltsis, I and Nowosad, K and Brouwer, RWW and Tylzanowski, P and van IJcken, WFJ and Huylebroeck, D and Grosveld, F and Kolovos, P}, title = {Low Input Targeted Chromatin Capture (Low-T2C).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2351}, number = {}, pages = {165-179}, pmid = {34382189}, issn = {1940-6029}, mesh = {Chromatin/chemistry/*genetics/metabolism ; *Chromatin Assembly and Disassembly ; Chromosome Mapping ; Computational Biology/*methods ; Gene Expression Regulation ; Gene Library ; Genomics/methods ; Reproducibility of Results ; }, abstract = {Targeted chromatin capture (T2C) is a 3C-based method and is used to study the 3D chromatin organization, interactomes and structural changes associated with gene regulation, progression through the cell cycle, and cell survival and development. Low input targeted chromatin capture (low-T2C) is an optimized version of the T2C protocol for low numbers of cells. Here, we describe the protocol for low-T2C, including all experimental steps and bioinformatics tools in detail.}, }
@article {pmid34381055, year = {2021}, author = {Yuan, J and Jiang, Q and Gong, T and Fan, D and Zhang, J and Chen, F and Zhu, X and Wang, X and Qiao, Y and Chen, H and Liu, Z and Su, J}, title = {Loss of grand histone H3 lysine 27 trimethylation domains mediated transcriptional activation in esophageal squamous cell carcinoma.}, journal = {NPJ genomic medicine}, volume = {6}, number = {1}, pages = {65}, pmid = {34381055}, issn = {2056-7944}, abstract = {Trimethylation of histone H3 lysine 27 trimethylation (H3K27me3) may be recruited by repressive Polycomb complexes to mediate gene silencing, which is critical for maintaining embryonic stem cell pluripotency and differentiation. However, the roles of aberrant H3K27me3 patterns in tumorigenesis are not fully understood. Here, we discovered that grand silencer domains (breadth > 50 kb) for H3K27me3 were significantly associated with epithelial cell differentiation and exhibited high gene essentiality and conservation in human esophageal epithelial cells. These grand H3K27me3 domains exhibited high modification signals involved in gene silencing, and preferentially occupied the entirety of topologically associating domains and interact with each other. We found that widespread loss of the grand H3K27me3 domains in of esophageal squamous cell carcinomas (ESCCs) were enriched in genes involved in epithelium and endothelium differentiation, which were significantly associated with overexpression with increase of active modifications of H3K4me3, H3K4me1, and H3K27ac marks, as well as DNA hypermethylation in the gene bodies. A total of 208 activated genes with loss of grand H3K27me3 domains in ESCC were identified, where the higher expression and mutation of T-box transcription factor 20 (TBX20) were associated with worse patients' outcomes. Our results showed that knockdown of TBX20 may have led to a striking defect in esophageal cancer cell growth and carcinogenesis-related pathway, including cell cycle and homologous recombination. Together, our results reveal that loss of grand H3K27me3 domains represent a catalog of remarkable activating regulators involved in carcinogenesis.}, }
@article {pmid34368157, year = {2021}, author = {Adeel, MM and Jiang, H and Arega, Y and Cao, K and Lin, D and Cao, C and Cao, G and Wu, P and Li, G}, title = {Structural Variations of the 3D Genome Architecture in Cervical Cancer Development.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {706375}, pmid = {34368157}, issn = {2296-634X}, abstract = {Human papillomavirus (HPV) integration is the major contributor to cervical cancer (CC) development by inducing structural variations (SVs) in the human genome. SVs are directly associated with the three-dimensional (3D) genome structure leading to cancer development. The detection of SVs is not a trivial task, and several genome-wide techniques have greatly helped in the identification of SVs in the cancerous genome. However, in cervical cancer, precise prediction of SVs mainly translocations and their effects on 3D-genome and gene expression still need to be explored. Here, we have used high-throughput chromosome conformation capture (Hi-C) data of cervical cancer to detect the SVs, especially the translocations, and validated it through whole-genome sequencing (WGS) data. We found that the cervical cancer 3D-genome architecture rearranges itself as compared to that in the normal tissue, and 24% of the total genome switches their A/B compartments. Moreover, translocation detection from Hi-C data showed the presence of high-resolution t(4;7) (q13.1; q31.32) and t(1;16) (q21.2; q22.1) translocations, which disrupted the expression of the genes located at and nearby positions. Enrichment analysis suggested that the disrupted genes were mainly involved in controlling cervical cancer-related pathways. In summary, we detect the novel SVs through Hi-C data and unfold the association among genome-reorganization, translocations, and gene expression regulation. The results help understand the underlying pathogenicity mechanism of SVs in cervical cancer development and identify the targeted therapeutics against cervical cancer.}, }
@article {pmid34351763, year = {2021}, author = {Wei, J and Tian, H and Zhou, R and Shao, Y and Song, F and Gao, YQ}, title = {Topological Constraints with Optimal Length Promote the Formation of Chromosomal Territories at Weakened Degree of Phase Separation.}, journal = {The journal of physical chemistry. B}, volume = {125}, number = {32}, pages = {9092-9101}, doi = {10.1021/acs.jpcb.1c03523}, pmid = {34351763}, issn = {1520-5207}, mesh = {*Cell Nucleus ; Chromatin ; *Chromosomes/genetics ; CpG Islands ; Humans ; Interphase ; }, abstract = {It is generally agreed that the nuclei of eukaryotic cells at interphase are partitioned into disjointed territories, with distinct regions occupied by certain chromosomes. However, the underlying mechanism for such territorialization is still under debate. Here we model chromosomes as coarse-grained block copolymers and to investigate the effect of loop domains (LDs) on the formation of compartments and territories based on dissipative particle dynamics. A critical length of LDs, which depends sensitively on the length of polymeric blocks, is obtained to minimize the degree of phase separation. This also applies to the two-polymer system: The critical length not only maximizes the degree of territorialization but also minimizes the degree of phase separation. Interestingly, by comparing with experimental data, we find the critical length for LDs and the corresponding length of blocks to be respectively very close to the mean length of topologically associating domains (TADs) and chromosomal segments with different densities of CpG islands for human chromosomes. The results indicate that topological constraints with optimal length can contribute to the formation of territories by weakening the degree of phase separation, which likely promotes the chromosomal flexibility in response to genetic regulations.}, }
@article {pmid34341417, year = {2021}, author = {Grabowicz, IE and Wilczyński, B and Kamińska, B and Roura, AJ and Wojtaś, B and Dąbrowski, MJ}, title = {The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15668}, pmid = {34341417}, issn = {2045-2322}, mesh = {*Chromatin ; Chromosomes ; Enhancer Elements, Genetic ; *Epigenesis, Genetic ; Evolution, Molecular ; *Glioma ; Humans ; }, abstract = {Genome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell-matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.}, }
@article {pmid34340871, year = {2022}, author = {Sexton, CE and Tillett, RL and Han, MV}, title = {The essential but enigmatic regulatory role of HERVH in pluripotency.}, journal = {Trends in genetics : TIG}, volume = {38}, number = {1}, pages = {12-21}, pmid = {34340871}, issn = {0168-9525}, support = {P20 GM121325/GM/NIGMS NIH HHS/United States ; }, mesh = {*Endogenous Retroviruses/metabolism ; Enhancer Elements, Genetic ; Humans ; *RNA, Long Noncoding/metabolism ; Stem Cells/metabolism ; }, abstract = {Human specific endogenous retrovirus H (HERVH) is highly expressed in both naive and primed stem cells and is essential for pluripotency. Despite the proven relationship between HERVH expression and pluripotency, there is no single definitive model for the function of HERVH. Instead, several hypotheses of a regulatory function have been put forward including HERVH acting as enhancers, long noncoding RNAs (lncRNAs), and most recently as markers of topologically associating domain (TAD) boundaries. Recently several enhancer-associated lncRNAs have been characterized, which bind to Mediator and are necessary for promoter-enhancer folding interactions. We propose a synergistic model of HERVH function combining relevant findings and discuss the current limitations for its role in regulation, including the lack of evidence for a pluripotency-associated target gene.}, }
@article {pmid34326481, year = {2021}, author = {Soochit, W and Sleutels, F and Stik, G and Bartkuhn, M and Basu, S and Hernandez, SC and Merzouk, S and Vidal, E and Boers, R and Boers, J and van der Reijden, M and Geverts, B and van Cappellen, WA and van den Hout, M and Ozgur, Z and van IJcken, WFJ and Gribnau, J and Renkawitz, R and Graf, T and Houtsmuller, A and Grosveld, F and Stadhouders, R and Galjart, N}, title = {CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells.}, journal = {Nature cell biology}, volume = {23}, number = {8}, pages = {881-893}, pmid = {34326481}, issn = {1476-4679}, mesh = {Animals ; CCCTC-Binding Factor/genetics/*physiology ; Chromatin/*metabolism ; *DNA Methylation ; Female ; *Gene Expression Regulation ; *Genome ; Green Fluorescent Proteins/genetics ; Male ; Mice ; Mitosis ; Mouse Embryonic Stem Cells ; Mutation ; Pluripotent Stem Cells/metabolism/*physiology ; Time Factors ; Transcription Elongation, Genetic ; }, abstract = {The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.}, }
@article {pmid34313981, year = {2021}, author = {Gupta, MK and Lenz, T and Le Roch, KG}, title = {Chromosomes Conformation Capture Coupled with Next-Generation Sequencing (Hi-C) in Plasmodium falciparum.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2369}, number = {}, pages = {15-25}, pmid = {34313981}, issn = {1940-6029}, support = {R01 AI136511/AI/NIAID NIH HHS/United States ; R21 AI142506/AI/NIAID NIH HHS/United States ; R01 AI142743/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosomes/genetics ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria ; *Plasmodium falciparum/genetics ; }, abstract = {Over the last decades, novel methods have been developed to study the role of chromosome positioning within the nucleus may play in gene regulation. Established proximity ligation-based chromosome conformation capture (3C) techniques such as Hi-C have revealed the existence of chromosome territories, functional nuclear landmarks, and topologically associating domains (TAPs) in most eukaryotic organisms. Adaptation of these methods in apicomplexan parasites has recently uncovered new aspects of 3D genome biology in virulence factors. Here, we describe the Hi-C protocol in the human malaria parasite, Plasmodium falciparum. This method can determine the genome organization in malaria parasites and its role in gene regulation and virulence.}, }
@article {pmid34311744, year = {2021}, author = {Li, X and Zeng, G and Li, A and Zhang, Z}, title = {DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {217}, pmid = {34311744}, issn = {1474-760X}, mesh = {*Algorithms ; Animals ; CCCTC-Binding Factor/genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; Chromatin/*chemistry ; *Chromatin Assembly and Disassembly ; Cluster Analysis ; DNA-Binding Proteins/genetics/metabolism ; Entropy ; Gene Expression ; *Genome ; Histones/genetics/metabolism ; Humans ; Mammals ; Single-Cell Analysis/*methods ; *Software ; }, abstract = {Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells.}, }
@article {pmid34311045, year = {2021}, author = {Long, Y and Liu, Z and Wang, P and Yang, H and Wang, Y and Zhang, S and Zhang, X and Wang, M}, title = {Disruption of topologically associating domains by structural variations in tetraploid cottons.}, journal = {Genomics}, volume = {113}, number = {5}, pages = {3405-3414}, doi = {10.1016/j.ygeno.2021.07.023}, pmid = {34311045}, issn = {1089-8646}, mesh = {Animals ; Chromatin ; Chromosomes ; Gene Expression Regulation ; *Genome ; Mammals/genetics ; *Tetraploidy ; }, abstract = {Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. We observed that approximately 16% of SVs occurred in TAD boundary regions that were called boundary affecting-structural variations (BA-SVs), and had a large effect on disrupting TAD organization. Nevertheless, SVs preferred occurring in TAD interior instead of TAD boundary, probably associated with the relaxed evolutionary selection pressure. We noticed the biased evolution of the At and Dt subgenomes of tetraploid cottons, in terms of SV-mediated disruption of 3D genome structure relative to diploids. In addition, we provide evidence showing that both SVs and TAD disruption could lead to expression difference of orthologous genes. This study advances our understanding of the effect of SVs on 3D genome organization and gene expression regulation in plants.}, }
@article {pmid34309794, year = {2022}, author = {Revikumar, A and Kashyap, V and Palollathil, A and Aravind, A and Raguraman, R and Kumar, KMK and Vijayakumar, M and Prasad, TSK and Raju, R}, title = {Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines.}, journal = {Journal of cell communication and signaling}, volume = {16}, number = {1}, pages = {129-135}, pmid = {34309794}, issn = {1873-9601}, abstract = {The G-quadruplexes (G4s) are a class of DNA secondary structures with guanine rich DNA sequences that can fold into four stranded non-canonical structures. At the genomic level, their pivotal role is well established in DNA replication, telomerase functions, constitution of topologically associating domains, and the regulation of gene expression. Genome instability mediated by altered G4 formation and assembly has been associated with multiple disorders including cancers and neurodegenerative disorders. Multiple tools have also been developed to predict the potential G4 regions in genomes and the whole genome G4 maps are also being derived through sequencing approaches. Enrichment of G4s in the cis-regulatory elements of genes associated with tumorigenesis has accelerated the quest for identification of G4-DNA binding ligands (G4DBLs) that can selectively bind and regulate the expression of such specific genes. In this context, the analysis of G4DBL responsive transcriptome in diverse cancer cell lines is inevitable for assessment of the specificity of novel G4DBLs. Towards this, we assembled the transcripts differentially regulated by different G4DBLs and have also identified a core set of genes regulated in diverse cancer cell lines in response to 3 or more of these ligands. With the mode of action of G4DBLs towards topology shifts, folding, or disruption of G4 structure being currently visualized, we believe that this dataset will serve as a platform for assembly of G4DBL responsive transcriptome for comparative analysis of G4DBLs in multiple cancer cells based on the expression of specific cis-regulatory G4 associated genes in the future.}, }
@article {pmid34295901, year = {2021}, author = {Tena, JJ and Santos-Pereira, JM}, title = {Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {702787}, pmid = {34295901}, issn = {2296-634X}, abstract = {Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.}, }
@article {pmid34292939, year = {2021}, author = {Willemin, A and Lopez-Delisle, L and Bolt, CC and Gadolini, ML and Duboule, D and Rodriguez-Carballo, E}, title = {Induction of a chromatin boundary in vivo upon insertion of a TAD border.}, journal = {PLoS genetics}, volume = {17}, number = {7}, pages = {e1009691}, pmid = {34292939}, issn = {1553-7404}, support = {F32 HD093555/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/genetics/metabolism ; Cell Cycle Proteins/genetics ; Chromatin/genetics/*physiology ; Chromatin Assembly and Disassembly ; DNA/genetics ; Enhancer Elements, Genetic/genetics ; Gene Expression/genetics ; Gene Expression Regulation/*genetics/physiology ; Gene Regulatory Networks/genetics/*physiology ; Genome/genetics/physiology ; Genomics/methods ; Mice ; Mice, Transgenic ; }, abstract = {Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.}, }
@article {pmid34290257, year = {2021}, author = {Fonseca, TL and Garcia, T and Fernandes, GW and Nair, TM and Bianco, AC}, title = {Neonatal thyroxine activation modifies epigenetic programming of the liver.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4446}, pmid = {34290257}, issn = {2041-1723}, support = {R01 DK058538/DK/NIDDK NIH HHS/United States ; R01 DK065055/DK/NIDDK NIH HHS/United States ; R01 DK077148/DK/NIDDK NIH HHS/United States ; R56 DK058538/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Chromatin/metabolism ; DNA Methylation ; *Epigenesis, Genetic ; Gene Expression ; Gene Expression Regulation, Developmental ; Iodide Peroxidase/genetics/metabolism ; Liver/growth &amp; development/*metabolism ; Mice ; Mice, Knockout ; Triiodothyronine/*metabolism ; }, abstract = {The type 2 deiodinase (D2) in the neonatal liver accelerates local thyroid hormone triiodothyronine (T3) production and expression of T3-responsive genes. Here we show that this surge in T3 permanently modifies hepatic gene expression. Liver-specific Dio2 inactivation (Alb-D2KO) transiently increases H3K9me3 levels during post-natal days 1-5 (P1-P5), and results in methylation of 1,508 DNA sites (H-sites) in the adult mouse liver. These sites are associated with 1,551 areas of reduced chromatin accessibility (RCA) within core promoters and 2,426 within intergenic regions, with reduction in the expression of 1,363 genes. There is strong spatial correlation between density of H-sites and RCA sites. Chromosome conformation capture (Hi-C) data reveals a set of 81 repressed genes with a promoter RCA in contact with an intergenic RCA ~300 Kbp apart, within the same topologically associating domain (χ[2 ]= 777; p < 0.00001). These data explain how the systemic hormone T3 acts locally during development to define future expression of hepatic genes.}, }
@article {pmid34290235, year = {2021}, author = {King, AJ and Songdej, D and Downes, DJ and Beagrie, RA and Liu, S and Buckley, M and Hua, P and Suciu, MC and Marieke Oudelaar, A and Hanssen, LLP and Jeziorska, D and Roberts, N and Carpenter, SJ and Francis, H and Telenius, J and Olijnik, AA and Sharpe, JA and Sloane-Stanley, J and Eglinton, J and Kassouf, MT and Orkin, SH and Pennacchio, LA and Davies, JOJ and Hughes, JR and Higgs, DR and Babbs, C}, title = {Reactivation of a developmentally silenced embryonic globin gene.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4439}, pmid = {34290235}, issn = {2041-1723}, support = {R01 HG003988/HG/NHGRI NIH HHS/United States ; 209181/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_00016/14/MRC_/Medical Research Council/United Kingdom ; MR/N00969X/1/MRC_/Medical Research Council/United Kingdom ; R01 HL032259/HL/NHLBI NIH HHS/United States ; MC_UU_12009/MRC_/Medical Research Council/United Kingdom ; 106130/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; MR/T014067/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/4/MRC_/Medical Research Council/United Kingdom ; 108785/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Acetylation ; Animals ; Chromatin/metabolism ; DNA-Binding Proteins/metabolism ; Enhancer Elements, Genetic ; Erythroid Cells/metabolism ; *Gene Expression Regulation, Developmental/drug effects ; *Gene Silencing/drug effects ; Histone Deacetylase Inhibitors/pharmacology ; Humans ; Mice ; Repressor Proteins/metabolism ; Transcription Factors/metabolism ; *Transcriptional Activation/drug effects ; alpha-Globins/genetics ; zeta-Globins/*genetics ; }, abstract = {The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues.}, }
@article {pmid34274970, year = {2021}, author = {Aavikko, M and Kaasinen, E and Andersson, N and Pentinmikko, N and Sulo, P and Donner, I and Pihlajamaa, P and Kuosmanen, A and Bramante, S and Katainen, R and Sipilä, LJ and Martin, S and Arola, J and Carpén, O and Heiskanen, I and Mecklin, JP and Taipale, J and Ristimäki, A and Lehti, K and Gucciardo, E and Katajisto, P and Schalin-Jäntti, C and Vahteristo, P and Aaltonen, LA}, title = {WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas.}, journal = {Human molecular genetics}, volume = {30}, number = {24}, pages = {2429-2440}, pmid = {34274970}, issn = {1460-2083}, mesh = {*Adenocarcinoma/genetics/pathology ; *Adenoma/genetics/pathology ; *Colorectal Neoplasms/genetics ; Humans ; Intestinal Mucosa/pathology ; *Neuroendocrine Tumors/genetics/pathology ; Wnt2 Protein ; }, abstract = {Many hereditary cancer syndromes are associated with an increased risk of small and large intestinal adenocarcinomas. However, conditions bearing a high risk to both adenocarcinomas and neuroendocrine tumors are yet to be described. We studied a family with 16 individuals in four generations affected by a wide spectrum of intestinal tumors, including hyperplastic polyps, adenomas, small intestinal neuroendocrine tumors, and colorectal and small intestinal adenocarcinomas. To assess the genetic susceptibility and understand the novel phenotype, we utilized multiple molecular methods, including whole genome sequencing, RNA sequencing, single cell sequencing, RNA in situ hybridization and organoid culture. We detected a heterozygous deletion at the cystic fibrosis locus (7q31.2) perfectly segregating with the intestinal tumor predisposition in the family. The deletion removes a topologically associating domain border between CFTR and WNT2, aberrantly activating WNT2 in the intestinal epithelium. These consequences suggest that the deletion predisposes to small intestinal neuroendocrine tumors and small and large intestinal adenocarcinomas, and reveals the broad tumorigenic effects of aberrant WNT activation in the human intestine.}, }
@article {pmid34253239, year = {2021}, author = {Li, Y and Xue, B and Zhang, M and Zhang, L and Hou, Y and Qin, Y and Long, H and Su, QP and Wang, Y and Guan, X and Jin, Y and Cao, Y and Li, G and Sun, Y}, title = {Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {206}, pmid = {34253239}, issn = {1474-760X}, mesh = {CCCTC-Binding Factor/antagonists &amp; inhibitors/genetics/metabolism ; Cell Cycle Proteins/antagonists &amp; inhibitors/genetics/metabolism ; Cell Line ; Cell Line, Tumor ; Chromatin/*chemistry ; Chromatin Assembly and Disassembly ; *DNA Replication ; DNA-Binding Proteins/antagonists &amp; inhibitors/genetics/metabolism ; G1 Phase Cell Cycle Checkpoints/*genetics ; Gene Expression ; HeLa Cells ; Humans ; In Situ Hybridization, Fluorescence ; Optical Imaging ; Osteoblasts/cytology/metabolism ; Proliferating Cell Nuclear Antigen/*genetics/metabolism ; RNA, Small Interfering/genetics/metabolism ; *Replication Origin ; Retinal Pigment Epithelium/cytology/metabolism ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined.<br><br>RESULTS: We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired.<br><br>CONCLUSION: Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.}, }
@article {pmid34245617, year = {2021}, author = {Kang, J and Kim, YW and Park, S and Kang, Y and Kim, A}, title = {Multiple CTCF sites cooperate with each other to maintain a TAD for enhancer-promoter interaction in the β-globin locus.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {8}, pages = {e21768}, doi = {10.1096/fj.202100105RR}, pmid = {34245617}, issn = {1530-6860}, mesh = {CCCTC-Binding Factor/genetics/*metabolism ; Cell Line ; Chromatin/genetics/*metabolism ; *Enhancer Elements, Genetic ; *Genetic Loci ; Humans ; *Promoter Regions, Genetic ; beta-Globins/*biosynthesis/genetics ; }, abstract = {Insulators are cis-regulatory elements that block enhancer activity and prevent heterochromatin spreading. The binding of CCCTC-binding factor (CTCF) protein is essential for insulators to play the roles in a chromatin context. The β-globin locus, consisting of multiple genes and enhancers, is flanked by two insulators 3'HS1 and HS5. However, it has been reported that the absence of these insulators did not affect the β-globin transcription. To explain the unexpected finding, we have deleted a CTCF motif at 3'HS1 or HS5 in the human β-globin locus and analyzed chromatin interactions around the locus. It was found that a topologically associating domain (TAD) containing the β-globin locus is maintained by neighboring CTCF sites in the CTCF motif-deleted loci. The additional deletions of neighboring CTCF motifs disrupted the β-globin TAD, resulting in decrease of the β-globin transcription. Chromatin interactions of the β-globin enhancers with gene promoter were weakened in the multiple CTCF motifs-deleted loci, even though the enhancers have still active chromatin features such as histone H3K27ac and histone H3 depletion. Genome-wide analysis using public CTCF ChIA-PET and ChIP-seq data showed that chromatin domains possessing multiple CTCF binding sites tend to contain super-enhancers like the β-globin enhancers. Taken together, our results show that multiple CTCF sites surrounding the β-globin locus cooperate with each other to maintain a TAD. The β-globin TAD appears to provide a compact spatial environment that enables enhancers to interact with promoter.}, }
@article {pmid34240140, year = {2021}, author = {Peinado, P and Andrades, A and Martorell-Marugán, J and Haswell, JR and Slack, FJ and Carmona-Sáez, P and Medina, PP}, title = {The SWI/SNF complex regulates the expression of miR-222, a tumor suppressor microRNA in lung adenocarcinoma.}, journal = {Human molecular genetics}, volume = {30}, number = {23}, pages = {2263-2271}, doi = {10.1093/hmg/ddab187}, pmid = {34240140}, issn = {1460-2083}, support = {R35 CA232105/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma of Lung/*genetics/*metabolism/pathology ; Cell Line, Tumor ; Chromosomal Proteins, Non-Histone/*metabolism ; DNA-Binding Proteins ; Enhancer Elements, Genetic ; Gene Expression Regulation, Neoplastic ; *Genes, Tumor Suppressor ; Humans ; MicroRNAs/*genetics ; Models, Biological ; Transcription Factors/*metabolism ; }, abstract = {SWitch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes are key epigenetic regulators that are recurrently mutated in cancer. Most studies of these complexes are focused on their role in regulating protein-coding genes. However, here, we show that SWI/SNF complexes control the expression of microRNAs. We used a SMARCA4-deficient model of lung adenocarcinoma (LUAD) to track changes in the miRNome upon SMARCA4 restoration. We found that SMARCA4-SWI/SNF complexes induced significant changes in the expression of cancer-related microRNAs. The most significantly dysregulated microRNA was miR-222, whose expression was promoted by SMARCA4-SWI/SNF complexes, but not by SMARCA2-SWI/SNF complexes via their direct binding to a miR-222 enhancer region. Importantly, miR-222 expression decreased cell viability, phenocopying the tumor suppressor role of SMARCA4-SWI/SNF complexes in LUAD. Finally, we showed that the miR-222 enhancer region resides in a topologically associating domain that does not contain any cancer-related protein-coding genes, suggesting that miR-222 may be involved in exerting the tumor suppressor role of SMARCA4. Overall, this study highlights the relevant role of the SWI/SNF complex in regulating the non-coding genome, opening new insights into the pathogenesis of LUAD.}, }
@article {pmid34234130, year = {2021}, author = {Bag, I and Chen, S and Rosin, LF and Chen, Y and Liu, CY and Yu, GY and Lei, EP}, title = {M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4170}, pmid = {34234130}, issn = {2041-1723}, mesh = {Animals ; Animals, Genetically Modified ; Cell Line ; Cell Nucleus/metabolism ; Chromatin/genetics/metabolism ; Chromatin Immunoprecipitation Sequencing ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/*genetics ; Gene Knockdown Techniques ; Genome, Insect ; Insulator Elements/genetics ; Male ; Microtubule-Associated Proteins/genetics/*metabolism ; Nuclear Proteins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; RNA-Seq ; Repressor Proteins/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; *Transcriptional Activation ; }, abstract = {Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.}, }
@article {pmid34228749, year = {2021}, author = {Srikanth, S and Jain, L and Zepeda-Mendoza, C and Cascio, L and Jones, K and Pauly, R and DuPont, B and Rogers, C and Sarasua, S and Phelan, K and Morton, C and Boccuto, L}, title = {Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253859}, pmid = {34228749}, issn = {1932-6203}, mesh = {Adolescent ; Child ; Child, Preschool ; Chromosome Deletion ; Chromosome Disorders/*genetics ; Chromosomes, Human, Pair 22/genetics ; Cohort Studies ; Female ; *Gene Rearrangement ; Genetic Variation ; Humans ; Male ; }, abstract = {Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic abnormalities (e.g., terminal or interstitial deletions, translocations, ring chromosomes, or SHANK3 variants). Position effects have been shown to affect gene expression and function and play a role in the clinical presentation of various genetic conditions. This study employed a topologically associating domain (TAD) analysis approach to investigate position effects of chromosomal rearrangements on selected candidate genes mapped to 22q13 in 81 individuals with PMS. Data collected were correlated with clinical information from these individuals and with expression and metabolic profiles of lymphoblastoid cells from selected cases. The data confirmed TAD predictions for genes encompassed in the deletions and the clinical and molecular data indicated clear differences among individuals with different 22q13 deletion sizes. The results of the study indicate a positive correlation between deletion size and phenotype severity in PMS and provide evidence of the contribution of other genes to the clinical variability in this developmental disorder by reduced gene expression and altered metabolomics.}, }
@article {pmid34201566, year = {2021}, author = {Erenpreisa, J and Krigerts, J and Salmina, K and Gerashchenko, BI and Freivalds, T and Kurg, R and Winter, R and Krufczik, M and Zayakin, P and Hausmann, M and Giuliani, A}, title = {Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis).}, journal = {Cells}, volume = {10}, number = {7}, pages = {}, pmid = {34201566}, issn = {2073-4409}, mesh = {Actomyosin/metabolism ; Animals ; Cell Line, Tumor ; Cell Nucleolus/metabolism ; Chickens ; DNA Replication Timing ; Embryonic Development/genetics ; Gene Expression Regulation ; Heterochromatin/*metabolism ; Humans ; *Models, Biological ; Organ Specificity/genetics ; Rats ; }, abstract = {Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.}, }
@article {pmid34183853, year = {2021}, author = {Pachano, T and Sánchez-Gaya, V and Ealo, T and Mariner-Faulí, M and Bleckwehl, T and Asenjo, HG and Respuela, P and Cruz-Molina, S and Muñoz-San Martín, M and Haro, E and van IJcken, WFJ and Landeira, D and Rada-Iglesias, A}, title = {Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness.}, journal = {Nature genetics}, volume = {53}, number = {7}, pages = {1036-1049}, pmid = {34183853}, issn = {1546-1718}, support = {862022/ERC_/European Research Council/International ; }, mesh = {Animals ; Chromatin/genetics/metabolism ; *CpG Islands ; *DNA Methylation ; Embryonic Stem Cells/metabolism ; *Enhancer Elements, Genetic ; *Epigenesis, Genetic ; *Gene Expression Regulation ; Gene Knock-In Techniques ; Mice ; Promoter Regions, Genetic ; }, abstract = {CpG islands (CGIs) represent a widespread feature of vertebrate genomes, being associated with ~70% of all gene promoters. CGIs control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance is barely known. Here we show that oCGIs are an essential component of poised enhancers that augment their long-range regulatory activity and control the responsiveness of their target genes. Using a knock-in strategy in mouse embryonic stem cells, we introduced poised enhancers with or without oCGIs within topologically associating domains harboring genes with different types of promoters. Analysis of the resulting cell lines revealed that oCGIs act as tethering elements that promote the physical and functional communication between poised enhancers and distally located genes, particularly those with large CGI clusters in their promoters. Therefore, by acting as genetic determinants of gene-enhancer compatibility, CGIs can contribute to gene expression control under both physiological and potentially pathological conditions.}, }
@article {pmid34182258, year = {2021}, author = {Yasuhara, T and Zou, L}, title = {Impacts of chromatin dynamics and compartmentalization on DNA repair.}, journal = {DNA repair}, volume = {105}, number = {}, pages = {103162}, doi = {10.1016/j.dnarep.2021.103162}, pmid = {34182258}, issn = {1568-7856}, mesh = {Cell Nucleus/*metabolism/ultrastructure ; Chromatin/*metabolism ; Chromatin Assembly and Disassembly ; *DNA Repair ; Eukaryota/genetics/metabolism ; Humans ; }, abstract = {The proper spatial organization of DNA, RNA, and proteins is critical for a variety of cellular processes. The genome is organized into numerous functional units, such as topologically associating domains (TADs), the formation of which is regulated by both proteins and RNA. In addition, a group of chromatin-bound proteins with the ability to undergo liquid-liquid phase separation (LLPS) can affect the spatial organization and compartmentalization of chromatin, RNA, and proteins by forming condensates, conferring unique properties to specific chromosomal regions. Although the regulation of DNA repair by histone modifications and chromatin accessibility is well established, the impacts of higher-order chromatin and protein organization on the DNA damage response (DDR) have not been appreciated until recently. In this review, we will focus on the movement of chromatin during the DDR, the compartmentalization of DDR proteins via LLPS, and the roles of membraneless nuclear bodies and transcription in DNA repair. With this backdrop, we will discuss the importance of the spatial organization of chromatin and proteins for the maintenance of genome integrity.}, }
@article {pmid34168075, year = {2021}, author = {Cai, Z and He, Y and Liu, S and Xue, Y and Quan, H and Zhang, L and Gao, YQ}, title = {Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing.}, journal = {Life science alliance}, volume = {4}, number = {8}, pages = {}, pmid = {34168075}, issn = {2575-1077}, mesh = {Animals ; Birds/*genetics ; Chromatin/chemistry/*genetics ; Computational Biology/methods ; *CpG Islands ; DNA Methylation ; Evolution, Molecular ; Humans ; Mammals/*genetics ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.}, }
@article {pmid34108480, year = {2021}, author = {Bauer, M and Vidal, E and Zorita, E and Üresin, N and Pinter, SF and Filion, GJ and Payer, B}, title = {Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3499}, pmid = {34108480}, issn = {2041-1723}, support = {R35 GM124926/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cellular Reprogramming/genetics ; Chromatin Assembly and Disassembly ; Induced Pluripotent Stem Cells/cytology/metabolism ; Mice ; RNA, Long Noncoding/genetics/metabolism ; Sex Chromatin/genetics/metabolism ; *Transcription, Genetic ; X Chromosome/genetics/*metabolism ; X Chromosome Inactivation/*genetics ; }, abstract = {A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the inactive mouse X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC reprogramming system and high-resolution Hi-C to produce a time course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we observe A/B-like compartments on the inactive X harbouring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, concomitant with downregulation of Xist. Importantly, we find that TAD formation precedes transcription and initiates from Xist-poor compartments. Here, we show that TAD formation and transcriptional reactivation are causally independent during X-reactivation while establishing Xist as a common denominator.}, }
@article {pmid34099928, year = {2021}, author = {Niu, L and Shen, W and Shi, Z and Tan, Y and He, N and Wan, J and Sun, J and Zhang, Y and Huang, Y and Wang, W and Fang, C and Li, J and Zheng, P and Cheung, E and Chen, Y and Li, L and Hou, C}, title = {Three-dimensional folding dynamics of the Xenopus tropicalis genome.}, journal = {Nature genetics}, volume = {53}, number = {7}, pages = {1075-1087}, pmid = {34099928}, issn = {1546-1718}, mesh = {Animals ; Apoptosis Regulatory Proteins/genetics ; Cell Cycle Proteins/genetics ; Chromatin/genetics/metabolism ; Chromatin Assembly and Disassembly ; Computational Biology/methods ; Embryonic Development/genetics ; Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; *Genome ; Genomics/methods ; *Models, Molecular ; *Nucleic Acid Conformation ; Phenotype ; Xenopus/embryology/*genetics ; Xenopus Proteins/genetics ; }, abstract = {Animal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.}, }
@article {pmid34099725, year = {2021}, author = {Sahin, M and Wong, W and Zhan, Y and Van Deynze, K and Koche, R and Leslie, CS}, title = {HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3366}, pmid = {34099725}, issn = {2041-1723}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; U01 DK128852/DK/NIDDK NIH HHS/United States ; U01 HG009395/HG/NHGRI NIH HHS/United States ; }, mesh = {Acetylation ; Algorithms ; Animals ; Cells, Cultured ; Chromatin/*genetics/metabolism ; Computational Biology/*methods ; Enhancer Elements, Genetic/*genetics ; Genomics/methods ; Histone Code/genetics ; Histones/metabolism ; Humans ; K562 Cells ; Lysine/metabolism ; Mice ; Promoter Regions, Genetic/*genetics ; }, abstract = {Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool for Hi-C/HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools and includes topologically associating domain (TAD) and A/B compartment callers. We found that HiC-DC+ can more accurately identify enhancer-promoter interactions in H3K27ac HiChIP, as validated by CRISPRi-FlowFISH experiments, compared to existing methods. Differential HiC-DC+ analyses of published HiChIP and Hi-C data sets in settings of cellular differentiation and cohesin perturbation systematically and quantitatively recovers biological findings, including enhancer hubs, TAD aggregation, and the relationship between promoter-enhancer loop dynamics and gene expression changes. HiC-DC+ therefore provides a principled statistical analysis tool to empower genome-wide studies of 3D chromatin architecture and function.}, }
@article {pmid34099491, year = {2021}, author = {Gillani, R and Seong, BKA and Crowdis, J and Conway, JR and Dharia, NV and Alimohamed, S and Haas, BJ and Han, K and Park, J and Dietlein, F and He, MX and Imamovic, A and Ma, C and Bassik, MC and Boehm, JS and Vazquez, F and Gusev, A and Liu, D and Janeway, KA and McFarland, JM and Stegmaier, K and Van Allen, EM}, title = {Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival.}, journal = {Cancer research}, volume = {81}, number = {15}, pages = {3971-3984}, pmid = {34099491}, issn = {1538-7445}, support = {T32 CA136432/CA/NCI NIH HHS/United States ; U01 CA233100/CA/NCI NIH HHS/United States ; U24 CA180922/CA/NCI NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; R35 CA210030/CA/NCI NIH HHS/United States ; R01 CA227388/CA/NCI NIH HHS/United States ; R50 CA211461/CA/NCI NIH HHS/United States ; R37 CA222574/CA/NCI NIH HHS/United States ; }, mesh = {Cell Survival/*genetics ; Gene Fusion/*genetics ; Humans ; Neoplasms/*genetics ; }, abstract = {Gene fusions frequently result from rearrangements in cancer genomes. In many instances, gene fusions play an important role in oncogenesis; in other instances, they are thought to be passenger events. Although regulatory element rearrangements and copy number alterations resulting from these structural variants are known to lead to transcriptional dysregulation across cancers, the extent to which these events result in functional dependencies with an impact on cancer cell survival is variable. Here we used CRISPR-Cas9 dependency screens to evaluate the fitness impact of 3,277 fusions across 645 cell lines from the Cancer Dependency Map. We found that 35% of cell lines harbored either a fusion partner dependency or a collateral dependency on a gene within the same topologically associating domain as a fusion partner. Fusion-associated dependencies revealed numerous novel oncogenic drivers and clinically translatable alterations. Broadly, fusions can result in partner and collateral dependencies that have biological and clinical relevance across cancer types. SIGNIFICANCE: This study provides insights into how fusions contribute to fitness in different cancer contexts beyond partner-gene activation events, identifying partner and collateral dependencies that may have direct implications for clinical care.}, }
@article {pmid34099014, year = {2021}, author = {Furlan-Magaril, M and Ando-Kuri, M and Arzate-Mejía, RG and Morf, J and Cairns, J and Román-Figueroa, A and Tenorio-Hernández, L and Poot-Hernández, AC and Andrews, S and Várnai, C and Virk, B and Wingett, SW and Fraser, P}, title = {The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {162}, pmid = {34099014}, issn = {1474-760X}, support = {BB/J004480/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Biological Clocks/genetics ; Chromatin/metabolism ; Circadian Rhythm/*genetics ; Enhancer Elements, Genetic ; Gene Expression Regulation ; *Genome ; Liver/metabolism ; Male ; Mice, Inbred C57BL ; Models, Genetic ; *Promoter Regions, Genetic ; Time Factors ; Transcription, Genetic ; }, abstract = {BACKGROUND: Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized.<br><br>RESULTS: Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes.<br><br>CONCLUSION: Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations.}, }
@article {pmid34093998, year = {2021}, author = {Chyr, J and Zhang, Z and Chen, X and Zhou, X}, title = {PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {2870-2880}, pmid = {34093998}, issn = {2001-0370}, abstract = {Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. In our study, we addressed the relationship between multi-omics data and higher-order chromatin structures using a newly developed machine-learning model called PredTAD. Our tool uses already-available and cost-effective datatypes such as transcription factor and histone modification ChIPseq data. Specifically, PredTAD utilizes both epigenetic and genetic features as well as neighboring information to classify the entire human genome as boundary or non-boundary regions. Our tool can predict boundary changes between normal and breast cancer genomes. Among the most important features for predicting boundary alterations were CTCF, subunits of cohesin (RAD21 and SMC3), and chromosome number, suggesting their roles in conserved and dynamic boundaries formation. Upon further analysis, we observed that genes near altered TAD boundaries were found to be involved in several important breast cancer signaling pathways such as Ras, Jak-STAT, and estrogen signaling pathways. We also discovered a TAD boundary alteration that contributes to RET oncogene overexpression. PredTAD can also successfully predict TAD boundary changes in other conditions and diseases. In conclusion, our newly developed machine learning tool allowed for a more complete understanding of the dynamic 3D chromatin structures involved in signaling pathway activation, altered gene expression, and disease state in breast cancer cells.}, }
@article {pmid34078267, year = {2021}, author = {Olgun, G and Nabi, A and Tastan, O}, title = {NoRCE: non-coding RNA sets cis enrichment tool.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {294}, pmid = {34078267}, issn = {1471-2105}, mesh = {Animals ; Genome ; Mice ; *MicroRNAs ; RNA, Untranslated/genetics ; Rats ; *Zebrafish/genetics ; }, abstract = {BACKGROUND: While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association.<br><br>RESULTS: We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding &amp; ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.<br><br>CONCLUSIONS: NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users' preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE .}, }
@article {pmid34071789, year = {2021}, author = {Peterson, SC and Samuelson, KB and Hanlon, SL}, title = {Multi-Scale Organization of the Drosophila melanogaster Genome.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34071789}, issn = {2073-4425}, support = {R00 HD099276/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Chromosomes, Insect/genetics ; Drosophila melanogaster/*genetics ; *Genome, Insect ; }, abstract = {Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.}, }
@article {pmid34034791, year = {2021}, author = {Lee, DI and Roy, S}, title = {GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {164}, pmid = {34034791}, issn = {1474-760X}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; R01 HG010045/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Cell Line ; Chromatin/*genetics ; Chromosomes/genetics ; Databases, Genetic ; *Genome ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; Regulatory Sequences, Nucleic Acid/genetics ; Time Factors ; }, abstract = {High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.}, }
@article {pmid34033138, year = {2021}, author = {Kim, J and Kang, J and Kim, YW and Kim, A}, title = {The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {6}, pages = {e21669}, doi = {10.1096/fj.202002337R}, pmid = {34033138}, issn = {1530-6860}, mesh = {Binding Sites ; CCCTC-Binding Factor/genetics/*metabolism ; Chromatin/*chemistry/genetics/metabolism ; *Enhancer Elements, Genetic ; Humans ; Promoter Regions, Genetic ; *Transcription, Genetic ; *Transcriptional Activation ; beta-Globins/*genetics/metabolism ; }, abstract = {The human β-globin locus control region (LCR) hypersensitive site 2 (HS2) is one of enhancers for transcription of the β-like globin genes in erythroid cells. Our previous study showed that the LCR HS2 has active chromatin structure before transcriptional induction of the β-globin gene, while another enhancer LCR HS3 is activated by the induction. To compare functional difference between them, we deleted each HS (ΔHS2 and ΔHS3) from the human β-globin locus in hybrid MEL/ch11 cells. Deletion of either HS2 or HS3 dramatically diminished the β-globin transcription and disrupted locus-wide histone H3K27ac and chromatin interaction between LCR HSs and gene. Surprisingly, ΔHS2 weakened interactions between CTCF sites forming the β-globin topologically associating domain (TAD), while ΔHS3 did not. CTCF occupancy and chromatin accessibility were reduced at the CTCF sites in the ΔHS2 locus. To further characterize the HS2, we deleted the maf-recognition elements for erythroid activator NF-E2 at HS2. This deletion decreased the β-globin transcription and enhancer-promoter interaction, but did not affect interactions between CTCF sites for the TAD. In light of these results, we propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and this role is beyond typical enhancer activity.}, }
@article {pmid34030950, year = {2022}, author = {Ulianov, SV and Razin, SV}, title = {The two waves in single-cell 3D genomics.}, journal = {Seminars in cell &amp; developmental biology}, volume = {121}, number = {}, pages = {143-152}, doi = {10.1016/j.semcdb.2021.05.021}, pmid = {34030950}, issn = {1096-3634}, mesh = {Genomics/*methods ; Humans ; Single-Cell Analysis/*methods ; }, abstract = {For decades, biochemical methods for the analysis of genome structure and function provided cell-population-averaged data that allowed general principles and tendencies to be disclosed. Microscopy-based studies, which immanently involve single-cell analysis, did not provide sufficient spatial resolution to investigate the particularly small details of 3D genome folding. Nevertheless, these studies demonstrated that mutual positions of chromosome territories within cell nuclei and individual genomic loci within chromosomal territories can vary significantly in individual cells. The development of new technologies in biochemistry and the advent of super-resolution microscopy in the last decade have made possible the full-scale study of 3D genome organization in individual cells. Maps of the 3D genome build based on C-data and super-resolution microscopy are highly consistent and, therefore, biologically relevant. The internal structures of individual chromosomes, loci, and topologically associating domains (TADs) are resolved as well as cell-cycle dynamics. 3D modeling allows one to investigate the physical mechanisms underlying genome folding. Finally, joint profiling of genome topology and epigenetic features will allow 3D genomics to handle complex cell-to-cell heterogeneity. In this review, we summarize the present state of studies into 3D genome organization in individual cells, analyze the technical problems of single-cell studies, and outline perspectives of 3D genomics.}, }
@article {pmid34019647, year = {2021}, author = {Requena, F and Abdallah, HH and García, A and Nitschké, P and Romana, S and Malan, V and Rausell, A}, title = {CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.}, journal = {Nucleic acids research}, volume = {49}, number = {W1}, pages = {W93-W103}, pmid = {34019647}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA Copy Number Variations ; Gene Expression ; Genome, Human ; Humans ; Internet ; Mice, Knockout ; Phenotype ; Protein Interaction Mapping ; Rare Diseases/diagnosis/*genetics ; Regulatory Sequences, Nucleic Acid ; *Software ; }, abstract = {Copy Number Variants (CNVs) are an important cause of rare diseases. Array-based Comparative Genomic Hybridization tests yield a ∼12% diagnostic rate, with ∼8% of patients presenting CNVs of unknown significance. CNVs interpretation is particularly challenging on genomic regions outside of those overlapping with previously reported structural variants or disease-associated genes. Recent studies showed that a more comprehensive evaluation of CNV features, leveraging both coding and non-coding impacts, can significantly improve diagnostic rates. However, currently available CNV interpretation tools are mostly gene-centric or provide only non-interactive annotations difficult to assess in the clinical practice. Here, we present CNVxplorer, a web server suited for the functional assessment of CNVs in a clinical diagnostic setting. CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs. It provides sequence constraint metrics, impact on regulatory elements and topologically associating domains, as well as expression patterns. Analyses offered cover (a) agreement with patient phenotypes; (b) visualizations of associations among genes, regulatory elements and transcription factors; (c) enrichment on functional and pathway annotations and (d) co-occurrence of terms across PubMed publications related to the query CNVs. A flexible evaluation workflow allows dynamic re-interrogation in clinical sessions. CNVxplorer is publicly available at http://cnvxplorer.com.}, }
@article {pmid34009337, year = {2021}, author = {Yuan, R and Zhang, J and Wang, Y and Zhu, X and Hu, S and Zeng, J and Liang, F and Tang, Q and Chen, Y and Chen, L and Zhu, W and Li, M and Mo, D}, title = {Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {28}, number = {2}, pages = {}, pmid = {34009337}, issn = {1756-1663}, mesh = {Animals ; Chromatin/*metabolism ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation Sequencing ; Embryo, Mammalian/*metabolism ; Embryonic Development ; Female ; Gene Expression Regulation, Developmental ; *Muscle Development ; Muscle, Skeletal/*growth &amp; development/metabolism ; Sequence Analysis, RNA ; Sus scrofa/*genetics/growth &amp; development/metabolism ; *Transcriptome ; }, abstract = {Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter-enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.}, }
@article {pmid34002095, year = {2021}, author = {Huang, H and Zhu, Q and Jussila, A and Han, Y and Bintu, B and Kern, C and Conte, M and Zhang, Y and Bianco, S and Chiariello, AM and Yu, M and Hu, R and Tastemel, M and Juric, I and Hu, M and Nicodemi, M and Zhuang, X and Ren, B}, title = {CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.}, journal = {Nature genetics}, volume = {53}, number = {7}, pages = {1064-1074}, pmid = {34002095}, issn = {1546-1718}, support = {U54 DK107977/DK/NIDDK NIH HHS/United States ; UM1 HG011585/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; K99 CA252020/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; CCCTC-Binding Factor/chemistry/*genetics/*metabolism ; Chromatin/*genetics/*metabolism ; Enhancer Elements, Genetic ; *Gene Expression Regulation ; Humans ; Insulator Elements ; Mice ; Mouse Embryonic Stem Cells/metabolism ; Promoter Regions, Genetic ; Protein Binding ; *Transcription, Genetic ; }, abstract = {Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.}, }
@article {pmid33973633, year = {2021}, author = {Wang, M and Li, J and Wang, P and Liu, F and Liu, Z and Zhao, G and Xu, Z and Pei, L and Grover, CE and Wendel, JF and Wang, K and Zhang, X}, title = {Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3621-3636}, pmid = {33973633}, issn = {1537-1719}, mesh = {*DNA Transposable Elements/genetics ; Genome, Plant ; Genomics ; *Gossypium/genetics ; Synteny ; }, abstract = {Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active ("A") and inactive ("B") compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K2 and A2 relative to D5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.}, }
@article {pmid33959385, year = {2021}, author = {Maksimenko, OG and Fursenko, DV and Belova, EV and Georgiev, PG}, title = {CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers.}, journal = {Acta naturae}, volume = {13}, number = {1}, pages = {31-46}, pmid = {33959385}, issn = {2075-8251}, abstract = {In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.}, }
@article {pmid33927397, year = {2021}, author = {Marinov, GK and Trevino, AE and Xiang, T and Kundaje, A and Grossman, AR and Greenleaf, WJ}, title = {Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum.}, journal = {Nature genetics}, volume = {53}, number = {5}, pages = {613-617}, pmid = {33927397}, issn = {1546-1718}, support = {U01 HG009431/HG/NHGRI NIH HHS/United States ; R01 HG008140/HG/NHGRI NIH HHS/United States ; U19 AI057266/AI/NIAID NIH HHS/United States ; P50 HG007735/HG/NHGRI NIH HHS/United States ; DP2 GM123485/GM/NIGMS NIH HHS/United States ; UM1 HG009436/HG/NHGRI NIH HHS/United States ; UM1 HG009442/HG/NHGRI NIH HHS/United States ; }, mesh = {Dinoflagellida/*genetics ; *Genome ; Models, Genetic ; *Transcription, Genetic ; }, abstract = {Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term 'dinoTADs') without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.}, }
@article {pmid33903158, year = {2021}, author = {Bohrer, CH and Larson, DR}, title = {The Stochastic Genome and Its Role in Gene Expression.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {13}, number = {10}, pages = {}, pmid = {33903158}, issn = {1943-0264}, mesh = {Animals ; *Gene Expression ; *Genome ; Mammals/*genetics ; Stochastic Processes ; }, abstract = {Mammalian genomes have distinct levels of spatial organization and structure that have been hypothesized to play important roles in transcription regulation. Although much has been learned about these architectural features with ensemble techniques, single-cell studies are showing a new universal trend: Genomes are stochastic and dynamic at every level of organization. Stochastic gene expression, on the other hand, has been studied for years. In this review, we probe whether there is a causative link between the two phenomena. We specifically discuss the functionality of chromatin state, topologically associating domains (TADs), and enhancer biology in light of their stochastic nature and their specific roles in stochastic gene expression. We highlight persistent fundamental questions in this area of research.}, }
@article {pmid33897976, year = {2021}, author = {Du, G and Li, H and Ding, Y and Jiang, S and Hong, H and Gan, J and Wang, L and Yang, Y and Li, Y and Huang, X and Sun, Y and Tao, H and Li, Y and Xu, X and Zheng, Y and Wang, J and Bai, X and Xu, K and Li, Y and Jiang, Q and Li, C and Chen, H and Bo, X}, title = {The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {1684-1693}, pmid = {33897976}, issn = {2001-0370}, abstract = {Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a "TAD hierarchical score (TH score)" for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.}, }
@article {pmid33880880, year = {2021}, author = {Zamariolli, M and Burssed, B and Moysés-Oliveira, M and Colovati, M and Bellucco, FTDS and Dos Santos, LC and Alvarez Perez, AB and Bragagnolo, S and Melaragno, MI}, title = {Novel MYT1 variants expose the complexity of oculo-auriculo-vertebral spectrum genetic mechanisms.}, journal = {American journal of medical genetics. Part A}, volume = {185}, number = {7}, pages = {2056-2064}, doi = {10.1002/ajmg.a.62217}, pmid = {33880880}, issn = {1552-4833}, mesh = {Branchial Region/pathology ; Brazil/epidemiology ; DNA Copy Number Variations/genetics ; DNA-Binding Proteins/*genetics ; Female ; *Genetic Predisposition to Disease ; Goldenhar Syndrome/epidemiology/*genetics/pathology ; Humans ; Male ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Transcription Factors/*genetics ; }, abstract = {Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder characterized by anomalies mainly involving the structures derived from the first and second pharyngeal arches. The spectrum presents with heterogeneous clinical features and complex etiology with genetic factors not yet completely understood. To date, MYT1 is the most important gene unambiguously associated with the spectrum and with functional data confirmation. In this work, we aimed to identify new single nucleotide variants (SNVs) affecting MYT1 in a cohort of 73 Brazilian patients diagnosed with OAVS. In addition, we investigated copy number variations (CNVs) encompassing this gene or its cis-regulatory elements and compared the frequency of these events in patients versus a cohort of 455 Brazilian control individuals. A new SNV, predicted as likely deleterious, was identified in five unrelated patients with OAVS. All five patients presented hearing impairment and orbital asymmetry suggesting an association with the variant. CNVs near MYT1, located in its neighboring topologically associating domain (TAD), were found to be enriched in patients when compared to controls, indicating a possible involvement of this region with OAVS pathogenicity. Our findings highlight the genetic complexity of the spectrum that seems to involve more than one variant type and inheritance patterns.}, }
@article {pmid33850120, year = {2021}, author = {Zhao, Y and Hou, Y and Xu, Y and Luan, Y and Zhou, H and Qi, X and Hu, M and Wang, D and Wang, Z and Fu, Y and Li, J and Zhang, S and Chen, J and Han, J and Li, X and Zhao, S}, title = {A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2217}, pmid = {33850120}, issn = {2041-1723}, mesh = {Animals ; Chromatin Immunoprecipitation Sequencing ; Epigenesis, Genetic ; *Epigenomics ; Gene Expression ; Genome ; Genome, Human ; HEK293 Cells ; Humans ; Mice ; RNA-Seq ; Receptors, G-Protein-Coupled/metabolism ; *Regulatory Sequences, Nucleic Acid ; Swine/*genetics ; Transcriptome ; }, abstract = {Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.}, }
@article {pmid33841414, year = {2021}, author = {Majumder, K and Morales, AJ}, title = {Utilization of Host Cell Chromosome Conformation by Viral Pathogens: Knowing When to Hold and When to Fold.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {633762}, pmid = {33841414}, issn = {1664-3224}, support = {F32 AI131468/AI/NIAID NIH HHS/United States ; K99 AI148511/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cell Transformation, Viral ; *Chromosomes, Human ; DNA, Viral/*genetics ; Epigenesis, Genetic ; Gammaherpesvirinae/*genetics/pathogenicity ; Gene Expression Regulation, Viral ; *Genome, Viral ; Herpesviridae Infections/genetics/*virology ; Host-Pathogen Interactions ; Humans ; Nucleic Acid Conformation ; Tumor Virus Infections/genetics/*virology ; *Virus Integration ; Virus Internalization ; Virus Latency ; Virus Replication ; }, abstract = {Though viruses have their own genomes, many depend on the nuclear environment of their hosts for replication and survival. A substantial body of work has therefore been devoted to understanding how viral and eukaryotic genomes interact. Recent advances in chromosome conformation capture technologies have provided unprecedented opportunities to visualize how mammalian genomes are organized and, by extension, how packaging of nuclear DNA impacts cellular processes. Recent studies have indicated that some viruses, upon entry into host cell nuclei, produce factors that alter host chromatin topology, and thus, impact the 3D organization of the host genome. Additionally, a variety of distinct viruses utilize host genome architectural factors to advance various aspects of their life cycles. Indeed, human gammaherpesviruses, known for establishing long-term reservoirs of latent infection in B lymphocytes, utilize 3D principles of genome folding to package their DNA and establish latency in host cells. This manipulation of host epigenetic machinery by latent viral genomes is etiologically linked to the onset of B cell oncogenesis. Small DNA viruses, by contrast, are tethered to distinct cellular sites that support virus expression and replication. Here, we briefly review the recent findings on how viruses and host genomes spatially communicate, and how this impacts virus-induced pathology.}, }
@article {pmid33838653, year = {2021}, author = {Xing, H and Wu, Y and Zhang, MQ and Chen, Y}, title = {Deciphering hierarchical organization of topologically associated domains through change-point testing.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {183}, pmid = {33838653}, issn = {1471-2105}, support = {R01MH109616/NH/NIH HHS/United States ; }, mesh = {Cell Nucleus ; *Chromatin/genetics ; *Chromosomes ; Computer Simulation ; Gene Expression Regulation ; Humans ; }, abstract = {BACKGROUND: The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them.<br><br>RESULTS: We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions.<br><br>CONCLUSIONS: HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions.}, }
@article {pmid33816958, year = {2020}, author = {Rozenwald, MB and Galitsyna, AA and Sapunov, GV and Khrameeva, EE and Gelfand, MS}, title = {A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features.}, journal = {PeerJ. Computer science}, volume = {6}, number = {}, pages = {e307}, pmid = {33816958}, issn = {2376-5992}, abstract = {Technological advances have lead to the creation of large epigenetic datasets, including information about DNA binding proteins and DNA spatial structure. Hi-C experiments have revealed that chromosomes are subdivided into sets of self-interacting domains called Topologically Associating Domains (TADs). TADs are involved in the regulation of gene expression activity, but the mechanisms of their formation are not yet fully understood. Here, we focus on machine learning methods to characterize DNA folding patterns in Drosophila based on chromatin marks across three cell lines. We present linear regression models with four types of regularization, gradient boosting, and recurrent neural networks (RNN) as tools to study chromatin folding characteristics associated with TADs given epigenetic chromatin immunoprecipitation data. The bidirectional long short-term memory RNN architecture produced the best prediction scores and identified biologically relevant features. Distribution of protein Chriz (Chromator) and histone modification H3K4me3 were selected as the most informative features for the prediction of TADs characteristics. This approach may be adapted to any similar biological dataset of chromatin features across various cell lines and species. The code for the implemented pipeline, Hi-ChiP-ML, is publicly available: https://github.com/MichalRozenwald/Hi-ChIP-ML.}, }
@article {pmid33796120, year = {2021}, author = {Miyazaki, K and Miyazaki, M}, title = {The Interplay Between Chromatin Architecture and Lineage-Specific Transcription Factors and the Regulation of Rag Gene Expression.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {659761}, pmid = {33796120}, issn = {1664-3224}, mesh = {Adaptive Immunity/genetics/immunology ; Cell Lineage/genetics/*immunology ; Chromatin/genetics/*immunology/metabolism ; Chromatin Assembly and Disassembly/genetics/*immunology ; DNA-Binding Proteins/genetics/*immunology/metabolism ; Gene Expression Regulation/immunology ; Homeodomain Proteins/genetics/*immunology/metabolism ; Humans ; Nuclear Proteins/genetics/*immunology/metabolism ; Promoter Regions, Genetic/genetics ; Transcription Factors/genetics/*immunology/metabolism ; }, abstract = {Cell type-specific gene expression is driven through the interplay between lineage-specific transcription factors (TFs) and the chromatin architecture, such as topologically associating domains (TADs), and enhancer-promoter interactions. To elucidate the molecular mechanisms of the cell fate decisions and cell type-specific functions, it is important to understand the interplay between chromatin architectures and TFs. Among enhancers, super-enhancers (SEs) play key roles in establishing cell identity. Adaptive immunity depends on the RAG-mediated assembly of antigen recognition receptors. Hence, regulation of the Rag1 and Rag2 (Rag1/2) genes is a hallmark of adaptive lymphoid lineage commitment. Here, we review the current knowledge of 3D genome organization, SE formation, and Rag1/2 gene regulation during B cell and T cell differentiation.}, }
@article {pmid33795867, year = {2021}, author = {Espinola, SM and Götz, M and Bellec, M and Messina, O and Fiche, JB and Houbron, C and Dejean, M and Reim, I and Cardozo Gizzi, AM and Lagha, M and Nollmann, M}, title = {Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development.}, journal = {Nature genetics}, volume = {53}, number = {4}, pages = {477-486}, pmid = {33795867}, issn = {1546-1718}, mesh = {Animals ; Cell Differentiation ; Cell Lineage/*genetics ; Chromatin/*chemistry/metabolism ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster/cytology/*genetics/growth &amp; development/metabolism ; Embryo, Nonmammalian ; Enhancer Elements, Genetic ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genomics ; Nuclear Proteins/*genetics/metabolism ; Promoter Regions, Genetic ; Single-Cell Analysis ; Transcription Factors/classification/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM-promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM-promoter interactions in defining transcriptional states, as well as distinct cell types.}, }
@article {pmid33767413, year = {2021}, author = {Davidson, IF and Peters, JM}, title = {Genome folding through loop extrusion by SMC complexes.}, journal = {Nature reviews. Molecular cell biology}, volume = {22}, number = {7}, pages = {445-464}, pmid = {33767413}, issn = {1471-0080}, mesh = {Adenosine Triphosphatases/chemistry/metabolism ; Animals ; Cell Cycle Proteins/chemistry/metabolism ; Chromatin/chemistry/metabolism ; Chromosomal Proteins, Non-Histone/chemistry/*metabolism ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; *Genome ; Humans ; Models, Biological ; Multiprotein Complexes/chemistry/metabolism ; Nucleic Acid Conformation ; }, abstract = {Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.}, }
@article {pmid33761883, year = {2021}, author = {Goldfarb, CN and Waxman, DJ}, title = {Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {212}, pmid = {33761883}, issn = {1471-2164}, support = {R01 DK121998/DK/NIDDK NIH HHS/United States ; R01 ES024421/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Constitutive Androstane Receptor ; Liver ; Mice ; Pyridines ; *RNA, Long Noncoding/genetics ; Transcriptome ; }, abstract = {BACKGROUND: While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for long non-coding (lnc)RNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection.<br><br>RESULTS: Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNA transcripts were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to TCPOBOP a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3).<br><br>CONCLUSIONS: Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and disease.}, }
@article {pmid33750794, year = {2021}, author = {Zhang, L and Zhao, J and Bi, H and Yang, X and Zhang, Z and Su, Y and Li, Z and Zhang, L and Sanderson, BJ and Liu, J and Ma, T}, title = {Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {62}, pmid = {33750794}, issn = {2662-6810}, abstract = {The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.}, }
@article {pmid33730165, year = {2021}, author = {Wang, L and Jia, G and Jiang, X and Cao, S and Chen, ZJ and Song, Q}, title = {Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.}, journal = {The Plant cell}, volume = {33}, number = {5}, pages = {1430-1446}, pmid = {33730165}, issn = {1532-298X}, mesh = {Chromatin/*chemistry ; Chromosomes, Plant/genetics ; Diploidy ; *Domestication ; Gene Duplication ; *Gene Expression Regulation, Plant ; Genome, Plant ; Phaseolus/genetics ; *Polyploidy ; Soybeans/anatomy &amp; histology/*genetics ; }, abstract = {Polyploidy or whole-genome duplication (WGD) is widespread in plants and is a key driver of evolution and speciation, accompanied by rapid and dynamic changes in genomic structure and gene expression. The 3D structure of the genome is intricately linked to gene expression, but its role in transcription regulation following polyploidy and domestication remains unclear. Here, we generated high-resolution (∼2 kb) Hi-C maps for cultivated soybean (Glycine max), wild soybean (Glycine soja), and common bean (Phaseolus vulgaris). We found polyploidization in soybean may induce architecture changes of topologically associating domains and subsequent diploidization led to chromatin topology alteration around chromosome-rearrangement sites. Compared with single-copy and small-scale duplicated genes, WGD genes displayed more long-range chromosomal interactions and were coupled with higher levels of gene expression and chromatin accessibilities but void of DNA methylation. Interestingly, chromatin loop reorganization was involved in expression divergence of the genes during soybean domestication. Genes with chromatin loops were under stronger artificial selection than genes without loops. These findings provide insights into the roles of dynamic chromatin structures on gene expression during polyploidization, diploidization, and domestication of soybean.}, }
@article {pmid33720766, year = {2021}, author = {Soto, C and Bryner, D and Neretti, N and Srivastava, A}, title = {Toward a Three-Dimensional Chromosome Shape Alphabet.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {28}, number = {6}, pages = {601-618}, pmid = {33720766}, issn = {1557-8666}, support = {R01 GM126558/GM/NIGMS NIH HHS/United States ; U01 CA200147/CA/NCI NIH HHS/United States ; R01 AG050582/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Chromosome Structures ; Chromosomes/chemistry/*genetics ; Computational Biology/*methods ; Humans ; }, abstract = {The study of the three-dimensional (3D) structure of chromosomes-the largest macromolecules in biology-is one of the most challenging to date in structural biology. Here, we develop a novel representation of 3D chromosome structures, as sequences of shape letters from a finite shape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct a Chromosome Shape Alphabet from an ensemble of chromosome 3D structures inferred from Hi-C data-via SIMBA3D or other methods-by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs' 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form the Chromosome Shape Letters (CSLs) of the alphabet. We provide a proof of concept for these CSLs by reconstructing independent test curves by using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize shapes in an ensemble of chromosome 3D structures by using generalized sequence logos.}, }
@article {pmid33677565, year = {2021}, author = {Tian, L and Ku, L and Yuan, Z and Wang, C and Su, H and Wang, S and Song, X and Dou, D and Ren, Z and Lai, J and Liu, T and Du, C and Chen, Y}, title = {Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines.}, journal = {Journal of experimental botany}, volume = {72}, number = {10}, pages = {3582-3596}, doi = {10.1093/jxb/erab087}, pmid = {33677565}, issn = {1460-2431}, mesh = {*Chromatin ; Epigenesis, Genetic ; Genome ; Genomics ; *Zea mays/genetics ; }, abstract = {Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.}, }
@article {pmid33631432, year = {2022}, author = {Liu, X and Sun, Q and Wang, Q and Hu, C and Chen, X and Li, H and Czajkowsky, DM and Shao, Z}, title = {Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {20}, number = {1}, pages = {101-109}, pmid = {33631432}, issn = {2210-3244}, mesh = {Animals ; Cell Line ; Chromatin ; Epithelial Cells ; Gene Expression Regulation ; *Genome ; *Genomics ; Mice ; }, abstract = {Recent studies have characterized the genomic structures of many eukaryotic cells, often focusing on their relation to gene expression. However, these studies have largely investigated cells grown in 2D cultures, although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higher-order genomic interactions, notably in compartment identity and strength as well as in topologically associating domain (TAD)-TAD interactions, but only minor differences are found at the TAD level. Our RNA-seq analysis reveals an up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells. These genes are associated with a subset of structural changes, suggesting that differences in genomic structure are critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changes in gene expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.}, }
@article {pmid33597753, year = {2021}, author = {Arnould, C and Rocher, V and Finoux, AL and Clouaire, T and Li, K and Zhou, F and Caron, P and Mangeot, PE and Ricci, EP and Mourad, R and Haber, JE and Noordermeer, D and Legube, G}, title = {Loop extrusion as a mechanism for formation of DNA damage repair foci.}, journal = {Nature}, volume = {590}, number = {7847}, pages = {660-665}, pmid = {33597753}, issn = {1476-4687}, support = {647344/ERC_/European Research Council/International ; R35 GM127029/GM/NIGMS NIH HHS/United States ; T32 GM007122/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Cycle Proteins/metabolism ; Cell Line ; Chromosomal Proteins, Non-Histone/metabolism ; DNA/*chemistry/genetics/*metabolism ; *DNA Breaks, Double-Stranded ; *DNA Repair ; Genome/genetics ; Histones/metabolism ; Humans ; *Nucleic Acid Conformation ; Nucleosomes/chemistry/genetics/metabolism ; Phosphorylation ; *Saccharomyces cerevisiae/cytology/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Tumor Suppressor p53-Binding Protein 1/metabolism ; }, abstract = {The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci[1]. It is unclear how these foci are rapidly assembled to establish a 'repair-prone' environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes[2,3]. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX-53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.}, }
@article {pmid33591308, year = {2021}, author = {Li, D and Sun, X and Yu, F and Perle, MA and Araten, D and Boeke, JD}, title = {Application of counter-selectable marker PIGA in engineering designer deletion cell lines and characterization of CRISPR deletion efficiency.}, journal = {Nucleic acids research}, volume = {49}, number = {5}, pages = {2642-2654}, pmid = {33591308}, issn = {1362-4962}, support = {P01 AG051449/AG/NIA NIH HHS/United States ; RM1 HG009491/HG/NHGRI NIH HHS/United States ; P50 GM107632/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Toxins/toxicity ; *CRISPR-Cas Systems ; *Cell Engineering ; Cell Line ; Chromosomes, Human, X ; Genetic Markers ; Heterozygote ; Humans ; Membrane Proteins/*genetics ; Mutation ; N-Acetylglucosaminyltransferases/genetics ; Pore Forming Cytotoxic Proteins/toxicity ; RNA/genetics ; *Sequence Deletion ; }, abstract = {The CRISPR/Cas9 system is a technology for genome engineering, which has been applied to indel mutations in genes as well as targeted gene deletion and replacement. Here, we describe paired gRNA deletions along the PIGA locus on the human X chromosome ranging from 17 kb to 2 Mb. We found no compelling linear correlation between deletion size and the deletion efficiency, and there is no substantial impact of topologically associating domains on deletion frequency. Using this precise deletion technique, we have engineered a series of designer deletion cell lines, including one with deletions of two X-chromosomal counterselectable (negative selection) markers, PIGA and HPRT1, and additional cell lines bearing each individual deletion. PIGA encodes a component of the glycosylphosphatidylinositol (GPI) anchor biosynthetic apparatus. The PIGA gene counterselectable marker has unique features, including existing single cell level assays for both function and loss of function of PIGA and the existence of a potent counterselectable agent, proaerolysin, which we use routinely for selection against cells expressing PIGA. These designer cell lines may serve as a general platform with multiple selection markers and may be particularly useful for large scale genome engineering projects such as Genome Project-Write (GP-write).}, }
@article {pmid33573880, year = {2021}, author = {Zheng, W and Yang, Z and Ge, X and Feng, Y and Wang, Y and Liu, C and Luan, Y and Cai, K and Vakal, S and You, F and Guo, W and Wang, W and Feng, Z and Li, F}, title = {Freeze substitution Hi-C, a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {3}, pages = {237-247}, doi = {10.1016/j.jgg.2020.11.002}, pmid = {33573880}, issn = {1673-8527}, mesh = {Animals ; Cost-Benefit Analysis ; *Drosophila melanogaster ; Freeze Substitution ; }, abstract = {Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in High-through chromosome conformation capture (Hi-C) to keep natural chromatin conformation intact. This requirement has impeded the advancement of 3D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time. Here, we develop a freeze substitution Hi-C (FS-Hi-C) technique that overcomes the need for fresh samples. FS-Hi-C can be used with samples stored in liquid nitrogen (LN2): the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution. After confirming that the FS step preserves the natural chromosome conformation during sample thawing, we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum. Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains, we found that FS-Hi-C outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-Hi-C will probably extend the application of 3D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date.}, }
@article {pmid33563719, year = {2021}, author = {Liao, Y and Zhang, X and Chakraborty, M and Emerson, JJ}, title = {Topologically associating domains and their role in the evolution of genome structure and function in Drosophila.}, journal = {Genome research}, volume = {31}, number = {3}, pages = {397-410}, pmid = {33563719}, issn = {1549-5469}, support = {K99 GM129411/GM/NIGMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromatin/*chemistry/*genetics ; Drosophila/*classification/*genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Female ; Genome, Insect/*genetics ; Genomics ; Male ; }, abstract = {Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.}, }
@article {pmid33545030, year = {2021}, author = {McArthur, E and Capra, JA}, title = {Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.}, journal = {American journal of human genetics}, volume = {108}, number = {2}, pages = {269-283}, pmid = {33545030}, issn = {1537-6605}, support = {F30 HG011200/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; }, mesh = {Cells, Cultured ; *Chromatin ; Embryonic Stem Cells ; *Evolution, Molecular ; Gene Expression Regulation ; *Genetic Variation ; *Genome, Human ; Genome-Wide Association Study ; Humans ; *Multifactorial Inheritance ; }, abstract = {Topologically associating domains (TADs) are fundamental units of three-dimensional (3D) nuclear organization. The regions bordering TADs-TAD boundaries-contribute to the regulation of gene expression by restricting interactions of cis-regulatory sequences to their target genes. TAD and TAD-boundary disruption have been implicated in rare-disease pathogenesis; however, we have a limited framework for integrating TADs and their variation across cell types into the interpretation of common-trait-associated variants. Here, we investigate an attribute of 3D genome architecture-the stability of TAD boundaries across cell types-and demonstrate its relevance to understanding how genetic variation in TADs contributes to complex disease. By synthesizing TAD maps across 37 diverse cell types with 41 genome-wide association studies (GWASs), we investigate the differences in disease association and evolutionary pressure on variation in TADs versus TAD boundaries. We demonstrate that genetic variation in TAD boundaries contributes more to complex-trait heritability, especially for immunologic, hematologic, and metabolic traits. We also show that TAD boundaries are more evolutionarily constrained than TADs. Next, stratifying boundaries by their stability across cell types, we find substantial variation. Compared to boundaries unique to a specific cell type, boundaries stable across cell types are further enriched for complex-trait heritability, evolutionary constraint, CTCF binding, and housekeeping genes. Thus, considering TAD boundary stability across cell types provides valuable context for understanding the genome's functional landscape and enabling variant interpretation that takes 3D structure into account.}, }
@article {pmid33542322, year = {2021}, author = {Halsall, JA and Andrews, S and Krueger, F and Rutledge, CE and Ficz, G and Reik, W and Turner, BM}, title = {Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3009}, pmid = {33542322}, issn = {2045-2322}, support = {C1015/A13794/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Acetylation ; Cell Cycle ; Chromatin/genetics ; Chromosomes/*genetics ; *Epigenesis, Genetic ; HeLa Cells ; Histone Code/*genetics ; Histones/genetics ; Humans ; Lysine ; Methylation ; Mitosis/genetics ; Nucleosomes/genetics ; Protein Processing, Post-Translational/*genetics ; }, abstract = {Chromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10-50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1-5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.}, }
@article {pmid33526923, year = {2021}, author = {Laffleur, B and Lim, J and Zhang, W and Chen, Y and Pefanis, E and Bizarro, J and Batista, CR and Wu, L and Economides, AN and Wang, J and Basu, U}, title = {Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells.}, journal = {Nature genetics}, volume = {53}, number = {2}, pages = {230-242}, pmid = {33526923}, issn = {1546-1718}, support = {P30 CA013696/CA/NCI NIH HHS/United States ; R01 AI099195/AI/NIAID NIH HHS/United States ; R01 AI134988/AI/NIAID NIH HHS/United States ; R01 AI143897/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; B-Lymphocytes/drug effects/*physiology ; CCCTC-Binding Factor/genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Embryonic Stem Cells/physiology ; Exosome Multienzyme Ribonuclease Complex/*genetics/metabolism ; Exosomes/genetics ; Green Fluorescent Proteins/genetics ; Mice, Knockout ; Mice, Transgenic ; Mutation ; RNA Processing, Post-Transcriptional ; RNA, Untranslated/*genetics ; Recombination, Genetic ; Somatic Hypermutation, Immunoglobulin/*physiology ; Tamoxifen/pharmacology ; }, abstract = {Noncoding RNAs are exquisitely titrated by the cellular RNA surveillance machinery for regulating diverse biological processes. The RNA exosome, the predominant 3' RNA exoribonuclease in mammalian cells, is composed of nine core and two catalytic subunits. Here, we developed a mouse model with a conditional allele to study the RNA exosome catalytic subunit DIS3. In DIS3-deficient B cells, integrity of the immunoglobulin heavy chain (Igh) locus in its topologically associating domain is affected, with accumulation of DNA-associated RNAs flanking CTCF-binding elements, decreased CTCF binding to CTCF-binding elements and disorganized cohesin localization. DIS3-deficient B cells also accumulate activation-induced cytidine deaminase-mediated asymmetric nicks, altering somatic hypermutation patterns and increasing microhomology-mediated end-joining DNA repair. Altered mutation patterns and Igh architectural defects in DIS3-deficient B cells lead to decreased class-switch recombination but increased chromosomal translocations. Our observations of DIS3-mediated architectural regulation at the Igh locus are reflected genome wide, thus providing evidence that noncoding RNA processing is an important mechanism for controlling genome organization.}, }
@article {pmid33523102, year = {2021}, author = {Franzini, S and Di Stefano, M and Micheletti, C}, title = {essHi-C: Essential component analysis of Hi-C matrices.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btab062}, pmid = {33523102}, issn = {1367-4811}, abstract = {MOTIVATION: Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C assays reflects in an inherent stochastic background of the interactions matrices, which inevitably convolve the features of interest with largely non-specific ones.<br><br>RESULTS: Here we introduce and discuss essHi-C, a method to isolate the specific, or essential component of Hi-C matrices from the non-specific portion of the spectrum that is compatible with random matrices. Systematic comparisons show that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth of topologically associating domains identification, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices.<br><br>AVAILABILITY: The essHi-C software package is available at: https://github.com/stefanofranzini/essHIC .<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid33512425, year = {2021}, author = {Qi, Q and Cheng, L and Tang, X and He, Y and Li, Y and Yee, T and Shrestha, D and Feng, R and Xu, P and Zhou, X and Pruett-Miller, S and Hardison, RC and Weiss, MJ and Cheng, Y}, title = {Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis.}, journal = {Blood}, volume = {137}, number = {10}, pages = {1327-1339}, pmid = {33512425}, issn = {1528-0020}, support = {R24 DK106766/DK/NIDDK NIH HHS/United States ; R35 GM133614/GM/NIGMS NIH HHS/United States ; R56 DK065806/DK/NIDDK NIH HHS/United States ; }, mesh = {Binding Sites ; CCCTC-Binding Factor/*metabolism ; Cell Line ; Cells, Cultured ; Enhancer Elements, Genetic ; Erythroid Cells/cytology/metabolism ; *Erythropoiesis ; Humans ; Promoter Regions, Genetic ; Protein Binding ; RNA-Binding Proteins/genetics/metabolism ; *Regulatory Elements, Transcriptional ; Transcriptional Activation ; }, abstract = {While constitutive CCCTC-binding factor (CTCF)-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell-type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell-type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single-nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR-Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell-type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell-type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.}, }
@article {pmid33508230, year = {2021}, author = {Luo, X and Liu, Y and Dang, D and Hu, T and Hou, Y and Meng, X and Zhang, F and Li, T and Wang, C and Li, M and Wu, H and Shen, Q and Hu, Y and Zeng, X and He, X and Yan, L and Zhang, S and Li, C and Su, B}, title = {3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis.}, journal = {Cell}, volume = {184}, number = {3}, pages = {723-740.e21}, doi = {10.1016/j.cell.2021.01.001}, pmid = {33508230}, issn = {1097-4172}, mesh = {Animals ; Base Sequence ; Brain/*embryology ; Chromatin/metabolism ; DNA Transposable Elements/genetics ; Enhancer Elements, Genetic/genetics ; *Evolution, Molecular ; Fetus/*embryology ; Gene Expression Regulation, Developmental ; *Genome ; Humans ; Macaca mulatta ; Mice ; Organogenesis/*genetics ; Species Specificity ; Synteny/genetics ; Transcription Factors/metabolism ; }, abstract = {Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque, and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. The human-specific loops are significantly enriched in enhancer-enhancer interactions, and the regulated genes show human-specific expression changes in the subplate, a transient zone of the developing brain critical for neural circuit formation and plasticity. Notably, many human-specific sequence changes are located in the human-specific TAD boundaries and loop anchors, which may generate new transcription factor binding sites and chromatin structures in human. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of brain development and evolution.}, }
@article {pmid33497970, year = {2021}, author = {Cavalheiro, GR and Pollex, T and Furlong, EE}, title = {To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?.}, journal = {Current opinion in genetics &amp; development}, volume = {67}, number = {}, pages = {119-129}, doi = {10.1016/j.gde.2020.12.015}, pmid = {33497970}, issn = {1879-0380}, mesh = {Animals ; Chromatin/genetics/*ultrastructure ; Chromatin Assembly and Disassembly/genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation/genetics ; Genome/*genetics ; Humans ; }, abstract = {The past decade has seen a huge jump in the resolution and scale at which we can interrogate the three-dimensional properties of the genome. This revealed different types of chromatin structures including topologically associating domains, partitioning genes and their enhancers into interacting domains. While the visualisation of these topologies and their dynamics has dramatically improved, our understanding of their underlying mechanisms and functional roles in gene expression has lagged behind. A suite of recent studies have addressed this using genetic manipulations to perturb topological features and loops at different scales. Here we assess the new biological insights gained on the functional relationship between genome topology and gene expression, with a particular focus on enhancer function.}, }
@article {pmid33497014, year = {2021}, author = {Beccari, L and Jaquier, G and Lopez-Delisle, L and Rodriguez-Carballo, E and Mascrez, B and Gitto, S and Woltering, J and Duboule, D}, title = {Dbx2 regulation in limbs suggests interTAD sharing of enhancers.}, journal = {Developmental dynamics : an official publication of the American Association of Anatomists}, volume = {250}, number = {9}, pages = {1280-1299}, pmid = {33497014}, issn = {1097-0177}, mesh = {Animals ; Extremities ; *Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Homeodomain Proteins/genetics/metabolism ; Limb Buds/metabolism ; Mammals/genetics/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopod, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction.<br><br>RESULTS: We show that HOX13 proteins bind to mammalian-specific sequences at the vicinity of the Dbx2 locus that have enhancer activity in developing digits. However, the functional inactivation of the DBX2 protein did not elicit any particular phenotype related to Hox genes inactivation in digits, suggesting either redundant or compensatory mechanisms. We report that the neighboring Nell2 and Ano6 genes are also expressed in distal limb buds and are in part controlled by the same Dbx2 enhancers despite being localized into two different topologically associating domains (TADs) flanking the Dbx2 locus.<br><br>CONCLUSIONS: We conclude that Hoxa13 and Hoxd genes cooperatively activate Dbx2 expression in developing digits through binding to mammalian specific regulatory sequences in the Dbx2 neighborhood. Furthermore, these enhancers can overcome TAD boundaries in either direction to co-regulate a set of genes located in distinct chromatin domains.}, }
@article {pmid33494803, year = {2021}, author = {Zhang, YW and Wang, MB and Li, SC}, title = {SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {45}, pmid = {33494803}, issn = {1474-760X}, mesh = {Algorithms ; Animals ; Cell Line ; Chromatin ; Epigenomics ; Gene Expression Regulation ; *Histone Code ; Histones ; Humans ; Software ; }, abstract = {Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.}, }
@article {pmid33479238, year = {2021}, author = {Madani Tonekaboni, SA and Haibe-Kains, B and Lupien, M}, title = {Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {499}, pmid = {33479238}, issn = {2041-1723}, support = {136963//CIHR/Canada ; 363288//CIHR/Canada ; }, mesh = {Animals ; Binding Sites/genetics ; Cell Differentiation/*genetics ; Chromatin/*genetics ; DNA Transposable Elements/genetics ; Enhancer Elements, Genetic/genetics ; Genome, Human/genetics ; Histone Code/*genetics ; Histones/*genetics ; Humans ; Lysine/*genetics ; Promoter Regions, Genetic/genetics ; }, abstract = {The human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating control elements and cis-regulatory elements, such as promoters, enhancers, and anchors of chromatin interactions. Uneven distribution of these features within chromosomes gives rise to clusters, such as topologically associating domains (TADs), lamina-associated domains, clusters of cis-regulatory elements or large organized chromatin lysine (K) domains (LOCKs). Here we show that LOCKs from diverse histone modifications discriminate primitive from differentiated cell types. Active LOCKs (H3K4me1, H3K4me3 and H3K27ac) cover a higher fraction of the genome in primitive compared to differentiated cell types while repressive LOCKs (H3K9me3, H3K27me3 and H3K36me3) do not. Active LOCKs in differentiated cells lie proximal to highly expressed genes while active LOCKs in primitive cells tend to be bivalent. Genes proximal to bivalent LOCKs are minimally expressed in primitive cells. Furthermore, bivalent LOCKs populate TAD boundaries and are preferentially bound by regulators of chromatin interactions, including CTCF, RAD21 and ZNF143. Together, our results argue that LOCKs discriminate primitive from differentiated cell populations.}, }
@article {pmid33456975, year = {2020}, author = {Melnikova, LS and Georgiev, PG and Golovnin, AK}, title = {The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes.}, journal = {Acta naturae}, volume = {12}, number = {4}, pages = {15-33}, pmid = {33456975}, issn = {2075-8251}, abstract = {The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of Drosophila and mammals, and it also briefly characterizes the proteins responsible for their functional activity. It was initially believed that the main properties of insulators are blocking of enhancers and the formation of independent transcription domains. We present experimental data proving that the chromatin loops formed by insulators play only an auxiliary role in enhancer blocking. The review also discusses the mechanisms involved in the formation of topologically associating domains and their role in the formation of the chromosomal architecture and regulation of gene transcription.}, }
@article {pmid33436846, year = {2021}, author = {Bediaga, NG and Coughlan, HD and Johanson, TM and Garnham, AL and Naselli, G and Schröder, J and Fearnley, LG and Bandala-Sanchez, E and Allan, RS and Smyth, GK and Harrison, LC}, title = {Multi-level remodelling of chromatin underlying activation of human T cells.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {528}, pmid = {33436846}, issn = {2045-2322}, mesh = {CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; Cells, Cultured ; Chromatin/*chemistry/*genetics ; Chromatin Assembly and Disassembly/*genetics/*physiology ; Gene Expression Regulation, Developmental/*genetics ; Humans ; Lymphocyte Activation/*genetics ; Male ; Nucleosomes/genetics ; T-Lymphocytes/*immunology ; Transcription Factors ; Transcription, Genetic/genetics ; }, abstract = {Remodelling of chromatin architecture is known to regulate gene expression and has been well characterized in cell lineage development but less so in response to cell perturbation. Activation of T cells, which triggers extensive changes in transcriptional programs, serves as an instructive model to elucidate how changes in chromatin architecture orchestrate gene expression in response to cell perturbation. To characterize coordinate changes at different levels of chromatin architecture, we analyzed chromatin accessibility, chromosome conformation and gene expression in activated human T cells. T cell activation was characterized by widespread changes in chromatin accessibility and interactions that were shared between activated CD4[+] and CD8[+] T cells, and with the formation of active regulatory regions associated with transcription factors relevant to T cell biology. Chromatin interactions that increased and decreased were coupled, respectively, with up- and down-regulation of corresponding target genes. Furthermore, activation was associated with disruption of long-range chromatin interactions and with partitioning of topologically associating domains (TADs) and remodelling of their TAD boundaries. Newly formed/strengthened TAD boundaries were associated with higher nucleosome occupancy and lower accessibility, linking changes in lower and higher order chromatin architecture. T cell activation exemplifies coordinate multi-level remodelling of chromatin underlying gene transcription.}, }
@article {pmid33436383, year = {2021}, author = {Ha, E and Bang, SY and Lim, J and Yun, JH and Kim, JM and Bae, JB and Lee, HS and Kim, BJ and Kim, K and Bae, SC}, title = {Genetic variants shape rheumatoid arthritis-specific transcriptomic features in CD4[+] T cells through differential DNA methylation, explaining a substantial proportion of heritability.}, journal = {Annals of the rheumatic diseases}, volume = {80}, number = {7}, pages = {876-883}, doi = {10.1136/annrheumdis-2020-219152}, pmid = {33436383}, issn = {1468-2060}, mesh = {Adult ; Aged ; Arthritis, Rheumatoid/*genetics/*immunology ; CD4-Positive T-Lymphocytes/*immunology ; DNA Methylation/*genetics/*immunology ; Female ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Male ; Middle Aged ; Transcriptome ; }, abstract = {OBJECTIVE: CD4[+] T cells have been suggested as the most disease-relevant cell type in rheumatoid arthritis (RA) in which RA-risk non-coding variants exhibit allele-specific effects on regulation of RA-driving genes. This study aimed to understand RA-specific signatures in CD4[+] T cells using multi-omics data, interpreting inter-omics relationships in shaping the RA transcriptomic landscape.<br><br>METHODS: We profiled genome-wide variants, gene expression and DNA methylation in CD4[+] T cells from 82 patients with RA and 40 healthy controls using high-throughput technologies. We investigated differentially expressed genes (DEGs) and differential methylated regions (DMRs) in RA and localised quantitative trait loci (QTLs) for expression and methylation. We then integrated these based on individual-level correlations to inspect DEG-regulating sources and investigated the potential regulatory roles of RA-risk variants by a partitioned-heritability enrichment analysis with RA genome-wide association summary statistics.<br><br>RESULTS: A large number of RA-specific DEGs were identified (n=2575), highlighting T cell differentiation and activation pathways. RA-specific DMRs, preferentially located in T cell regulatory regions, were correlated with the expression levels of 548 DEGs mostly in the same topologically associating domains. In addition, expressional variances in 771 and 83 DEGs were partially explained by expression QTLs for DEGs and methylation QTLs (meQTLs) for DEG-correlated DMRs, respectively. A large number of RA variants were moderately to strongly correlated with meQTLs. DEG-correlated DMRs, enriched with meQTLs, had strongly enriched heritability of RA.<br><br>CONCLUSION: Our findings revealed that the methylomic changes, driven by RA heritability-explaining variants, shape the differential expression of a substantial fraction of DEGs in CD4[+] T cells in patients with RA, reinforcing the importance of a multidimensional approach in disease-relevant tissues.}, }
@article {pmid33422934, year = {2021}, author = {Peters, JM}, title = {How DNA loop extrusion mediated by cohesin enables V(D)J recombination.}, journal = {Current opinion in cell biology}, volume = {70}, number = {}, pages = {75-83}, doi = {10.1016/j.ceb.2020.11.007}, pmid = {33422934}, issn = {1879-0410}, mesh = {Animals ; *Cell Cycle Proteins/genetics ; Chromatin ; *Chromosomal Proteins, Non-Histone/genetics ; Mice ; *V(D)J Recombination ; }, abstract = {'Structural maintenance of chromosomes' (SMC) complexes are required for the folding of genomic DNA into loops. Theoretical considerations and single-molecule experiments performed with the SMC complexes cohesin and condensin indicate that DNA folding occurs via loop extrusion. Recent work indicates that this process is essential for the assembly of antigen receptor genes by V(D)J recombination in developing B and T cells of the vertebrate immune system. Here, I review how recent studies of the mouse immunoglobulin heavy chain locus Igh have provided evidence for this hypothesis and how the formation of chromatin loops by cohesin and regulation of this process by CTCF and Wapl might ensure that all variable gene segments in this locus (VH segments) participate in recombination with a re-arranged DJH segment, to ensure generation of a maximally diverse repertoire of B-cell receptors and antibodies.}, }
@article {pmid33420075, year = {2021}, author = {Sun, Q and Perez-Rathke, A and Czajkowsky, DM and Shao, Z and Liang, J}, title = {High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {205}, pmid = {33420075}, issn = {2041-1723}, support = {R35 GM127084/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biophysics ; Chromatin/*chemistry ; *Chromatin Assembly and Disassembly ; Chromosomes, Insect/chemistry/genetics ; Computational Biology ; Drosophila/*genetics ; *Embryonic Development ; Genetic Heterogeneity ; Genome ; Models, Molecular ; Molecular Conformation ; }, abstract = {Single-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5-6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.}, }
@article {pmid33419466, year = {2021}, author = {Jia, J and Xie, Y and Cheng, J and Kong, C and Wang, M and Gao, L and Zhao, F and Guo, J and Wang, K and Li, G and Cui, D and Hu, T and Zhao, G and Wang, D and Ru, Z and Zhang, Y}, title = {Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {26}, pmid = {33419466}, issn = {1474-760X}, mesh = {China ; Chromatin ; *Chromosomes, Plant ; DNA Transposable Elements ; Evolution, Molecular ; Genes, Plant/genetics ; *Genome, Plant ; Plant Breeding ; *Polyploidy ; Translocation, Genetic ; Triticum/*genetics ; }, abstract = {BACKGROUND: Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown.<br><br>RESULTS: We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China&#xa0;carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity.<br><br>CONCLUSIONS: The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.}, }
@article {pmid33414725, year = {2020}, author = {Russo, R and Marra, R and Rosato, BE and Iolascon, A and Andolfo, I}, title = {Genetics and Genomics Approaches for Diagnosis and Research Into Hereditary Anemias.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {613559}, pmid = {33414725}, issn = {1664-042X}, abstract = {The hereditary anemias are a relatively heterogeneous set of disorders that can show wide clinical and genetic heterogeneity, which often hampers correct clinical diagnosis. The classical diagnostic workflow for these conditions generally used to start with analysis of the family and personal histories, followed by biochemical and morphological evaluations, and ending with genetic testing. However, the diagnostic framework has changed more recently, and genetic testing is now a suitable approach for differential diagnosis of these patients. There are several approaches to this genetic testing, the choice of which depends on phenotyping, genetic heterogeneity, and gene size. For patients who show complete phenotyping, single-gene testing remains recommended. However, genetic analysis now includes next-generation sequencing, which is generally based on custom-designed targeting panels and whole-exome sequencing. The use of next-generation sequencing also allows the identification of new causative genes, and of polygenic conditions and genetic factors that modify disease severity of hereditary anemias. In the research field, whole-genome sequencing is useful for the identification of non-coding causative mutations, which might account for the disruption of transcriptional factor occupancy sites and cis-regulatory elements. Moreover, advances in high-throughput sequencing techniques have now resulted in the identification of genome-wide profiling of the chromatin structures known as the topologically associating domains. These represent a recurrent disease mechanism that exposes genes to inappropriate regulatory elements, causing errors in gene expression. This review focuses on the challenges of diagnosis and research into hereditary anemias, with indications of both the advantages and disadvantages. Finally, we consider the future perspectives for the use of next-generation sequencing technologies in this era of precision medicine.}, }
@article {pmid33407087, year = {2021}, author = {Deschamps, S and Crow, JA and Chaidir, N and Peterson-Burch, B and Kumar, S and Lin, H and Zastrow-Hayes, G and May, GD}, title = {Chromatin loop anchors contain core structural components of the gene expression machinery in maize.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {23}, pmid = {33407087}, issn = {1471-2164}, mesh = {*Chromatin/genetics ; Chromatin Assembly and Disassembly ; Gene Expression ; Genome, Plant ; *Zea mays/genetics ; }, abstract = {BACKGROUND: Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity.<br><br>RESULTS: Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that <&#x2009;7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions.<br><br>CONCLUSIONS: Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.}, }
@article {pmid33398174, year = {2021}, author = {Kubo, N and Ishii, H and Xiong, X and Bianco, S and Meitinger, F and Hu, R and Hocker, JD and Conte, M and Gorkin, D and Yu, M and Li, B and Dixon, JR and Hu, M and Nicodemi, M and Zhao, H and Ren, B}, title = {Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.}, journal = {Nature structural &amp; molecular biology}, volume = {28}, number = {2}, pages = {152-161}, pmid = {33398174}, issn = {1545-9985}, support = {U54 DK107977/DK/NIDDK NIH HHS/United States ; T32 GM008666/GM/NIGMS NIH HHS/United States ; U54 DK107965/DK/NIDDK NIH HHS/United States ; UM1 HG011585/HG/NHGRI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; CCCTC-Binding Factor/*metabolism ; Cell Line ; Chromatin/*metabolism ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Mice ; Mouse Embryonic Stem Cells/cytology/*metabolism ; Neural Stem Cells/cytology/*metabolism ; Promoter Regions, Genetic ; Protein Binding ; Transcriptional Activation ; }, abstract = {The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.}, }
@article {pmid33397980, year = {2021}, author = {Ulianov, SV and Zakharova, VV and Galitsyna, AA and Kos, PI and Polovnikov, KE and Flyamer, IM and Mikhaleva, EA and Khrameeva, EE and Germini, D and Logacheva, MD and Gavrilov, AA and Gorsky, AS and Nechaev, SK and Gelfand, MS and Vassetzky, YS and Chertovich, AV and Shevelyov, YY and Razin, SV}, title = {Order and stochasticity in the folding of individual Drosophila genomes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {41}, pmid = {33397980}, issn = {2041-1723}, mesh = {Animals ; Biopolymers/metabolism ; Chromatin/genetics ; Databases, Genetic ; Drosophila melanogaster/*genetics ; Epigenesis, Genetic ; *Genome, Insect ; Haploidy ; Models, Genetic ; *Nucleic Acid Conformation ; Stochastic Processes ; X Chromosome/genetics ; }, abstract = {Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.}, }
@article {pmid33396256, year = {2020}, author = {Decker, B and Liput, M and Abdellatif, H and Yergeau, D and Bae, Y and Jornet, JM and Stachowiak, EK and Stachowiak, MK}, title = {Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1-The Genome Archipelago Model.}, journal = {International journal of molecular sciences}, volume = {22}, number = {1}, pages = {}, pmid = {33396256}, issn = {1422-0067}, mesh = {Animals ; CCCTC-Binding Factor/genetics/*metabolism ; Cell Differentiation ; Cell Nucleus/*genetics ; Chromatin/genetics/*metabolism ; Chromosomes/genetics ; Embryonic Stem Cells/*cytology/metabolism ; *Genome ; Mice ; Molecular Conformation ; *Neurogenesis ; Receptor, Fibroblast Growth Factor, Type 1/genetics/*metabolism ; }, abstract = {During the development of mouse embryonic stem cells (ESC) to neuronal committed cells (NCC), coordinated changes in the expression of 2851 genes take place, mediated by the nuclear form of FGFR1. In this paper, widespread differences are demonstrated in the ESC and NCC inter- and intra-chromosomal interactions, chromatin looping, the formation of CTCF- and nFGFR1-linked Topologically Associating Domains (TADs) on a genome-wide scale and in exemplary HoxA-D loci. The analysis centered on HoxA cluster shows that blocking FGFR1 disrupts the loop formation. FGFR1 binding and genome locales are predictive of the genome interactions; likewise, chromatin interactions along with nFGFR1 binding are predictive of the genome function and correlate with genome regulatory attributes and gene expression. This study advances a topologically integrated genome archipelago model that undergoes structural transformations through the formation of nFGFR1-associated TADs. The makeover of the TAD islands serves to recruit distinct ontogenic programs during the development of the ESC to NCC.}, }
@article {pmid33382983, year = {2021}, author = {Takemata, N and Bell, SD}, title = {Multi-scale architecture of archaeal chromosomes.}, journal = {Molecular cell}, volume = {81}, number = {3}, pages = {473-487.e6}, pmid = {33382983}, issn = {1097-4164}, support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Compartmentation ; Chromatin/*genetics ; Chromatin Assembly and Disassembly ; *Chromosomes, Archaeal ; DNA, Archaeal/*genetics ; Gene Expression Regulation, Archaeal ; Nucleotide Motifs ; Ribosomes/genetics/metabolism ; Sulfolobus acidocaldarius/*genetics/metabolism ; Sulfolobus solfataricus/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. We reveal that chromosomes of Sulfolobus archaea are organized into CID-like topological domains in addition to previously described larger A/B compartment-type structures. We uncover local rules governing the identity of the topological domains and their boundaries. We also identify long-range loop structures and provide evidence of a hub-like structure that colocalizes genes involved in ribosome biogenesis. In addition to providing high-resolution descriptions of archaeal chromosome architectures, our data provide evidence of multiple modes of organization in prokaryotic chromosomes and yield insights into the evolution of eukaryotic chromosome conformation.}, }
@article {pmid33360765, year = {2021}, author = {Rullens, PMJ and Kind, J}, title = {Attach and stretch: Emerging roles for genome-lamina contacts in shaping the 3D genome.}, journal = {Current opinion in cell biology}, volume = {70}, number = {}, pages = {51-57}, doi = {10.1016/j.ceb.2020.11.006}, pmid = {33360765}, issn = {1879-0410}, mesh = {Animals ; Cell Nucleus ; Chromatin ; *Genome ; Intermediate Filaments ; Nuclear Envelope ; *Nuclear Lamina ; }, abstract = {A large proportion of the metazoan genome is spatially segregated at the nuclear periphery through genomic contacts with the nuclear lamina, a thin meshwork of lamin filaments that lines the inner-nuclear membrane. Lamina-associated domains are believed to contribute to the regulation of gene transcription and to provide structural three-dimensional support to the organization of the genome in A and B compartments and topologically associating domains. In this review, we will evaluate recent work addressing the role of lamina-associated domains in three-dimensional genome organization and propose experimental frameworks that may expand our understanding of their interdependence.}, }
@article {pmid33334380, year = {2020}, author = {Kruse, K and Hug, CB and Vaquerizas, JM}, title = {FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {303}, pmid = {33334380}, issn = {1474-760X}, support = {MC_UP_1605/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Chromatin ; Chromosomes/*chemistry ; Computational Biology ; Embryonic Stem Cells ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; *Molecular Conformation ; }, abstract = {Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data (https://github.com/vaquerizaslab/fanc). Due to its compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.}, }
@article {pmid33284803, year = {2020}, author = {Torosin, NS and Anand, A and Golla, TR and Cao, W and Ellison, CE}, title = {3D genome evolution and reorganization in the Drosophila melanogaster species group.}, journal = {PLoS genetics}, volume = {16}, number = {12}, pages = {e1009229}, pmid = {33284803}, issn = {1553-7404}, support = {R01 GM130698/GM/NIGMS NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; }, mesh = {Animals ; Chromatin/*genetics ; *Chromatin Assembly and Disassembly ; Chromosomes, Insect/*genetics ; Conserved Sequence ; Drosophila melanogaster ; *Evolution, Molecular ; Gene Rearrangement ; *Genome, Insect ; Transcription, Genetic ; }, abstract = {Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts and there is evidence that deletion of TAD boundaries leads to aberrant expression of neighboring genes. While the mechanisms of TAD formation have been well-studied, current knowledge on the patterns of TAD evolution across species is limited. Due to the integral role TADs play in gene regulation, their structure and organization is expected to be conserved during evolution. However, more recent research suggests that TAD structures diverge relatively rapidly. We use Hi-C chromosome conformation capture to measure evolutionary conservation of whole TADs and TAD boundary elements between D. melanogaster and D. triauraria, two early-branching species from the melanogaster species group which diverged ∼15 million years ago. We find that the majority of TADs have been reorganized since the common ancestor of D. melanogaster and D. triauraria, via a combination of chromosomal rearrangements and gain/loss of TAD boundaries. TAD reorganization between these two species is associated with a localized effect on gene expression, near the site of disruption. By separating TADs into subtypes based on their chromatin state, we find that different subtypes are evolving under different evolutionary forces. TADs enriched for broadly expressed, transcriptionally active genes are evolving rapidly, potentially due to positive selection, whereas TADs enriched for developmentally-regulated genes remain conserved, presumably due to their importance in restricting gene-regulatory element interactions. These results provide novel insight into the evolutionary dynamics of TADs and help to reconcile contradictory reports related to the evolutionary conservation of TADs and whether changes in TAD structure affect gene expression.}, }
@article {pmid33273453, year = {2020}, author = {Guerrero-Martínez, JA and Ceballos-Chávez, M and Koehler, F and Peiró, S and Reyes, JC}, title = {TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6196}, pmid = {33273453}, issn = {2041-1723}, mesh = {Animals ; Chromatin/*metabolism ; *Enhancer Elements, Genetic ; Gene Expression Regulation ; Genome ; HEK293 Cells ; Humans ; MCF-7 Cells ; Mice ; Multigene Family ; RNA, Messenger/genetics/metabolism ; Transforming Growth Factor beta/*metabolism ; }, abstract = {The Transforming Growth Factor-β (TGFβ) signaling pathway controls transcription by regulating enhancer activity. How TGFβ-regulated enhancers are selected and what chromatin changes are associated with TGFβ-dependent enhancers regulation are still unclear. Here we report that TGFβ treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGFβ. This enhancer opening depends on both the canonical and non-canonical TGFβ pathways. Most TGFβ-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGFβ regulatory domains (TRD). CRISPR-mediated inactivation of enhancers within TRDs impairs TGFβ-dependent regulation of all co-regulated genes, demonstrating that enhancer targeting is more promiscuous than previously anticipated. The area of TRD influence is restricted by topologically associating domains (TADs) borders, causing a bias towards co-regulation within TADs.}, }
@article {pmid33268790, year = {2020}, author = {Sanders, JT and Freeman, TF and Xu, Y and Golloshi, R and Stallard, MA and Hill, AM and San Martin, R and Balajee, AS and McCord, RP}, title = {Radiation-induced DNA damage and repair effects on 3D genome organization.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6178}, pmid = {33268790}, issn = {2041-1723}, support = {R35 GM133557/GM/NIGMS NIH HHS/United States ; }, mesh = {Ataxia Telangiectasia/genetics/metabolism/pathology ; Ataxia Telangiectasia Mutated Proteins/deficiency/*genetics ; Cell Cycle/genetics/*radiation effects ; Cell Line ; DNA/*genetics/metabolism ; DNA Damage ; *DNA Repair ; Fibroblasts/metabolism/pathology/radiation effects ; Gene Expression ; Genome, Human/*radiation effects ; High-Throughput Nucleotide Sequencing ; Histones/genetics/metabolism ; Humans ; Lymphocytes/metabolism/pathology/radiation effects ; Organ Specificity ; X-Rays ; }, abstract = {The three-dimensional structure of chromosomes plays an important role in gene expression regulation and also influences the repair of radiation-induced DNA damage. Genomic aberrations that disrupt chromosome spatial domains can lead to diseases including cancer, but how the 3D genome structure responds to DNA damage is poorly understood. Here, we investigate the impact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells and ataxia telangiectasia mutated (ATM) patient cells. We irradiate fibroblasts, lymphoblasts, and ATM-deficient fibroblasts with 5 Gy X-rays and perform Hi-C at 30 minutes, 24 hours, or 5 days after irradiation. We observe that 3D genome changes after irradiation are cell type-specific, with lymphoblastoid cells generally showing more contact changes than irradiated fibroblasts. However, all tested repair-proficient cell types exhibit an increased segregation of topologically associating domains (TADs). This TAD boundary strengthening after irradiation is not observed in ATM deficient fibroblasts and may indicate the presence of a mechanism to protect 3D genome structure integrity during DNA damage repair.}, }
@article {pmid33239788, year = {2020}, author = {Yang, H and Luan, Y and Liu, T and Lee, HJ and Fang, L and Wang, Y and Wang, X and Zhang, B and Jin, Q and Ang, KC and Xing, X and Wang, J and Xu, J and Song, F and Sriranga, I and Khunsriraksakul, C and Salameh, T and Li, D and Choudhary, MNK and Topczewski, J and Wang, K and Gerhard, GS and Hardison, RC and Wang, T and Cheng, KC and Yue, F}, title = {A map of cis-regulatory elements and 3D genome structures in zebrafish.}, journal = {Nature}, volume = {588}, number = {7837}, pages = {337-343}, pmid = {33239788}, issn = {1476-4687}, support = {U01 HG009391/HG/NHGRI NIH HHS/United States ; R01 HG009906/HG/NHGRI NIH HHS/United States ; R01 HG007175/HG/NHGRI NIH HHS/United States ; R01 DK107735/DK/NIDDK NIH HHS/United States ; U01 CA200060/CA/NCI NIH HHS/United States ; R01 ES024992/ES/NIEHS NIH HHS/United States ; R24 DK106766/DK/NIDDK NIH HHS/United States ; R25 DA027995/DA/NIDA NIH HHS/United States ; U24 ES026699/ES/NIEHS NIH HHS/United States ; R35 GM124820/GM/NIGMS NIH HHS/United States ; R01 HG007354/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Brain/metabolism ; Conserved Sequence/genetics ; DNA Methylation ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic ; Evolution, Molecular ; Female ; Gene Expression Profiling ; Gene Regulatory Networks/genetics ; Genome/*genetics ; Heterochromatin/chemistry/genetics/metabolism ; Humans ; *Imaging, Three-Dimensional ; Male ; Mice ; *Molecular Imaging ; Organ Specificity ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Single-Cell Analysis ; Species Specificity ; Zebrafish/*genetics ; }, abstract = {The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species[1]. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.}, }
@article {pmid33229569, year = {2020}, author = {Rodríguez-Carballo, E and Lopez-Delisle, L and Willemin, A and Beccari, L and Gitto, S and Mascrez, B and Duboule, D}, title = {Chromatin topology and the timing of enhancer function at the HoxD locus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {49}, pages = {31231-31241}, pmid = {33229569}, issn = {1091-6490}, mesh = {Animals ; CCCTC-Binding Factor/*genetics ; Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; Embryonic Development/*genetics ; Enhancer Elements, Genetic/*genetics ; Extremities/growth &amp; development ; Gene Expression Regulation, Developmental/genetics ; Genes, Homeobox/*genetics ; Limb Buds/growth &amp; development ; Mice ; }, abstract = {The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.}, }
@article {pmid33203573, year = {2021}, author = {Eres, IE and Gilad, Y}, title = {A TAD Skeptic: Is 3D Genome Topology Conserved?.}, journal = {Trends in genetics : TIG}, volume = {37}, number = {3}, pages = {216-223}, pmid = {33203573}, issn = {0168-9525}, support = {R35 GM131726/GM/NIGMS NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; Conserved Sequence/*genetics ; *Evolution, Molecular ; Genome, Human/genetics ; Genomics ; Humans ; Protein Domains/*genetics ; }, abstract = {The notion that topologically associating domains (TADs) are highly conserved across species is prevalent in the field of 3D genomics. However, what exactly is meant by 'highly conserved' and what are the actual comparative data that support this notion? To address these questions, we performed a historical review of the relevant literature and retraced numerous citation chains to reveal the primary data that were used as the basis for the widely accepted conclusion that TADs are highly conserved across evolution. A thorough review of the available evidence suggests the answer may be more complex than what is commonly presented.}, }
@article {pmid33182325, year = {2020}, author = {Ehrlich, KC and Baribault, C and Ehrlich, M}, title = {Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33182325}, issn = {1422-0067}, support = {NS04885/NH/NIH HHS/United States ; }, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Adult ; Aged ; Brain/*metabolism ; Cells, Cultured ; Child, Preschool ; Chromatin/genetics ; DNA Methylation/genetics ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/*genetics ; Epigenomics/methods ; Exons/genetics ; Female ; Gene Expression Regulation/genetics ; Humans ; Male ; Middle Aged ; Muscle Proteins/*genetics ; Muscle, Skeletal/*metabolism ; Promoter Regions, Genetic/genetics ; Transcription, Genetic/genetics ; Up-Regulation/genetics ; }, abstract = {KLHL and the related KBTBD genes encode components of the Cullin-E3 ubiquitin ligase complex and typically target tissue-specific proteins for degradation, thereby affecting differentiation, homeostasis, metabolism, cell signaling, and the oxidative stress response. Despite their importance in cell function and disease (especially, KLHL40, KLHL41, KBTBD13, KEAP1, and ENC1), previous studies of epigenetic factors that affect transcription were predominantly limited to promoter DNA methylation. Using diverse tissue and cell culture whole-genome profiles, we examined 17 KLHL or KBTBD genes preferentially expressed in skeletal muscle or brain to identify tissue-specific enhancer and promoter chromatin, open chromatin (DNaseI hypersensitivity), and DNA hypomethylation. Sixteen of the 17 genes displayed muscle- or brain-specific enhancer chromatin in their gene bodies, and most exhibited specific intergenic enhancer chromatin as well. Seven genes were embedded in super-enhancers (particularly strong, tissue-specific clusters of enhancers). The enhancer chromatin regions typically displayed foci of DNA hypomethylation at peaks of open chromatin. In addition, we found evidence for an intragenic enhancer in one gene upregulating expression of its neighboring gene, specifically for KLHL40/HHATL and KLHL38/FBXO32 gene pairs. Many KLHL/KBTBD genes had tissue-specific promoter chromatin at their 5' ends, but surprisingly, two (KBTBD11 and KLHL31) had constitutively unmethylated promoter chromatin in their 3' exons that overlaps a retrotransposed KLHL gene. Our findings demonstrate the importance of expanding epigenetic analyses beyond the 5' ends of genes in studies of normal and abnormal gene regulation.}, }
@article {pmid33155082, year = {2022}, author = {Chang, L and Li, M and Shao, S and Li, C and Ai, S and Xue, B and Hou, Y and Zhang, Y and Li, R and Fan, X and He, A and Li, C and Sun, Y}, title = {Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells.}, journal = {Protein &amp; cell}, volume = {13}, number = {4}, pages = {258-280}, pmid = {33155082}, issn = {1674-8018}, mesh = {*Chromatin ; Chromosomes ; Genome ; Humans ; *Lamin Type B/genetics ; }, abstract = {The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.}, }
@article {pmid33154377, year = {2020}, author = {Nora, EP and Caccianini, L and Fudenberg, G and So, K and Kameswaran, V and Nagle, A and Uebersohn, A and Hajj, B and Saux, AL and Coulon, A and Mirny, LA and Pollard, KS and Dahan, M and Bruneau, BG}, title = {Molecular basis of CTCF binding polarity in genome folding.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5612}, pmid = {33154377}, issn = {2041-1723}, support = {R01 GM114190/GM/NIGMS NIH HHS/United States ; U54 DK107980/DK/NIDDK NIH HHS/United States ; UM1 HL098179/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Animals ; Binding Sites ; CCCTC-Binding Factor/*chemistry/genetics/*metabolism ; Cell Cycle Proteins/chemistry/metabolism ; Cell Line ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/chemistry/metabolism ; Chromosomes, Mammalian/*chemistry/genetics/metabolism ; Cricetinae ; Drosophila ; Mice ; Mutation ; Nucleotide Motifs ; Protein Binding ; Structure-Activity Relationship ; }, abstract = {Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains unclear. By combining ChIP-seq and single molecule live imaging we report that CTCF positions cohesin, but does not control its overall binding dynamics on chromatin. Using an inducible complementation system, we find that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remains at CTCF sites in this mutant, albeit with reduced enrichment. Given the orientation of CTCF motifs presents the N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites translates into genome folding patterns.}, }
@article {pmid33151112, year = {2020}, author = {Kong, N and Jung, I}, title = {Long-range chromatin interactions in pathogenic gene expression control.}, journal = {Transcription}, volume = {11}, number = {5}, pages = {211-216}, pmid = {33151112}, issn = {2154-1272}, mesh = {Chromatin/chemistry/*genetics/metabolism ; Disease/*genetics ; Gene Expression ; Humans ; }, abstract = {A large number of distal cis-regulatory elements (cREs) have been annotated in the human genome, which plays a central role in orchestrating spatiotemporal gene expression. Since many cREs regulate non-adjacent genes, long-range cRE-promoter interactions are an important factor in the functional characterization of the engaged cREs. In this regard, recent studies have demonstrated that identification of long-range target genes can decipher the effect of genetic mutations residing within cREs on abnormal gene expression. In addition, investigation of altered long-range cREs-promoter interactions induced by chromosomal rearrangements has revealed their critical roles in pathogenic gene expression. In this review, we briefly discuss how the analysis of 3D chromatin structure can help us understand the functional impact of cREs harboring disease-associated genetic variants and how chromosomal rearrangements disrupting topologically associating domains can lead to pathogenic gene expression.}, }
@article {pmid33101859, year = {2020}, author = {Chu, X and Wang, J}, title = {Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {7}, number = {20}, pages = {2001572}, pmid = {33101859}, issn = {2198-3844}, abstract = {As an essential and fundamental process of life, cell development involves large-scale reorganization of the 3D genome architecture, which forms the basis of gene regulation. Here, a landscape-switching model is developed to explore the microscopic chromosomal structural origin of embryonic stem cell (ESC) differentiation and somatic cell reprogramming. It is shown that chromosome structure exhibits significant compartment-switching in the unit of topologically associating domain. It is found that the chromosome during differentiation undergoes monotonic compaction with spatial repositioning of active and inactive chromosomal loci toward the chromosome surface and interior, respectively. In contrast, an overexpanded chromosome, which exhibits universal localization of loci at the chromosomal surface with erasing the structural characteristics formed in the somatic cells, is observed during reprogramming. An early distinct differentiation pathway from the ESC to the terminally differentiated cell, giving rise to early bifurcation on the Waddington landscape for the ESC differentiation is suggested. The theoretical model herein including the non-equilibrium effects, draws a picture of the highly irreversible cell differentiation and reprogramming processes, in line with the experiments. The predictions provide a physical understanding of cell differentiation and reprogramming from the chromosomal structural and dynamical perspective and can be tested by future experiments.}, }
@article {pmid33099628, year = {2020}, author = {Li, Y and Gao, G and Lin, Y and Hu, S and Luo, Y and Wang, G and Jin, L and Wang, Q and Wang, J and Tang, Q and Li, M}, title = {Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome.}, journal = {GigaScience}, volume = {9}, number = {10}, pages = {}, pmid = {33099628}, issn = {2047-217X}, mesh = {Animals ; Chromosomes/genetics ; Female ; *Geese/genetics ; *Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; }, abstract = {BACKGROUND: The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing.<br><br>FINDINGS: We generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for &#x223c;88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions.<br><br>CONCLUSIONS: We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.}, }
@article {pmid33091336, year = {2020}, author = {Gu, B and Comerci, CJ and McCarthy, DG and Saurabh, S and Moerner, WE and Wysocka, J}, title = {Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging.}, journal = {Molecular cell}, volume = {80}, number = {4}, pages = {699-711.e7}, pmid = {33091336}, issn = {1097-4164}, support = {R35 GM118067/GM/NIGMS NIH HHS/United States ; R35 GM131757/GM/NIGMS NIH HHS/United States ; T32 GM120007/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/genetics/*metabolism ; Cell Cycle Proteins/genetics/*metabolism ; Cells, Cultured ; Chromatin/genetics/*metabolism ; Chromosomal Proteins, Non-Histone/genetics/*metabolism ; Chromosomes, Mammalian ; Embryonic Stem Cells/*cytology/metabolism ; Genetic Loci ; Genome ; Image Processing, Computer-Assisted ; Mice ; Microscopy, Fluorescence/*methods ; Proteins/genetics/*metabolism ; *Transcription, Genetic ; }, abstract = {CCCTC-binding factor (CTCF) and cohesin play critical roles in organizing mammalian genomes into topologically associating domains (TADs). Here, by combining genetic engineering with quantitative super-resolution stimulated emission depletion (STED) microscopy, we demonstrate that in living cells, CTCF forms clusters typically containing 2-8 molecules. A fraction of CTCF clusters, enriched for those with ≥3 molecules, are coupled with cohesin complexes with a characteristic physical distance suggestive of a defined molecular interaction. Acute degradation of the cohesin unloader WAPL or transcriptional inhibition (TI) result in increased CTCF clustering. Furthermore, the effect of TI on CTCF clusters is alleviated by the acute loss of the cohesin subunit SMC3. Our study provides quantitative characterization of CTCF clusters in living cells, uncovers the opposing effects of cohesin and transcription on CTCF clustering, and highlights the power of quantitative super-resolution microscopy as a tool to bridge the gap between biochemical and genomic methodologies in chromatin research.}, }
@article {pmid33090716, year = {2020}, author = {Tinker, RJ and Burghel, GJ and Garg, S and Steggall, M and Cuvertino, S and Banka, S}, title = {Haploinsufficiency of ATP6V0C possibly underlies 16p13.3 deletions that cause microcephaly, seizures, and neurodevelopmental disorder.}, journal = {American journal of medical genetics. Part A}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajmg.a.61905}, pmid = {33090716}, issn = {1552-4833}, abstract = {We recently contributed to the description of eight individuals with a novel condition caused by 16p13.3 microdeletions encompassing TBC1D24, ATP6V0C, and PDPK1 and resulting in epilepsy, microcephaly and neurodevelopmental problems. The phenotypic spectrum, the minimum overlapping region and the underlying disease mechanism for this disorder remain to be clarified. Here we report a 3.5-year-old male, with microcephaly, autism spectrum disorder and a de novo 16p13.3 microdeletion. We performed detailed in silico analysis to show that the minimum overlapping region for the condition is ~80Kb encompassing five protein coding genes. Analysis of loss of function constraint metrics, transcript-aware evaluation of the population variants, GeVIR scores, analysis of reported pathogenic point variants, detailed review of the known functions of gene products and their animal models showed that the haploinsufficiency of ATP6V0C likely underlies the phenotype of this condition. Protein-protein interaction network, gene phenology and analysis of topologically associating domain showed that it was unlikely that the disorder has an epistatic or regulatory basis. 16p13.3 deletions encompassing ATP6V0C cause a neurodevelopmental disorder. Our results broaden the phenotypic spectrum of this disorder and clarify the likely underlying disease mechanism for the condition.}, }
@article {pmid33077913, year = {2020}, author = {Szabo, Q and Donjon, A and Jerković, I and Papadopoulos, GL and Cheutin, T and Bonev, B and Nora, EP and Bruneau, BG and Bantignies, F and Cavalli, G}, title = {Regulation of single-cell genome organization into TADs and chromatin nanodomains.}, journal = {Nature genetics}, volume = {52}, number = {11}, pages = {1151-1157}, pmid = {33077913}, issn = {1546-1718}, support = {P01 HL089707/HL/NHLBI NIH HHS/United States ; UM1 HL098179/HL/NHLBI NIH HHS/United States ; 788972/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; EP-C-15-010/EPA/EPA/United States ; 100136MA/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Differentiation/genetics ; Cell Line ; Chromatin/*chemistry ; Chromosome Painting ; Drosophila/genetics ; Embryonic Stem Cells/*ultrastructure ; In Situ Hybridization, Fluorescence ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Conformation ; Nanostructures ; Nuclear Microscopy ; *Protein Domains ; }, abstract = {The genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs)[1-4]. However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy. TAD structures and physical insulation associated with their borders are variable between individual cells, yet chromatin intermingling is enriched within TADs compared to adjacent TADs in most cells. The spatial segregation of TADs is further exacerbated during cell differentiation. Favored interactions within TADs are regulated by cohesin and CTCF through distinct mechanisms: cohesin generates chromatin contacts and intermingling while CTCF prevents inter-TAD contacts. Furthermore, TADs are subdivided into discrete nanodomains, which persist in cells depleted of CTCF or cohesin, whereas disruption of nucleosome contacts alters their structural organization. Altogether, these results provide a physical basis for the folding of individual chromosomes at the nanoscale.}, }
@article {pmid33075237, year = {2021}, author = {Paik, S and Maule, F and Gallo, M}, title = {Dysregulation of chromatin organization in pediatric and adult brain tumors: oncoepigenomic contributions to tumorigenesis and cancer stem cell properties.}, journal = {Genome}, volume = {64}, number = {4}, pages = {326-336}, doi = {10.1139/gen-2020-0097}, pmid = {33075237}, issn = {1480-3321}, mesh = {Adult ; Brain Neoplasms/*genetics ; Carcinogenesis/*genetics ; Cell Differentiation ; Child ; *Chromatin ; DNA Methylation ; Disease ; Epigenesis, Genetic ; Epigenomics ; Genome ; Humans ; Neoplasms ; *Neoplastic Stem Cells ; }, abstract = {The three-dimensional (3D) organization of the genome is a crucial enabler of cell fate, identity, and function. In this review, we will focus on the emerging role of altered 3D genome organization in the etiology of disease, with a special emphasis on brain cancers. We discuss how different genetic alterations can converge to disrupt the epigenome in childhood and adult brain tumors, by causing aberrant DNA methylation and by affecting the amounts and genomic distribution of histone post-translational modifications. We also highlight examples that illustrate how epigenomic alterations have the potential to affect 3D genome architecture in brain tumors. Finally, we will propose the concept of "epigenomic erosion" to explain the transition from stem-like cells to differentiated cells in hierarchically organized brain cancers.}, }
@article {pmid33073863, year = {2020}, author = {Huang, Y and Neijts, R and de Laat, W}, title = {How chromosome topologies get their shape: views from proximity ligation and microscopy methods.}, journal = {FEBS letters}, volume = {594}, number = {21}, pages = {3439-3449}, doi = {10.1002/1873-3468.13961}, pmid = {33073863}, issn = {1873-3468}, mesh = {Animals ; Chromosomes/*chemistry/*metabolism ; Humans ; Microscopy/*methods ; Models, Molecular ; Molecular Conformation ; }, abstract = {The 3D organization of our genome is an important determinant for the transcriptional output of a gene in (patho)physiological contexts. The spatial organization of linear chromosomes within nucleus is dominantly inferred using two distinct approaches, chromosome conformation capture (3C) and DNA fluorescent in situ hybridization (DNA-FISH). While 3C and its derivatives score genomic interaction frequencies based on proximity ligation events, DNA-FISH methods measure physical distances between genomic loci. Despite these approaches probe different characteristics of chromosomal topologies, they provide a coherent picture of how chromosomes are organized in higher-order structures encompassing chromosome territories, compartments, and topologically associating domains. Yet, at the finer topological level of promoter-enhancer communication, the imaging-centered and the 3C methods give more divergent and sometimes seemingly paradoxical results. Here, we compare and contrast observations made applying visual DNA-FISH and molecular 3C approaches. We emphasize that the 3C approach, due to its inherently competitive ligation step, measures only 'relative' proximities. A 3C interaction enriched between loci, therefore does not necessarily translates into a decrease in absolute spatial distance. Hence, we advocate caution when modeling chromosome conformations.}, }
@article {pmid33060757, year = {2020}, author = {Iwasaki, Y and Ikemura, T and Kurokawa, K and Okada, N}, title = {Implication of a new function of human tDNAs in chromatin organization.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17440}, pmid = {33060757}, issn = {2045-2322}, mesh = {A549 Cells ; Activating Transcription Factor 3/metabolism ; Amino Acid Motifs ; Chromatin/*chemistry ; Computational Biology ; Databases, Factual ; E1A-Associated p300 Protein/metabolism ; Genome, Human ; HeLa Cells ; Hep G2 Cells ; Humans ; K562 Cells ; Protein Domains ; RNA, Transfer/*metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Repressor Proteins/metabolism ; Synteny ; Transcription Factors/*metabolism ; Transcription Factors, TFIII/metabolism ; }, abstract = {Transfer RNA genes (tDNAs) are essential genes that encode tRNAs in all species. To understand new functions of tDNAs, other than that of encoding tRNAs, we used ENCODE data to examine binding characteristics of transcription factors (TFs) for all tDNA regions (489 loci) in the human genome. We divided the tDNAs into three groups based on the number of TFs that bound to them. At the two extremes were tDNAs to which many TFs bound (Group 1) and those to which no TFs bound (Group 3). Several TFs involved in chromatin remodeling such as ATF3, EP300 and TBL1XR1 bound to almost all Group 1 tDNAs. Furthermore, almost all Group 1 tDNAs included DNase I hypersensitivity sites and may thus interact with other chromatin regions through their bound TFs, and they showed highly conserved synteny across tetrapods. In contrast, Group 3 tDNAs did not possess these characteristics. These data suggest the presence of a previously uncharacterized function of these tDNAs. We also examined binding of CTCF to tDNAs and their involvement in topologically associating domains (TADs) and lamina-associated domains (LADs), which suggest a new perspective on the evolution and function of tDNAs.}, }
@article {pmid33028366, year = {2020}, author = {Saha, P and Sowpati, DT and Soujanya, M and Srivastava, I and Mishra, RK}, title = {Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes.}, journal = {Epigenetics &amp; chromatin}, volume = {13}, number = {1}, pages = {41}, pmid = {33028366}, issn = {1756-8935}, support = {EpiHed//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/International ; JRF/SRF fellowship//University Grants Commission/International ; }, mesh = {Animals ; Centromere/genetics/*metabolism ; Chromobox Protein Homolog 5 ; Chromosomal Proteins, Non-Histone/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; *Epigenesis, Genetic ; Heterochromatin/genetics/*metabolism ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/metabolism ; }, abstract = {BACKGROUND: Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression.<br><br>RESULTS: Here, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes.<br><br>CONCLUSIONS: Distinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.}, }
@article {pmid33022222, year = {2020}, author = {de Bruijn, SE and Fiorentino, A and Ottaviani, D and Fanucchi, S and Melo, US and Corral-Serrano, JC and Mulders, T and Georgiou, M and Rivolta, C and Pontikos, N and Arno, G and Roberts, L and Greenberg, J and Albert, S and Gilissen, C and Aben, M and Rebello, G and Mead, S and Raymond, FL and Corominas, J and Smith, CEL and Kremer, H and Downes, S and Black, GC and Webster, AR and Inglehearn, CF and van den Born, LI and Koenekoop, RK and Michaelides, M and Ramesar, RS and Hoyng, CB and Mundlos, S and Mhlanga, MM and Cremers, FPM and Cheetham, ME and Roosing, S and Hardcastle, AJ}, title = {Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa.}, journal = {American journal of human genetics}, volume = {107}, number = {5}, pages = {802-814}, pmid = {33022222}, issn = {1537-6605}, support = {MC_UU_00024/1/MRC_/Medical Research Council/United Kingdom ; 205041/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_U123160651/MRC_/Medical Research Council/United Kingdom ; MR/R012121/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Amino Acid Sequence ; Cell Differentiation ; Cellular Reprogramming ; Child ; Chromosome Mapping ; Chromosomes, Human, Pair 17/*chemistry ; Cohort Studies ; Enhancer Elements, Genetic ; Female ; Fibroblasts/metabolism/pathology ; Gene Expression ; Genes, Dominant ; Genome, Human ; Humans ; Induced Pluripotent Stem Cells/metabolism/pathology ; Male ; Nuclear Proteins/*genetics/metabolism ; Organoids/metabolism/pathology ; Phosphoric Diester Hydrolases/*genetics/metabolism ; Polymorphism, Genetic ; Primary Cell Culture ; Retinal Cone Photoreceptor Cells/*metabolism/pathology ; Retinitis Pigmentosa/diagnosis/*genetics/metabolism/pathology ; Transcription Factors/*genetics/metabolism ; Whole Genome Sequencing ; }, abstract = {The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.}, }
@article {pmid33020667, year = {2020}, author = {Akdemir, KC and Le, VT and Kim, JM and Killcoyne, S and King, DA and Lin, YP and Tian, Y and Inoue, A and Amin, SB and Robinson, FS and Nimmakayalu, M and Herrera, RE and Lynn, EJ and Chan, K and Seth, S and Klimczak, LJ and Gerstung, M and Gordenin, DA and O'Brien, J and Li, L and Deribe, YL and Verhaak, RG and Campbell, PJ and Fitzgerald, R and Morrison, AJ and Dixon, JR and Andrew Futreal, P}, title = {Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure.}, journal = {Nature genetics}, volume = {52}, number = {11}, pages = {1178-1188}, pmid = {33020667}, issn = {1546-1718}, support = {DP5 OD023071/OD/NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; ZIA ES103266/ImNIH/Intramural NIH HHS/United States ; P50 CA127001/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Cell Line, Tumor ; Chromatin/*chemistry ; Chromosomes, Human, X/genetics ; DNA Mismatch Repair ; DNA Mutational Analysis ; DNA, Neoplasm ; Datasets as Topic ; Female ; *Genome, Human ; Humans ; Male ; *Mutation ; Neoplasms/*genetics ; Protein Conformation ; Protein Domains ; Protein Folding ; X Chromosome Inactivation ; }, abstract = {Somatic mutations in driver genes may ultimately lead to the development of cancer. Understanding how somatic mutations accumulate in cancer genomes and the underlying factors that generate somatic mutations is therefore crucial for developing novel therapeutic strategies. To understand the interplay between spatial genome organization and specific mutational processes, we studied 3,000 tumor-normal-pair whole-genome datasets from 42 different human cancer types. Our analyses reveal that the change in somatic mutational load in cancer genomes is co-localized with topologically-associating-domain boundaries. Domain boundaries constitute a better proxy to track mutational load change than replication timing measurements. We show that different mutational processes lead to distinct somatic mutation distributions where certain processes generate mutations in active domains, and others generate mutations in inactive domains. Overall, the interplay between three-dimensional genome organization and active mutational processes has a substantial influence on the large-scale mutation-rate variations observed in human cancers.}, }
@article {pmid32987449, year = {2021}, author = {Goel, VY and Hansen, AS}, title = {The macro and micro of chromosome conformation capture.}, journal = {Wiley interdisciplinary reviews. Developmental biology}, volume = {10}, number = {6}, pages = {e395}, pmid = {32987449}, issn = {1759-7692}, support = {R00 GM130896/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Nucleus ; *Chromatin/genetics ; *Chromosomes/genetics ; Genome ; Promoter Regions, Genetic ; }, abstract = {The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.}, }
@article {pmid32986691, year = {2020}, author = {Xie, WJ and Qi, Y and Zhang, B}, title = {Characterizing chromatin folding coordinate and landscape with deep learning.}, journal = {PLoS computational biology}, volume = {16}, number = {9}, pages = {e1008262}, pmid = {32986691}, issn = {1553-7358}, support = {R35 GM133580/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromatin/chemistry/*metabolism ; Computer Simulation ; *Deep Learning ; Genome ; Histone Code ; Models, Biological ; Protein Conformation ; Thermodynamics ; }, abstract = {Genome organization is critical for setting up the spatial environment of gene transcription, and substantial progress has been made towards its high-resolution characterization. The underlying molecular mechanism for its establishment is much less understood. We applied a deep-learning approach, variational autoencoder (VAE), to analyze the fluctuation and heterogeneity of chromatin structures revealed by single-cell imaging and to identify a reaction coordinate for chromatin folding. This coordinate connects the seemingly random structures observed in individual cohesin-depleted cells as intermediate states along a folding pathway that leads to the formation of topologically associating domains (TAD). We showed that folding into wild-type-like structures remain energetically favorable in cohesin-depleted cells, potentially as a result of the phase separation between the two chromatin segments with active and repressive histone marks. The energetic stabilization, however, is not strong enough to overcome the entropic penalty, leading to the formation of only partially folded structures and the disappearance of TADs from contact maps upon averaging. Our study suggests that machine learning techniques, when combined with rigorous statistical mechanical analysis, are powerful tools for analyzing structural ensembles of chromatin.}, }
@article {pmid32970351, year = {2021}, author = {Chan, WF and Coughlan, HD and Iannarella, N and Smyth, GK and Johanson, TM and Keenan, CR and Allan, RS}, title = {Identification and characterization of the long noncoding RNA Dreg1 as a novel regulator of Gata3.}, journal = {Immunology and cell biology}, volume = {99}, number = {3}, pages = {323-332}, doi = {10.1111/imcb.12408}, pmid = {32970351}, issn = {1440-1711}, mesh = {Chromatin ; Enhancer Elements, Genetic/genetics ; GATA3 Transcription Factor/genetics/metabolism ; Promoter Regions, Genetic ; *RNA, Long Noncoding/genetics ; }, abstract = {The eukaryotic genome is three-dimensionally segregated into discrete globules of topologically associating domains (TADs), within which numerous cis-regulatory elements such as enhancers and promoters interact to regulate gene expression. In this study, we identify a T-cell-specific sub-TAD containing the Gata3 locus, and reveal a previously uncharacterized long noncoding RNA (Dreg1) within a distant enhancer lying approximately 280 kb downstream of Gata3. Dreg1 expression is highly correlated with that of Gata3 during early immune system development and T helper type 2 cell differentiation. Inhibition and overexpression of Dreg1 suggest that it may be involved in the establishment, but not in the maintenance of Gata3 expression. Overall, we propose that Dreg1 is a novel regulator of Gata3 and may inform therapeutic strategies in diseases such allergy and lymphoma, where Gata3 has a pathological role.}, }
@article {pmid32968472, year = {2019}, author = {Wang, YXR and Sarkar, P and Ursu, O and Kundaje, A and Bickel, PJ}, title = {NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA.}, journal = {The annals of applied statistics}, volume = {13}, number = {3}, pages = {1511-1536}, pmid = {32968472}, issn = {1932-6157}, support = {DP2 GM123485/GM/NIGMS NIH HHS/United States ; }, abstract = {Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. One specific feature of the 3D organization is known as topologically associating domains (TADs), which are densely interacting, contiguous chromatin regions playing important roles in regulating gene expression. A few algorithms have been proposed to detect TADs. In particular, the structure of Hi-C data naturally inspires application of community detection methods. However, one of the drawbacks of community detection is that most methods take exchangeability of the nodes in the network for granted; whereas the nodes in this case, that is, the positions on the chromosomes, are not exchangeable. We propose a network model for detecting TADs using Hi-C data that takes into account this nonexchangeability. in addition, our model explicitly makes use of cell-type specific CTCF binding sites as biological covariates and can be used to identify conserved TADs across multiple cell types. The model leads to a likelihood objective that can be efficiently optimized via relaxation. We also prove that when suitably initialized, this model finds the underlying TAD structure with high probability. using simulated data, we show the advantages of our method and the caveats of popular community detection methods, such as spectral clustering, in this application. Applying our method to real Hi-C data, we demonstrate the domains identified have desirable epigenetic features and compare them across different cell types.}, }
@article {pmid32968280, year = {2020}, author = {Mitter, M and Gasser, C and Takacs, Z and Langer, CCH and Tang, W and Jessberger, G and Beales, CT and Neuner, E and Ameres, SL and Peters, JM and Goloborodko, A and Micura, R and Gerlich, DW}, title = {Conformation of sister chromatids in the replicated human genome.}, journal = {Nature}, volume = {586}, number = {7827}, pages = {139-144}, pmid = {32968280}, issn = {1476-4687}, support = {P 27947/FWF_/Austrian Science Fund FWF/Austria ; 281198/ERC_/European Research Council/International ; F 8002/FWF_/Austrian Science Fund FWF/Austria ; 693949/ERC_/European Research Council/International ; F 8011/FWF_/Austrian Science Fund FWF/Austria ; P 31691/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Cell Cycle Proteins/metabolism ; Chromatids/*chemistry/genetics/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; *Chromosome Pairing ; DNA/analysis/biosynthesis ; *DNA Replication ; Genome, Human/*genetics ; Heterochromatin/chemistry/genetics/metabolism ; Humans ; *Nucleic Acid Conformation ; }, abstract = {The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)[1,2] analysis has revealed a complex genomic landscape of internal chromosomal structures in vertebrate cells[3-7], but the identical sequence of sister chromatids has made it difficult to determine how they topologically interact in replicated chromosomes. Here we describe sister-chromatid-sensitive Hi-C (scsHi-C), which is based on labelling of nascent DNA with 4-thio-thymidine and nucleoside conversion chemistry. Genome-wide conformation maps of human chromosomes reveal that sister-chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister-chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired and are characterized by facultative heterochromatin and insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister-chromatid topologies and our scsHi-C technology will make it possible to investigate how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.}, }
@article {pmid32967822, year = {2020}, author = {Miron, E and Oldenkamp, R and Brown, JM and Pinto, DMS and Xu, CS and Faria, AR and Shaban, HA and Rhodes, JDP and Innocent, C and de Ornellas, S and Hess, HF and Buckle, V and Schermelleh, L}, title = {Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.}, journal = {Science advances}, volume = {6}, number = {39}, pages = {}, pmid = {32967822}, issn = {2375-2548}, support = {MC_UU_00016/1/MRC_/Medical Research Council/United Kingdom ; MR/K01577X/1/MRC_/Medical Research Council/United Kingdom ; MR/N00969X/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.}, }
@article {pmid32948616, year = {2020}, author = {Fu, AX and Lui, KN and Tang, CS and Ng, RK and Lai, FP and Lau, ST and Li, Z and Garcia-Barcelo, MM and Sham, PC and Tam, PK and Ngan, ES and Yip, KY}, title = {Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease.}, journal = {Genome research}, volume = {30}, number = {11}, pages = {1618-1632}, pmid = {32948616}, issn = {1549-5469}, mesh = {Class II Phosphatidylinositol 3-Kinases/genetics/metabolism ; *Enhancer Elements, Genetic ; Genetic Variation ; Hirschsprung Disease/*genetics ; Humans ; Introns ; NFI Transcription Factors/metabolism ; *Promoter Regions, Genetic ; Proto-Oncogene Proteins c-ret/genetics ; Whole Genome Sequencing ; ras Guanine Nucleotide Exchange Factors/genetics ; }, abstract = {It is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times that of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals; and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multiscale information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell stage-specific regulatory roles of three top novel regulatory elements on our list, respectively in the RET, RASGEF1A, and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the patients affects the binding of the gliogenesis regulator NFIA, with a corresponding up-regulation of multiple genes in the same topologically associating domain.}, }
@article {pmid32896099, year = {2021}, author = {Serna-Pujol, N and Salinas-Pena, M and Mugianesi, F and Lopez-Anguita, N and Torrent-Llagostera, F and Izquierdo-Bouldstridge, A and Marti-Renom, MA and Jordan, A}, title = {TADs enriched in histone H1.2 strongly overlap with the B compartment, inaccessible chromatin, and AT-rich Giemsa bands.}, journal = {The FEBS journal}, volume = {288}, number = {6}, pages = {1989-2013}, doi = {10.1111/febs.15549}, pmid = {32896099}, issn = {1742-4658}, mesh = {*Azure Stains ; Base Composition/*genetics ; Breast Neoplasms/genetics/metabolism/pathology ; Cell Line, Tumor ; Chromatin/*genetics/metabolism ; Chromatin Assembly and Disassembly/*genetics ; Epigenesis, Genetic ; Epigenomics/methods ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Histones/*genetics/metabolism ; Humans ; }, abstract = {Giemsa staining of metaphase chromosomes results in a characteristic banding useful for identification of chromosomes and its alterations. We have investigated in silico whether Giemsa bands (G bands) correlate with epigenetic and topological features of the interphase genome. Staining of G-positive bands decreases with GC content; nonetheless, G-negative bands are GC heterogeneous. High GC bands are enriched in active histone marks, RNA polymerase II, and SINEs and associate with gene richness, gene expression, and early replication. Low GC bands are enriched in repressive marks, lamina-associated domains, and LINEs. Histone H1 variants distribute heterogeneously among G bands: H1X is enriched at high GC bands and H1.2 is abundant at low GC, compacted bands. According to epigenetic features and H1 content, G bands can be organized in clusters useful to compartmentalize the genome. Indeed, we have obtained Hi-C chromosome interaction maps and compared topologically associating domains (TADs) and A/B compartments to G banding. TADs with high H1.2/H1X ratio strongly overlap with B compartment, late replicating, and inaccessible chromatin and low GC bands. We propose that GC content is a strong driver of chromatin compaction and 3D genome organization, that Giemsa staining recapitulates this organization denoted by high-throughput techniques, and that H1 variants distribute at distinct chromatin domains. DATABASES: Hi-C data on T47D breast cancer cells have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE147627.}, }
@article {pmid32820401, year = {2021}, author = {Forcato, M and Bicciato, S}, title = {Computational Analysis of Hi-C Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2157}, number = {}, pages = {103-125}, doi = {10.1007/978-1-0716-0664-3_7}, pmid = {32820401}, issn = {1940-6029}, mesh = {Chromatin/*chemistry/*metabolism ; Computational Biology/*methods ; Humans ; Nucleic Acid Conformation ; }, abstract = {The chromatin organization in the 3D nuclear space is essential for genome functionality. This spatial organization encompasses different topologies at diverse scale lengths with chromosomes occupying distinct volumes and individual chromosomes folding into compartments, inside which the chromatin fiber is packed in large domains (as the topologically associating domains, TADs) and forms short-range interactions (as enhancer-promoter loops). The widespread adoption of high-throughput techniques derived from chromosome conformation capture (3C) has been instrumental in investigating the nuclear organization of chromatin. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D structures, as in principle it can detect any pair of restriction fragments connected as a result of ligation by proximity. However, the analysis of the enormous amount of genomic data produced by Hi-C techniques requires the application of complex, multistep computational procedures that may constitute a difficult task also for expert computational biologists. In this chapter, we describe the computational analysis of Hi-C data obtained from the lymphoblastoid cell line GM12878, detailing the processing of raw data, the generation and normalization of the Hi-C contact map, the detection of TADs and chromatin interactions, and their visualization and annotation.}, }
@article {pmid32820398, year = {2021}, author = {Di Stefano, M and Castillo, D and Serra, F and Farabella, I and Goodstadt, MN and Marti-Renom, MA}, title = {Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2157}, number = {}, pages = {35-63}, doi = {10.1007/978-1-0716-0664-3_4}, pmid = {32820398}, issn = {1940-6029}, mesh = {Animals ; Chromatin/genetics/metabolism ; Chromosomes, Human/genetics/*metabolism ; Genome, Human/genetics/physiology ; Humans ; }, abstract = {Chromatin Conformation Capture techniques have unveiled several layers of chromosome organization such as the segregation in compartments, the folding in topologically associating domains (TADs), and site-specific looping interactions. The discovery of this genome hierarchical organization emerged from the computational analysis of chromatin capture data. With the increasing availability of such data, automatic pipelines for the robust comparison, grouping, and classification of multiple experiments are needed. Here we present a pipeline based on the TADbit framework that emphasizes reproducibility, automation, quality check, and statistical robustness. This comprehensive modular pipeline covers all the steps from the sequencing products to the visualization of reconstructed 3D models of the chromatin.}, }
@article {pmid32806598, year = {2020}, author = {Nath, N and Hagenau, L and Weiss, S and Tzvetkova, A and Jensen, LR and Kaderali, L and Port, M and Scherthan, H and Kuss, AW}, title = {Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts.}, journal = {International journal of molecular sciences}, volume = {21}, number = {16}, pages = {}, pmid = {32806598}, issn = {1422-0067}, mesh = {Chromosomes, Human, Pair 19/genetics ; DNA/*genetics/*radiation effects ; DNA Copy Number Variations/genetics ; Databases, Genetic ; Fibroblasts/*pathology/*radiation effects ; *Genome, Human ; Gingiva/*cytology ; Humans ; INDEL Mutation/genetics ; Translocation, Genetic ; X-Rays ; }, abstract = {While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.}, }
@article {pmid32805187, year = {2020}, author = {Zhang, X and Lei, F and Wang, XM and Deng, KQ and Ji, YX and Zhang, Y and Li, H and Zhang, XD and Lu, Z and Zhang, P}, title = {NULP1 Alleviates Cardiac Hypertrophy by Suppressing NFAT3 Transcriptional Activity.}, journal = {Journal of the American Heart Association}, volume = {9}, number = {16}, pages = {e016419}, pmid = {32805187}, issn = {2047-9980}, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/deficiency/genetics/*metabolism ; Cardiomegaly/diagnostic imaging/genetics/*metabolism/therapy ; Echocardiography ; Gene Deletion ; Humans ; Immunoprecipitation/methods ; Mice ; Mice, Knockout ; Mice, Transgenic ; Myocytes, Cardiac/metabolism ; NFATC Transcription Factors/antagonists &amp; inhibitors/genetics/*metabolism ; Oligopeptides/pharmacology ; Phosphoric Monoester Hydrolases/metabolism ; Rats ; Rats, Sprague-Dawley ; Repressor Proteins/deficiency/genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Background The development of pathological cardiac hypertrophy involves the coordination of a series of transcription activators and repressors, while their interplay to trigger pathological gene reprogramming remains unclear. NULP1 (nuclear localized protein 1) is a member of the basic helix-loop-helix family of transcription factors and its biological functions in pathological cardiac hypertrophy are barely understood. Methods and Results Immunoblot and immunostaining analyses showed that NULP1 expression was consistently reduced in the failing hearts of patients and hypertrophic mouse hearts and rat cardiomyocytes. Nulp1 knockout exacerbates aortic banding-induced cardiac hypertrophy pathology, which was significantly blunted by transgenic overexpression of Nulp1. Signal pathway screening revealed the nuclear factor of activated T cells (NFAT) pathway to be dramatically suppressed by NULP1. Coimmunoprecipitation showed that NULP1 directly interacted with the topologically associating domain of NFAT3 via its C-terminal region, which was sufficient to suppress NFAT3 transcriptional activity. Inactivation of the NFAT pathway by VIVIT peptides in vivo rescued the aggravated pathogenesis of cardiac hypertrophy resulting from Nulp1 deficiency. Conclusions NULP1 is an endogenous suppressor of NFAT3 signaling under hypertrophic stress and thus negatively regulates the pathogenesis of cardiac hypertrophy. Targeting overactivated NFAT by NULP1 may be a novel therapeutic strategy for the treatment of pathological cardiac hypertrophy and heart failure.}, }
@article {pmid32782014, year = {2020}, author = {Nanni, L and Ceri, S and Logie, C}, title = {Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {197}, pmid = {32782014}, issn = {1474-760X}, mesh = {CCCTC-Binding Factor/*metabolism ; *Genome, Human ; Humans ; }, abstract = {BACKGROUND: Topologically associating domains (TADs) are genomic regions of self-interaction. Additionally, it is known that TAD boundaries are enriched in CTCF binding sites. In turn, CTCF sites are known to be asymmetric, whereby the convergent configuration of a pair of CTCF sites leads to the formation of a chromatin loop in vivo. However, to date, it has been unclear how to reconcile TAD structure with CTCF-based chromatin loops.<br><br>RESULTS: We approach this problem by analysing CTCF binding site strengths and classifying clusters of CTCF sites along the genome on the basis of their relative orientation. Analysis of CTCF site orientation classes as a function of their spatial distribution along the human genome reveals that convergent CTCF site clusters are depleted while divergent CTCF clusters are enriched in the 5- to 100-kb range. We then analyse the distribution of CTCF binding sites as a function of TAD boundary conservation across seven primary human blood cell types. This reveals divergent CTCF site enrichment at TAD boundaries. Furthermore, convergent arrays of CTCF sites separate the left and right sections of TADs that harbour internal CTCF sites, resulting in unequal TAD 'halves'.<br><br>CONCLUSIONS: The orientation-based CTCF binding site cluster classification that we present reconciles TAD boundaries and CTCF site clusters in a mechanistically elegant fashion. This model suggests that the emergent structure of nuclear chromatin in the form of TADs relies on the obligate alternation of divergent and convergent CTCF site clusters that occur at different length scales along the genome.}, }
@article {pmid32767399, year = {2020}, author = {Khazeem, MM and Cowell, IG and Harkin, LF and Casement, JW and Austin, CA}, title = {Transcription of carbonyl reductase 1 is regulated by DNA topoisomerase II beta.}, journal = {FEBS letters}, volume = {594}, number = {20}, pages = {3395-3405}, doi = {10.1002/1873-3468.13904}, pmid = {32767399}, issn = {1873-3468}, mesh = {Carbonyl Reductase (NADPH)/*genetics/metabolism ; Cell Line ; DNA Topoisomerases, Type II/*metabolism ; Epigenesis, Genetic ; Gene Expression Profiling ; *Gene Expression Regulation ; Genome, Human ; Humans ; Promoter Regions, Genetic ; *Transcription, Genetic ; }, abstract = {DNA topoisomerase II beta (TOP2B) has a role in transcriptional regulation. Here, to further investigate transcriptional regulation by TOP2B, we used RNA-sequencing and real-time PCR to analyse the differential gene expression profiles of wild-type and two independent TOP2B-null pre-B Nalm-6 cell lines, one generated by targeted insertion and the other using CRISPR-Cas9 gene editing. We identified carbonyl reductase 1 (CBR1) among the most significantly downregulated genes in these TOP2B-null cells. Reduced CBR1 expression was accompanied by loss of binding of the transcription factors USF2 and MAX to the CBR1 promoter. We describe possible mechanisms by which loss of TOP2B results in CBR1 downregulation. To our knowledge, this is the first report of a link between TOP2B and CBR1.}, }
@article {pmid32746892, year = {2020}, author = {Heurteau, A and Perrois, C and Depierre, D and Fosseprez, O and Humbert, J and Schaak, S and Cuvier, O}, title = {Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {193}, pmid = {32746892}, issn = {1474-760X}, mesh = {Animals ; Cell Line ; DNA-Binding Proteins/*metabolism ; Drosophila ; Drosophila Proteins/*metabolism ; Eye Proteins/*metabolism ; Genome, Insect ; Heterochromatin/*metabolism ; Histone Code ; Histone Methyltransferases/*metabolism ; }, }
@article {pmid32680543, year = {2020}, author = {Matthews, BJ and Waxman, DJ}, title = {Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver.}, journal = {Epigenetics &amp; chromatin}, volume = {13}, number = {1}, pages = {30}, pmid = {32680543}, issn = {1756-8935}, support = {R01 DK121998/DK/NIDDK NIH HHS/United States ; DK121998/DK/NIDDK NIH HHS/United States ; DK33765/DK/NIDDK NIH HHS/United States ; DGE-1247312//National Science Foundation/International ; }, mesh = {Animals ; CCCTC-Binding Factor/chemistry/metabolism ; Cell Cycle Proteins/metabolism ; Chromatin/*metabolism ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/metabolism ; Enhancer Elements, Genetic ; Female ; *Genome ; Liver/*metabolism ; Male ; Mice ; *Sex ; }, abstract = {Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.}, }
@article {pmid32663239, year = {2020}, author = {Liang, M and Soomro, A and Tasneem, S and Abatti, LE and Alizada, A and Yuan, X and Uusküla-Reimand, L and Antounians, L and Alvi, SA and Paterson, AD and Rivard, G&#xc9; and Scott, IC and Mitchell, JA and Hayward, CPM and Wilson, MD}, title = {Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder.}, journal = {Blood}, volume = {136}, number = {23}, pages = {2679-2690}, pmid = {32663239}, issn = {1528-0020}, support = {201603PJT-364832/CAPMC/CIHR/Canada ; }, mesh = {Animals ; *Enhancer Elements, Genetic ; *Factor V Deficiency/genetics/metabolism/pathology ; Female ; *Gene Duplication ; *Gene Expression Regulation ; Humans ; Megakaryocytes/*metabolism/pathology ; *Membrane Proteins/biosynthesis/genetics ; Zebrafish ; }, abstract = {Quebec platelet disorder (QPD) is an autosomal dominant bleeding disorder with a unique, platelet-dependent, gain-of-function defect in fibrinolysis, without systemic fibrinolysis. The hallmark feature of QPD is a >100-fold overexpression of PLAU, specifically in megakaryocytes. This overexpression leads to a >100-fold increase in platelet stores of urokinase plasminogen activator (PLAU/uPA); subsequent plasmin-mediated degradation of diverse α-granule proteins; and platelet-dependent, accelerated fibrinolysis. The causative mutation is a 78-kb tandem duplication of PLAU. How this duplication causes megakaryocyte-specific PLAU overexpression is unknown. To investigate the mechanism that causes QPD, we used epigenomic profiling, comparative genomics, and chromatin conformation capture approaches to study PLAU regulation in cultured megakaryocytes from participants with QPD and unaffected controls. QPD duplication led to ectopic interactions between PLAU and a conserved megakaryocyte enhancer found within the same topologically associating domain (TAD). Our results support a unique disease mechanism whereby the reorganization of sub-TAD genome architecture results in a dramatic, cell-type-specific blood disorder phenotype.}, }
@article {pmid32619215, year = {2020}, author = {Danieli, A and Papantonis, A}, title = {Spatial genome architecture and the emergence of malignancy.}, journal = {Human molecular genetics}, volume = {29}, number = {R2}, pages = {R197-R204}, doi = {10.1093/hmg/ddaa128}, pmid = {32619215}, issn = {1460-2083}, mesh = {*Chromatin Assembly and Disassembly ; Chromosomes, Human/*chemistry/genetics ; Genome, Human ; Humans ; Neoplasms/etiology/*pathology ; *Promoter Regions, Genetic ; }, abstract = {Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter-enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.}, }
@article {pmid32579944, year = {2020}, author = {Zhang, K and Wu, DY and Zheng, H and Wang, Y and Sun, QR and Liu, X and Wang, LY and Xiong, WJ and Wang, Q and Rhodes, JDP and Xu, K and Li, L and Lin, Z and Yu, G and Xia, W and Huang, B and Du, Z and Yao, Y and Nasmyth, KA and Klose, RJ and Miao, YL and Xie, W}, title = {Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA.}, journal = {Molecular cell}, volume = {79}, number = {2}, pages = {234-250.e9}, doi = {10.1016/j.molcel.2020.06.001}, pmid = {32579944}, issn = {1097-4164}, support = {209400/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Cycle Proteins/*physiology ; Cell Line ; Cell Nucleus ; Chromatin/*physiology ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/*physiology ; Computational Biology/methods ; Datasets as Topic ; Embryonic Development ; Female ; Male ; Mice ; Mice, Inbred C57BL ; *Nuclear Transfer Techniques ; Zygote/*physiology ; }, abstract = {Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of 3D chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that, during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger topologically associating domains (TADs) at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell-specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.}, }
@article {pmid32572210, year = {2020}, author = {Luppino, JM and Park, DS and Nguyen, SC and Lan, Y and Xu, Z and Yunker, R and Joyce, EF}, title = {Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.}, journal = {Nature genetics}, volume = {52}, number = {8}, pages = {840-848}, pmid = {32572210}, issn = {1546-1718}, support = {R35 GM128903/GM/NIGMS NIH HHS/United States ; T32 GM008216/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Cycle Proteins/*genetics ; Cell Line, Tumor ; Chromatin/genetics ; Chromosomal Proteins, Non-Histone/*genetics ; Genome, Human/*genetics ; HCT116 Cells ; Humans ; Protein Binding/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Transcription, Genetic/genetics ; }, abstract = {The human genome can be segmented into topologically associating domains (TADs), which have been proposed to spatially sequester genes and regulatory elements through chromatin looping. Interactions between TADs have also been suggested, presumably because of variable boundary positions across individual cells. However, the nature, extent and consequence of these dynamic boundaries remain unclear. Here, we combine high-resolution imaging with Oligopaint technology to quantify the interaction frequencies across both weak and strong boundaries. We find that chromatin intermingling across population-defined boundaries is widespread but that the extent of permissibility is locus-specific. Cohesin depletion, which abolishes domain formation at the population level, does not induce ectopic interactions but instead reduces interactions across all boundaries tested. In contrast, WAPL or CTCF depletion increases inter-domain contacts in a cohesin-dependent manner. Reduced chromatin intermingling due to cohesin loss affects the topology and transcriptional bursting frequencies of genes near boundaries. We propose that cohesin occasionally bypasses boundaries to promote incorporation of boundary-proximal genes into neighboring domains.}, }
@article {pmid32568101, year = {2020}, author = {Chen, SL and Hu, F and Wang, DW and Qin, ZY and Liang, Y and Dai, YJ}, title = {Prognosis and regulation of an adenylyl cyclase network in acute myeloid leukemia.}, journal = {Aging}, volume = {12}, number = {12}, pages = {11864-11877}, pmid = {32568101}, issn = {1945-4589}, mesh = {Adenylyl Cyclases/*genetics/metabolism ; Antineoplastic Combined Chemotherapy Protocols/pharmacology/therapeutic use ; Apoptosis/genetics ; Biomarkers, Tumor/*genetics/metabolism ; Cell Line, Tumor ; Cell Survival/drug effects ; Computational Biology ; Datasets as Topic ; Drug Screening Assays, Antitumor ; Drug Synergism ; Gene Expression Profiling ; *Gene Expression Regulation, Leukemic ; Gene Regulatory Networks/drug effects/genetics ; Humans ; Kaplan-Meier Estimate ; Leukemia, Myeloid, Acute/*genetics/mortality/pathology ; MAP Kinase Signaling System/drug effects/genetics ; Mutation ; Prognosis ; Protein Interaction Maps/drug effects/genetics ; Protein Kinase Inhibitors/pharmacology/therapeutic use ; }, abstract = {We explored the roles of adenylyl cyclases (ADCYs) in acute myeloid leukemia (AML). Expression ADCYs in AML and their effect on prognosis was analyzed using data from Oncomine, GEPIA and cBioPortal databases. Frequently altered neighbor genes (FANGs) of ADCYs were detected using the 3D Genome Browser, after which the functions of these FANGs were predicted using Metascape tools. Cell viability and apoptosis were assessed using CCK-8 and Annexin V-FITC/PI kits. Expression levels of ADCYs were higher in AML cells lines and in bone marrow-derived mononuclear cells from AML patients than in control cells, and were predictive of a poor prognosis. A total of 58 ADCY FANGs were identified from the topologically associating domains on the basis of the Hi-C data. Functional analysis of these FANGs revealed abnormal activation of the MAPK signaling pathway. Drug sensitivity tests showed that fasudil plus trametinib or sapanisertib had a synergistic effect suppressing AML cell viability and increasing apoptosis. These findings suggest that dysregulation of ADCY expression leads to altered signaling in the MAPK pathway in AML and that the ADCY expression profile may be predictive of prognosis in AML patients.}, }
@article {pmid32554599, year = {2020}, author = {Maharjan, M and McKowen, JK and Hart, CM}, title = {Overlapping but Distinct Sequences Play Roles in the Insulator and Promoter Activities of the Drosophila BEAF-Dependent scs' Insulator.}, journal = {Genetics}, volume = {215}, number = {4}, pages = {1003-1012}, pmid = {32554599}, issn = {1943-2631}, mesh = {Animals ; Chromatin/*genetics ; Chromosomes/*genetics ; DNA-Binding Proteins/*genetics/metabolism ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster/*genetics/growth &amp; development/metabolism ; Eye Proteins/*genetics/metabolism ; Female ; *Insulator Elements ; *Promoter Regions, Genetic ; }, abstract = {Chromatin domain insulators are thought to help partition the genome into genetic units called topologically associating domains (TADs). In Drosophila, TADs are often separated by inter-TAD regions containing active housekeeping genes and associated insulator binding proteins. This raises the question of whether insulator binding proteins are involved primarily in chromosomal TAD architecture or gene activation, or if these two activities are linked. The Boundary Element-Associated Factor of 32 kDa (BEAF-32, or BEAF for short) is usually found in inter-TADs. BEAF was discovered based on binding to the scs' insulator, and is important for the insulator activity of scs' and other BEAF binding sites. There are divergent promoters in scs' with a BEAF binding site by each. Here, we dissect the scs' insulator to identify DNA sequences important for insulator and promoter activity, focusing on the half of scs' with a high affinity BEAF binding site. We find that the BEAF binding site is important for both insulator and promoter activity, as is another sequence we refer to as LS4. Aside from that, different sequences play roles in insulator and promoter activity. So while there is overlap and BEAF is important for both, insulator and promoter activity can be separated.}, }
@article {pmid32514124, year = {2020}, author = {Stik, G and Vidal, E and Barrero, M and Cuartero, S and Vila-Casadesús, M and Mendieta-Esteban, J and Tian, TV and Choi, J and Berenguer, C and Abad, A and Borsari, B and le Dily, F and Cramer, P and Marti-Renom, MA and Stadhouders, R and Graf, T}, title = {CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.}, journal = {Nature genetics}, volume = {52}, number = {7}, pages = {655-661}, pmid = {32514124}, issn = {1546-1718}, mesh = {Antigens, Differentiation/metabolism ; B-Lymphocytes/*physiology ; CCCTC-Binding Factor/genetics/*physiology ; Cell Line, Tumor ; Cell Proliferation/physiology ; Chromatin/physiology ; Gene Expression Regulation ; Humans ; Macrophages/*physiology ; Molecular Conformation ; Myelopoiesis/genetics/*physiology ; Protein Conformation ; }, abstract = {Three-dimensional organization of the genome is important for transcriptional regulation[1-7]. In mammals, CTCF and the cohesin complex create submegabase structures with elevated internal chromatin contact frequencies, called topologically associating domains (TADs)[8-12]. Although TADs can contribute to transcriptional regulation, ablation of TAD organization by disrupting CTCF or the cohesin complex causes modest gene expression changes[13-16]. In contrast, CTCF is required for cell cycle regulation[17], embryonic development and formation of various adult cell types[18]. To uncouple the role of CTCF in cell-state transitions and cell proliferation, we studied the effect of CTCF depletion during the conversion of human leukemic B cells into macrophages with minimal cell division. CTCF depletion disrupts TAD organization but not cell transdifferentiation. In contrast, CTCF depletion in induced macrophages impairs the full-blown upregulation of inflammatory genes after exposure to endotoxin. Our results demonstrate that CTCF-dependent genome topology is not strictly required for a functional cell-fate conversion but facilitates a rapid and efficient response to an external stimulus.}, }
@article {pmid32499403, year = {2020}, author = {Kang, H and Shokhirev, MN and Xu, Z and Chandran, S and Dixon, JR and Hetzer, MW}, title = {Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation.}, journal = {Genes &amp; development}, volume = {34}, number = {13-14}, pages = {913-930}, pmid = {32499403}, issn = {1549-5477}, support = {DP5 OD023071/OD/NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R01 GM126829/GM/NIGMS NIH HHS/United States ; R01 NS096786/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Cell Cycle Checkpoints/genetics ; Chromatin/*metabolism ; Chromosomes/genetics/metabolism ; Enhancer Elements, Genetic ; Genome/genetics ; Histone Code/*genetics ; Histones/*metabolism ; Humans ; Mitosis/*genetics ; Promoter Regions, Genetic ; Protein Binding ; Protein Processing, Post-Translational/*genetics ; Time Factors ; Transcriptional Activation/*genetics ; }, abstract = {During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.}, }
@article {pmid32486876, year = {2020}, author = {Papanicolaou, N and Bonetti, A}, title = {The New Frontier of Functional Genomics: From Chromatin Architecture and Noncoding RNAs to Therapeutic Targets.}, journal = {SLAS discovery : advancing life sciences R &amp; D}, volume = {25}, number = {6}, pages = {568-580}, pmid = {32486876}, issn = {2472-5560}, mesh = {Chromatin/*genetics ; Genome, Human ; Genome-Wide Association Study ; *Genomics ; Humans ; Molecular Targeted Therapy/*trends ; Promoter Regions, Genetic/genetics ; RNA, Untranslated/*genetics ; }, abstract = {Common diseases are complex, multifactorial disorders whose pathogenesis is influenced by the interplay of genetic predisposition and environmental factors. Genome-wide association studies have interrogated genetic polymorphisms across genomes of individuals to test associations between genotype and susceptibility to specific disorders, providing insights into the genetic architecture of several complex disorders. However, genetic variants associated with the susceptibility to common diseases are often located in noncoding regions of the genome, such as tissue-specific enhancers or long noncoding RNAs, suggesting that regulatory elements might play a relevant role in human diseases. Enhancers are cis-regulatory genomic sequences that act in concert with promoters to regulate gene expression in a precise spatiotemporal manner. They can be located at a considerable distance from their cognate target promoters, increasing the difficulty of their identification. Genomes are organized in domains of chromatin folding, namely topologically associating domains (TADs). Identification of enhancer-promoter interactions within TADs has revealed principles of cell-type specificity across several organisms and tissues. The vast majority of mammalian genomes are pervasively transcribed, accounting for a previously unappreciated complexity of the noncoding RNA fraction. Particularly, long noncoding RNAs have emerged as key players for the establishment of chromatin architecture and regulation of gene expression. In this perspective, we describe the new advances in the fields of transcriptomics and genome organization, focusing on the role of noncoding genomic variants in the predisposition of common diseases. Finally, we propose a new framework for the identification of the next generation of pharmacological targets for common human diseases.}, }
@article {pmid32483172, year = {2020}, author = {Oudelaar, AM and Beagrie, RA and Gosden, M and de Ornellas, S and Georgiades, E and Kerry, J and Hidalgo, D and Carrelha, J and Shivalingam, A and El-Sagheer, AH and Telenius, JM and Brown, T and Buckle, VJ and Socolovsky, M and Higgs, DR and Hughes, JR}, title = {Dynamics of the 4D genome during in vivo lineage specification and differentiation.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2722}, pmid = {32483172}, issn = {2041-1723}, support = {G1000801/MRC_/Medical Research Council/United Kingdom ; MR/N00969X/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/MRC_/Medical Research Council/United Kingdom ; MC_UU_12009/15/MRC_/Medical Research Council/United Kingdom ; R01 DK100915/DK/NIDDK NIH HHS/United States ; MC_UU_00016/12/MRC_/Medical Research Council/United Kingdom ; BB/R008655/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_PC_15069/MRC_/Medical Research Council/United Kingdom ; BB/M025624/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J001694/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_U137961145/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 209181/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12009/4/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/4/MRC_/Medical Research Council/United Kingdom ; MC_UU_12009/13/MRC_/Medical Research Council/United Kingdom ; MC_U137961144/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/14/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cell Differentiation/*genetics ; Cells, Cultured ; Chromatin/genetics ; Chromosomes, Mammalian/genetics ; Enhancer Elements, Genetic/*genetics ; Female ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Developmental ; Genome/*genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Mice ; Mice, Inbred C57BL ; Mouse Embryonic Stem Cells/cytology/metabolism ; Promoter Regions, Genetic/*genetics ; Stem Cells/cytology/*metabolism ; }, abstract = {Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.}, }
@article {pmid32473574, year = {2020}, author = {Sparks, TM and Harabula, I and Pombo, A}, title = {Evolving methodologies and concepts in 4D nucleome research.}, journal = {Current opinion in cell biology}, volume = {64}, number = {}, pages = {105-111}, pmid = {32473574}, issn = {1879-0410}, support = {U54 DK107977/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Chromatin/metabolism ; Genome ; Genomics ; Humans ; Nucleosomes/*metabolism ; *Research ; }, abstract = {The genome requires tight regulation in space and time to maintain viable cell functions. Advances in our understanding of the 3D genome show a complex hierarchical network of structures, involving compartments, membraneless bodies, topologically associating domains, lamina associated domains, protein- or RNA-mediated loops, enhancer-promoter contacts, and accessible chromatin regions, with chromatin state regulation through epigenetic and transcriptional mechanisms. Further technology developments are poised to increase genomic resolution, dissect single-cell behaviors, including in vivo dynamics of genome folding, and provide mechanistic perspectives that identify further 3D genome players by integrating multiomics information. We highlight recent key developments in 4D nucleome methodologies and give a perspective on their future directions.}, }
@article {pmid32470376, year = {2020}, author = {Melo, US and Schöpflin, R and Acuna-Hidalgo, R and Mensah, MA and Fischer-Zirnsak, B and Holtgrewe, M and Klever, MK and Türkmen, S and Heinrich, V and Pluym, ID and Matoso, E and Bernardo de Sousa, S and Louro, P and Hülsemann, W and Cohen, M and Dufke, A and Latos-Bieleńska, A and Vingron, M and Kalscheuer, V and Quintero-Rivera, F and Spielmann, M and Mundlos, S}, title = {Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases.}, journal = {American journal of human genetics}, volume = {106}, number = {6}, pages = {872-884}, pmid = {32470376}, issn = {1537-6605}, mesh = {Chromatin Assembly and Disassembly/genetics ; Chromosome Breakpoints ; Chromosomes, Human/*genetics ; Cohort Studies ; Developmental Disabilities/*genetics ; Genome, Human/*genetics ; Humans ; *Molecular Conformation ; SOX9 Transcription Factor/genetics ; Segmental Duplications, Genomic/genetics ; Translocation, Genetic/*genetics ; }, abstract = {Genome-wide analysis methods, such as array comparative genomic hybridization (CGH) and whole-genome sequencing (WGS), have greatly advanced the identification of structural variants (SVs) in the human genome. However, even with standard high-throughput sequencing techniques, complex rearrangements with multiple breakpoints are often difficult to resolve, and predicting their effects on gene expression and phenotype remains a challenge. Here, we address these problems by using high-throughput chromosome conformation capture (Hi-C) generated from cultured cells of nine individuals with developmental disorders (DDs). Three individuals had previously been identified as harboring duplications at the SOX9 locus and six had been identified with translocations. Hi-C resolved the positions of the duplications and was instructive in interpreting their distinct pathogenic effects, including the formation of new topologically associating domains (neo-TADs). Hi-C was very sensitive in detecting translocations, and it revealed previously unrecognized complex rearrangements at the breakpoints. In several cases, we observed the formation of fused-TADs promoting ectopic enhancer-promoter interactions that were likely to be involved in the disease pathology. In summary, we show that Hi-C is a sensible method for the detection of complex SVs in a clinical setting. The results help interpret the possible pathogenic effects of the SVs in individuals with DDs.}, }
@article {pmid32460018, year = {2020}, author = {Lazar, JE and Stehling-Sun, S and Nandakumar, V and Wang, H and Chee, DR and Howard, NP and Acosta, R and Dunn, D and Diegel, M and Neri, F and Castillo, A and Ibarrientos, S and Lee, K and Lescano, N and Van Biber, B and Nelson, J and Halow, J and Sandstrom, R and Bates, D and Urnov, FD and Stamatoyannopoulos, JA and Funnell, APW}, title = {Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling.}, journal = {Cell reports}, volume = {31}, number = {8}, pages = {107676}, doi = {10.1016/j.celrep.2020.107676}, pmid = {32460018}, issn = {2211-1247}, support = {UM1 HG009444/HG/NHGRI NIH HHS/United States ; U54 HG007010/HG/NHGRI NIH HHS/United States ; }, mesh = {Chromatin Assembly and Disassembly/*genetics ; DNA/*genetics ; DNA Helicases/*metabolism ; Gene Expression/*genetics ; Humans ; Nuclear Proteins/*metabolism ; Transcription Factors/*metabolism ; }, abstract = {The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. We use precision genome engineering to reawaken homozygously inactivated SMARCA4, a central ATPase of the human SWI/SNF chromatin remodeling complex, in lung adenocarcinoma cells. Here, we combine DNase I hypersensitivity, histone modification, and transcriptional profiling to show that SMARCA4 dramatically increases both the number and magnitude of accessible chromatin sites genome-wide, chiefly by unmasking sites of low regulatory factor occupancy. By contrast, transcriptional changes are concentrated within well-demarcated remodeling domains wherein expression of specific genes is gated by both distal element activation and promoter chromatin configuration. Our results provide a perspective on how global chromatin remodeling activity is translated to gene expression via regulatory DNA.}, }
@article {pmid32439634, year = {2020}, author = {Boyle, S and Flyamer, IM and Williamson, I and Sengupta, D and Bickmore, WA and Illingworth, RS}, title = {A central role for canonical PRC1 in shaping the 3D nuclear landscape.}, journal = {Genes &amp; development}, volume = {34}, number = {13-14}, pages = {931-949}, pmid = {32439634}, issn = {1549-5477}, support = {MC_UU_00007/2/MRC_/Medical Research Council/United Kingdom ; MR/S007644/1/MRC_/Medical Research Council/United Kingdom ; MR/K017047/1/MRC_/Medical Research Council/United Kingdom ; BBSRC_BB/H008500/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; Cell Nucleus/*genetics ; Embryo, Mammalian ; Genome/*genetics ; Mice ; Mouse Embryonic Stem Cells ; Polycomb Repressive Complex 1/*genetics/*metabolism ; Polycomb-Group Proteins/metabolism ; Protein Binding ; Ubiquitin-Protein Ligases/genetics/metabolism ; }, abstract = {Polycomb group (PcG) proteins silence gene expression by chemically and physically modifying chromatin. A subset of PcG target loci are compacted and cluster in the nucleus; a conformation that is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organization and their relationship with transcription remains poorly understood. Here we examine the role of Polycomb-repressive complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells (mESCs). Using a combination of imaging and Hi-C analyses, we show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale. Impairment of PRC1 enzymatic activity does not directly disrupt these interactions. We demonstrate that PcG targets coalesce in vivo, and that developmentally induced expression of one of the target loci disrupts this spatial arrangement. Finally, we show that transcriptional activation and the loss of PRC1-mediated interactions are separable events. These findings provide important insights into the function of PRC1, while highlighting the complexity of this regulatory system.}, }
@article {pmid32424124, year = {2020}, author = {Chen, CH and Zheng, R and Tokheim, C and Dong, X and Fan, J and Wan, C and Tang, Q and Brown, M and Liu, JS and Meyer, CA and Liu, XS}, title = {Determinants of transcription factor regulatory range.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2472}, pmid = {32424124}, issn = {2041-1723}, support = {U24 CA237617/CA/NCI NIH HHS/United States ; }, mesh = {Acetylation ; Animals ; Cell Line ; Chromatin/metabolism ; *Gene Expression Regulation ; Genome-Wide Association Study ; Histones/metabolism ; Lysine/metabolism ; Mice ; Models, Genetic ; Polymorphism, Single Nucleotide/genetics ; Protein Binding/genetics ; Quantitative Trait Loci/genetics ; Transcription Factors/*metabolism ; Transcription Initiation Site ; }, abstract = {Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.}, }
@article {pmid32403166, year = {2020}, author = {Sumiyama, K and Tanave, A}, title = {The regulatory landscape of the Dlx gene system in branchial arches: Shared characteristics among Dlx bigene clusters and evolution.}, journal = {Development, growth &amp; differentiation}, volume = {62}, number = {5}, pages = {355-362}, doi = {10.1111/dgd.12671}, pmid = {32403166}, issn = {1440-169X}, mesh = {Animals ; Branchial Region/*metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Developmental/*genetics ; Homeodomain Proteins/*genetics/metabolism ; Humans ; Multigene Family/*genetics ; Transcription Factors/*genetics/metabolism ; }, abstract = {The mammalian Dlx genes encode homeobox-type transcription factors and are physically organized as convergent bigene clusters. The paired Dlx genes share tissue specificity in the expression profile. Genetic regulatory mechanisms, such as intergenic enhancer sharing between paired Dlx genes, have been proposed to explain this conservation of bigene structure. All mammalian Dlx genes have expression and function in developing craniofacial structures, especially in the first and second pharyngeal arches (branchial arches). Each Dlx cluster (Dlx1/2, Dlx3/4, and Dlx5/6) has overlapping, nested expression in the branchial arches which is called the "Dlx code" and plays a key role in organizing craniofacial structure and evolution. Here we summarize cis-regulatory studies on branchial arch expression of the three Dlx bigene clusters and show some shared characteristics among the clusters, including cis-regulatory motifs, TAD (Topologically Associating Domain) boundaries, CTCF loops, and distal enhancer landscapes, together with a molecular condensate model for activation of the Dlx bigene cluster.}, }
@article {pmid32385148, year = {2020}, author = {Bian, Q and Anderson, EC and Yang, Q and Meyer, BJ}, title = {Histone H3K9 methylation promotes formation of genome compartments in Caenorhabditis elegans via chromosome compaction and perinuclear anchoring.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {21}, pages = {11459-11470}, pmid = {32385148}, issn = {1091-6490}, support = {R01 GM030702/GM/NIGMS NIH HHS/United States ; R35 GM131845/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chromosomal Proteins, Non-Histone/genetics/metabolism ; Chromosomes/genetics/*metabolism ; Gene Expression Regulation ; Genome ; Heterochromatin/genetics/metabolism ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Histones/genetics/*metabolism ; Lysine/genetics/*metabolism ; Methylation ; Mutation ; X Chromosome/genetics/metabolism ; }, abstract = {Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization in Caenorhabditis elegans and investigate roles for compartments in regulating gene expression. Distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other both in cis and in trans, while interacting less frequently with central regions, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genes met-2 and set-25 significantly impaired formation of inactive Arm and active Center compartments. cec-4 mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: Perinuclear anchoring of chromosome arms via CEC-4 to promote their cis association, and an anchoring-independent mechanism that compacts individual chromosome arms. In both met-2 set-25 and cec-4 mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene-expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X established by the dosage compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.}, }
@article {pmid32384149, year = {2020}, author = {Yang, M and Safavi, S and Woodward, EL and Duployez, N and Olsson-Arvidsson, L and Ungerbäck, J and Sigvardsson, M and Zaliova, M and Zuna, J and Fioretos, T and Johansson, B and Nord, KH and Paulsson, K}, title = {13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.}, journal = {Blood}, volume = {136}, number = {8}, pages = {946-956}, pmid = {32384149}, issn = {1528-0020}, mesh = {Cell Line ; Chromatin Assembly and Disassembly/genetics/physiology ; Chromosome Deletion ; Chromosome Disorders/complications/*genetics ; Chromosomes, Human, Pair 13/genetics ; Cohort Studies ; DNA Copy Number Variations/genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation, Leukemic ; Humans ; Microarray Analysis ; Polymorphism, Single Nucleotide ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*genetics ; RNA-Seq ; Up-Regulation/genetics ; Whole Genome Sequencing ; fms-Like Tyrosine Kinase 3/*genetics ; }, abstract = {Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene in 13q12.2 are among the most common driver events in acute leukemia, leading to increased cell proliferation and survival through activation of the phosphatidylinositol 3-kinase/AKT-, RAS/MAPK-, and STAT5-signaling pathways. In this study, we examine the pathogenetic impact of somatic hemizygous 13q12.2 microdeletions in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) using 5 different patient cohorts (in total including 1418 cases). The 13q12.2 deletions occur immediately 5' of FLT3 and involve the PAN3 locus. By detailed analysis of the 13q12.2 segment, we show that the deletions lead to loss of a topologically associating domain border and an enhancer of FLT3. This results in increased cis interactions between the FLT3 promoter and another enhancer located distally to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expected to lead to ligand-independent activation of the receptor and downstream signaling. The 13q12.2 deletions are highly enriched in the high-hyperdiploid BCP ALL subtype (frequency 3.9% vs 0.5% in other BCP ALL) and in cases that subsequently relapsed. Taken together, our study describes a novel mechanism of FLT3 involvement in leukemogenesis by upregulation via chromatin remodeling and enhancer hijacking. These data further emphasize the role of FLT3 as a driver gene in BCP ALL.}, }
@article {pmid32334414, year = {2020}, author = {Pérez-Rico, YA and Barillot, E and Shkumatava, A}, title = {Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish.}, journal = {iScience}, volume = {23}, number = {5}, pages = {101046}, pmid = {32334414}, issn = {2589-0042}, abstract = {CCCTC-binding factor (CTCF) is a conserved architectural protein that plays crucial roles in gene regulation and three-dimensional (3D) chromatin organization. To better understand mechanisms and evolution of vertebrate genome organization, we analyzed genome occupancy of CTCF in zebrafish utilizing an endogenously epitope-tagged CTCF knock-in allele. Zebrafish CTCF shares similar facets with its mammalian counterparts, including binding to enhancers, active promoters and repeat elements, and bipartite sequence motifs of its binding sites. However, we found that in vivo CTCF binding is not enriched at boundaries of topologically associating domains (TADs) in developing zebrafish, whereas TAD demarcation by chromatin marks did not differ from mammals. Our data suggest that general mechanisms underlying 3D chromatin organization, and in particular the involvement of CTCF in this process, differ between distant vertebrate species.}, }
@article {pmid32324846, year = {2020}, author = {Zhang, Z and Wang, Q and Liu, Y and Sun, Q and Li, H and Czajkowsky, DM and Shao, Z}, title = {Massive reorganization of the genome during primary monocyte differentiation into macrophage.}, journal = {Acta biochimica et biophysica Sinica}, volume = {52}, number = {5}, pages = {546-553}, doi = {10.1093/abbs/gmaa026}, pmid = {32324846}, issn = {1745-7270}, mesh = {*Cell Differentiation ; Female ; *Genome, Human ; Humans ; Macrophages/cytology/*metabolism ; Male ; Monocytes/cytology/*metabolism ; }, abstract = {Monocyte-to-macrophage trans-differentiation has long been studied to better understand this immunological response and aspects of developmental processes more generally. A key question is the nature of the corresponding changes in chromatin conformation and its relationship to the transcriptome during this process. This question is especially intriguing since this trans-differentiation is not associated with progression through mitosis, often considered a necessary step for gross changes in chromosomal structure. Here, we characterized the transcriptional and genomic structural changes during macrophage development of primary human monocytes using RNA-seq and in situ Hi-C. We found that, during this transition, the genome architecture undergoes a massive remodeling to a degree not observed before between structured genomes, with changes in ~90% of the topologically associating domains (TADs). These changes in the TADs are associated with changed expression of immunological genes. These structural changes, however, differ extensively from those described recently in a study of the leukemia cell line, THP-1. Furthermore, up-regulation of the AP-1 family of genes that effected functionally important changes in the genomic structure during the differentiation of the THP-1 cells was not corroborated with the primary cells. Taken together, our results provide a comprehensive characterization of the changes in genomic structure during the monocyte-to-macrophage transition, establish a framework for the elucidation of processes underlying differentiation without proliferation, and demonstrate the importance of verifying with primary cells the mechanisms discovered with cultured cells.}, }
@article {pmid32315832, year = {2020}, author = {Luo, Z and Wang, X and Jiang, H and Wang, R and Chen, J and Chen, Y and Xu, Q and Cao, J and Gong, X and Wu, J and Yang, Y and Li, W and Han, C and Cheng, CY and Rosenfeld, MG and Sun, F and Song, X}, title = {Reorganized 3D Genome Structures Support Transcriptional Regulation in Mouse Spermatogenesis.}, journal = {iScience}, volume = {23}, number = {4}, pages = {101034}, pmid = {32315832}, issn = {2589-0042}, abstract = {Three-dimensional chromatin structures undergo dynamic reorganization during mammalian spermatogenesis; however, their impacts on gene regulation remain unclear. Here, we focused on understanding the structure-function regulation of meiotic chromosomes by Hi-C and other omics techniques in mouse spermatogenesis across five stages. Beyond confirming recent reports regarding changes in compartmentalization and reorganization of topologically associating domains (TADs), we further demonstrated that chromatin loops are present prior to and after, but not at, the pachytene stage. By integrating Hi-C and RNA-seq data, we showed that the switching of A/B compartments between spermatogenic stages is tightly associated with meiosis-specific mRNAs and piRNAs expression. Moreover, our ATAC-seq data indicated that chromatin accessibility per se is not responsible for the TAD and loop diminishment at pachytene. Additionally, our ChIP-seq data demonstrated that CTCF and cohesin remain bound at TAD boundary regions throughout meiosis, suggesting that dynamic reorganization of TADs does not require CTCF and cohesin clearance.}, }
@article {pmid32313950, year = {2020}, author = {Kantidze, OL and Razin, SV}, title = {Weak interactions in higher-order chromatin organization.}, journal = {Nucleic acids research}, volume = {48}, number = {9}, pages = {4614-4626}, pmid = {32313950}, issn = {1362-4962}, mesh = {Chromatin/*chemistry ; DNA, Superhelical ; RNA ; Static Electricity ; }, abstract = {The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.}, }
@article {pmid32301703, year = {2020}, author = {Amândio, AR and Lopez-Delisle, L and Bolt, CC and Mascrez, B and Duboule, D}, title = {A complex regulatory landscape involved in the development of mammalian external genitals.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32301703}, issn = {2050-084X}, support = {NICHD F32HD0935/NH/NIH HHS/United States ; 310030B_138662/SNSF_/Swiss National Science Foundation/Switzerland ; 588029/ERC_/European Research Council/International ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; Chromatin/*metabolism ; Enhancer Elements, Genetic/*genetics ; Genes, Homeobox/genetics ; Genitalia/*metabolism ; Mammals/*genetics ; Mice ; Multigene Family/genetics ; Promoter Regions, Genetic ; }, abstract = {Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. We used a TAD flanking the mouse HoxD cluster to study how these regulatory architectures are formed and deconstructed once their function achieved. We describe this TAD as a functional unit, with several regulatory sequences acting together to elicit a transcriptional response. With one exception, deletion of these sequences didn't modify the transcriptional outcome, a result at odds with a conventional view of enhancer function. The deletion and inversion of a CTCF site located near these regulatory sequences did not affect transcription of the target gene. Slight modifications were nevertheless observed, in agreement with the loop extrusion model. We discuss these unexpected results considering both conventional and alternative explanations relying on the accumulation of poorly specific factors within the TAD backbone.}, }
@article {pmid32299027, year = {2020}, author = {Noordermeer, D and Feil, R}, title = {Differential 3D chromatin organization and gene activity in genomic imprinting.}, journal = {Current opinion in genetics &amp; development}, volume = {61}, number = {}, pages = {17-24}, doi = {10.1016/j.gde.2020.03.004}, pmid = {32299027}, issn = {1879-0380}, mesh = {Alleles ; Allelic Imbalance/genetics ; Animals ; CCCTC-Binding Factor/*genetics ; Chromatin/*genetics/ultrastructure ; CpG Islands/genetics ; DNA Methylation/genetics ; Gene Expression Regulation/genetics ; Genomic Imprinting/*genetics ; Histones/genetics ; Humans ; RNA, Long Noncoding/*genetics ; }, abstract = {Genomic imprinting gives rise to parent-of-origin dependent allelic gene expression. Most imprinted genes cluster in domains where differentially methylated regions (DMRs)-carrying CpG methylation on one parental allele-regulate their activity. Several imprinted DMRs bind CTCF on the non-methylated allele. CTCF structures TADs ('Topologically Associating Domains'), which are structural units of transcriptional regulation. Recent investigations show that imprinted domains are embedded within TADs that are similar on both parental chromosomes. Within these TADs, however, allelic subdomains are structured by combinations of mono-allelic and bi-allelic CTCF binding that guide imprinted expression. This emerging view indicates that imprinted chromosomal domains should be considered at the overarching TAD level, and questions how CTCF integrates with other regulatory proteins and lncRNAs to achieve imprinted transcriptional programs.}, }
@article {pmid32286279, year = {2020}, author = {Chen, M and Zhu, Q and Li, C and Kou, X and Zhao, Y and Li, Y and Xu, R and Yang, L and Yang, L and Gu, L and Wang, H and Liu, X and Jiang, C and Gao, S}, title = {Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1813}, pmid = {32286279}, issn = {2041-1723}, mesh = {Animals ; Cellular Reprogramming ; Chromatin/*metabolism ; Embryo, Mammalian/*metabolism ; Embryonic Development ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation, Developmental ; Genome ; Histones/metabolism ; Lysine/metabolism ; Metaphase ; Methylation ; Mice ; *Nuclear Transfer Techniques ; Promoter Regions, Genetic/genetics ; Zygote/metabolism ; }, abstract = {The oocyte cytoplasm can reprogram the somatic cell nucleus into a totipotent state, but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examine higher order chromatin structures of mouse SCNT embryos using a low-input Hi-C method. We find that donor cell chromatin transforms to the metaphase state rapidly after SCNT along with the dissolution of typical 3D chromatin structure. Intriguingly, the genome undergoes a mitotic metaphase-like to meiosis metaphase II-like transition following activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerge following metaphase exit. TADs are further removed until the 2-cell stage before being progressively reestablished. Obvious defects including stronger TAD boundaries, aberrant super-enhancer and promoter interactions are found in SCNT embryos. These defects are partially caused by inherited H3K9me3, and can be rescued by Kdm4d overexpression. These observations provide insight into chromatin architecture reorganization during SCNT embryo development.}, }
@article {pmid32241291, year = {2020}, author = {Wang, G and Meng, Q and Xia, B and Zhang, S and Lv, J and Zhao, D and Li, Y and Wang, X and Zhang, L and Cooke, JP and Cao, Q and Chen, K}, title = {TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {84}, pmid = {32241291}, issn = {1474-760X}, support = {P50 CA180995/CA/NCI NIH HHS/United States ; R01 HL133254/HL/NHLBI NIH HHS/United States ; HL133254/NH/NIH HHS/United States ; GM125632/NH/NIH HHS/United States ; R01 CA208257/CA/NCI NIH HHS/United States ; R01 GM125632/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Cell Line, Tumor ; Chromatin/metabolism ; *Chromosomes, Mammalian ; *Epigenesis, Genetic ; Epigenomics/methods ; Histone Code ; Humans ; Mice ; Sequence Analysis, DNA ; *Transcription, Genetic ; }, abstract = {We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and mergers of TADs with high accuracy in simulation analyses and defines hundreds of TAD splits and mergers between pairs of different cell types, such as endothelial cells and fibroblasts. Our work reveals a key role for TAD remodeling in epigenetic regulation of transcription and delivers the first tool for the community to perform dynamic analysis of TAD splits and mergers in numerous biological and disease models.}, }
@article {pmid32240449, year = {2020}, author = {Pontvianne, F and Grob, S}, title = {Three-dimensional nuclear organization in Arabidopsis thaliana.}, journal = {Journal of plant research}, volume = {133}, number = {4}, pages = {479-488}, pmid = {32240449}, issn = {1618-0860}, mesh = {Animals ; *Arabidopsis/genetics ; *Cell Nucleus/genetics ; Chromatin ; }, abstract = {In recent years, the study of plant three-dimensional nuclear architecture received increasing attention. Enabled by technological advances, our knowledge on nuclear architecture has greatly increased and we can now access large data sets describing its manifold aspects. The principles of nuclear organization in plants do not significantly differ from those in animals. Plant nuclear organization comprises various scales, ranging from gene loops to topologically associating domains to nuclear compartmentalization. However, whether plant three-dimensional chromosomal features also exert similar functions as in animals is less clear. This review discusses recent advances in the fields of three-dimensional chromosome folding and nuclear compartmentalization and describes a novel silencing mechanism, which is closely linked to nuclear architecture.}, }
@article {pmid32213324, year = {2020}, author = {Krietenstein, N and Abraham, S and Venev, SV and Abdennur, N and Gibcus, J and Hsieh, TS and Parsi, KM and Yang, L and Maehr, R and Mirny, LA and Dekker, J and Rando, OJ}, title = {Ultrastructural Details of Mammalian Chromosome Architecture.}, journal = {Molecular cell}, volume = {78}, number = {3}, pages = {554-565.e7}, pmid = {32213324}, issn = {1097-4164}, support = {R01 GM114190/GM/NIGMS NIH HHS/United States ; U54 DK107980/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; Cells, Cultured ; Chromatin/chemistry ; Chromosomes, Human/*ultrastructure ; Chromosomes, Mammalian/ultrastructure ; Embryonic Stem Cells/cytology ; Fibroblasts/cytology ; Humans ; Male ; Mammals/genetics ; Nucleosomes/metabolism/ultrastructure ; Signal-To-Noise Ratio ; }, abstract = {Over the past decade, 3C-related methods have provided remarkable insights into chromosome folding in vivo. To overcome the limited resolution of prior studies, we extend a recently developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts. Micro-C robustly captures known features of chromosome folding including compartment organization, topologically associating domains, and interactions between CTCF binding sites. In addition, Micro-C provides a detailed map of nucleosome positions and localizes contact domain boundaries with nucleosomal precision. Compared to Hi-C, Micro-C exhibits an order of magnitude greater dynamic range, allowing the identification of ∼20,000 additional loops in each cell type. Many newly identified peaks are localized along extrusion stripes and form transitive grids, consistent with their anchors being pause sites impeding cohesin-dependent loop extrusion. Our analyses comprise the highest-resolution maps of chromosome folding in human cells to date, providing a valuable resource for studies of chromosome organization.}, }
@article {pmid32213323, year = {2020}, author = {Hsieh, TS and Cattoglio, C and Slobodyanyuk, E and Hansen, AS and Rando, OJ and Tjian, R and Darzacq, X}, title = {Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.}, journal = {Molecular cell}, volume = {78}, number = {3}, pages = {539-553.e8}, pmid = {32213323}, issn = {1097-4164}, support = {R00 GM130896/GM/NIGMS NIH HHS/United States ; 003061/HHMI/Howard Hughes Medical Institute/United States ; U01 EB021236/EB/NIBIB NIH HHS/United States ; U54 DK107980/DK/NIDDK NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; K99 GM130896/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/genetics ; Chromatin/*chemistry/genetics/*metabolism ; Chromatin Assembly and Disassembly/*genetics ; DNA Polymerase II/genetics/metabolism ; Embryonic Stem Cells/physiology ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genome Components ; Mice ; Promoter Regions, Genetic ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic ; }, abstract = {Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here, we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci, often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin folding and gene regulation.}, }
@article {pmid32203470, year = {2020}, author = {Kloetgen, A and Thandapani, P and Ntziachristos, P and Ghebrechristos, Y and Nomikou, S and Lazaris, C and Chen, X and Hu, H and Bakogianni, S and Wang, J and Fu, Y and Boccalatte, F and Zhong, H and Paietta, E and Trimarchi, T and Zhu, Y and Van Vlierberghe, P and Inghirami, GG and Lionnet, T and Aifantis, I and Tsirigos, A}, title = {Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia.}, journal = {Nature genetics}, volume = {52}, number = {4}, pages = {388-400}, pmid = {32203470}, issn = {1546-1718}, support = {R01 CA133379/CA/NCI NIH HHS/United States ; R01 CA194923/CA/NCI NIH HHS/United States ; R01 CA228135/CA/NCI NIH HHS/United States ; R01 CA149655/CA/NCI NIH HHS/United States ; R01 GM127538/GM/NIGMS NIH HHS/United States ; R01 CA216421/CA/NCI NIH HHS/United States ; R01 CA202025/CA/NCI NIH HHS/United States ; UG1 CA233332/CA/NCI NIH HHS/United States ; U54 CA193419/CA/NCI NIH HHS/United States ; R35 CA220499/CA/NCI NIH HHS/United States ; P01 CA229086/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; 639784/ERC_/European Research Council/International ; U10 CA180820/CA/NCI NIH HHS/United States ; R00 CA188293/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; CCCTC-Binding Factor/genetics ; Carcinogenesis/genetics ; Cell Line, Tumor ; Chromatin/*genetics ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/genetics ; Humans ; Jurkat Cells ; Mice ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/*genetics ; Promoter Regions, Genetic/genetics ; T-Lymphocytes/*physiology ; }, abstract = {Differences in three-dimensional (3D) chromatin architecture can influence the integrity of topologically associating domains (TADs) and rewire specific enhancer-promoter interactions, impacting gene expression and leading to human disease. Here we investigate the 3D chromatin architecture in T cell acute lymphoblastic leukemia (T-ALL) by using primary human leukemia specimens and examine the dynamic responses of this architecture to pharmacological agents. Systematic integration of matched in situ Hi-C, RNA-seq and CTCF ChIP-seq datasets revealed widespread differences in intra-TAD chromatin interactions and TAD boundary insulation in T-ALL. Our studies identify and focus on a TAD 'fusion' event associated with absence of CTCF-mediated insulation, enabling direct interactions between the MYC promoter and a distal super-enhancer. Moreover, our data also demonstrate that small-molecule inhibitors targeting either oncogenic signal transduction or epigenetic regulation can alter specific 3D interactions found in leukemia. Overall, our study highlights the impact, complexity and dynamic nature of 3D chromatin architecture in human acute leukemia.}, }
@article {pmid32199341, year = {2020}, author = {Ibrahim, DM and Mundlos, S}, title = {The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization.}, journal = {Current opinion in genetics &amp; development}, volume = {61}, number = {}, pages = {1-8}, doi = {10.1016/j.gde.2020.02.015}, pmid = {32199341}, issn = {1879-0380}, mesh = {Animals ; Chromatin/*genetics/ultrastructure ; Chromatin Assembly and Disassembly/genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome/*genetics ; Humans ; Mice ; }, abstract = {The causal relationship between 3D chromatin domains and gene regulation has been of considerable debate in recent years. Initial Hi-C studies profiling the 3D chromatin structure of the genome described evolutionarily conserved Topologically Associating Domains (TADs) that correlated with gene expression. Subsequent evidence from mouse models and human disease directly linked TADs to gene regulation. However, a number of focused genetic and genome-wide studies questioned the relevance of 3D chromatin domains for orchestrating gene expression, ultimately yielding a more multi-layered view of 3D chromatin structure and gene regulation. We review the evidence for and against the importance of 3D chromatin structure for gene regulation and argue for a more comprehensive classification of regulatory chromatin domains that integrates 3D chromatin structure with genomic, functional, and evolutionary conservation.}, }
@article {pmid32193349, year = {2020}, author = {Carstens, S and Nilges, M and Habeck, M}, title = {Bayesian inference of chromatin structure ensembles from population-averaged contact data.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {14}, pages = {7824-7830}, pmid = {32193349}, issn = {1091-6490}, mesh = {*Bayes Theorem ; Chromatin/genetics/*ultrastructure ; Chromosomes/genetics/*ultrastructure ; Genome, Human/*genetics ; Humans ; Molecular Conformation ; }, abstract = {Mounting experimental evidence suggests a role for the spatial organization of chromatin in crucial processes of the cell nucleus such as transcription regulation. Chromosome conformation capture techniques allow us to characterize chromatin structure by mapping contacts between chromosomal loci on a genome-wide scale. The most widespread modality is to measure contact frequencies averaged over a population of cells. Single-cell variants exist, but suffer from low contact numbers and have not yet gained the same resolution as population methods. While intriguing biological insights have already been garnered from ensemble-averaged data, information about three-dimensional (3D) genome organization in the underlying individual cells remains largely obscured because the contact maps show only an average over a huge population of cells. Moreover, computational methods for structure modeling of chromatin have mostly focused on fitting a single consensus structure, thereby ignoring any cell-to-cell variability in the model itself. Here, we propose a fully Bayesian method to infer ensembles of chromatin structures and to determine the optimal number of states in a principled, objective way. We illustrate our approach on simulated data and compute multistate models of chromatin from chromosome conformation capture carbon copy (5C) data. Comparison with independent data suggests that the inferred ensembles represent the underlying sample population faithfully. Harnessing the rich information contained in multistate models, we investigate cell-to-cell variability of chromatin organization into topologically associating domains, thus highlighting the ability of our approach to deliver insights into chromatin organization of great biological relevance.}, }
@article {pmid32191860, year = {2020}, author = {Shinkai, S and Sugawara, T and Miura, H and Hiratani, I and Onami, S}, title = {Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization.}, journal = {Biophysical journal}, volume = {118}, number = {9}, pages = {2220-2228}, pmid = {32191860}, issn = {1542-0086}, mesh = {Animals ; Cell Nucleus ; *Chromatin/genetics ; *Chromosomes/genetics ; DNA ; Mice ; Mouse Embryonic Stem Cells ; }, abstract = {The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the microscale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose a new, to our knowledge, microrheology for Hi-C data to analyze the dynamic compliance property as a measure of rigidness and flexibility of genomic regions along with the time evolution. Our method allows the conversion of an Hi-C matrix into the spectrum of the dynamic rheological property along the genomic coordinate of a single chromosome. To demonstrate the power of the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD regions. The spectrum clearly shows the dynamic viscoelasticity of chromatin domain formation at different timescales. Furthermore, we characterized the appearance of synchronous and liquid-like intercompartment interactions in differentiated cells. Together, our microrheology data derived from Hi-C data provide physical insights into the dynamics of the 3D genome organization.}, }
@article {pmid32165395, year = {2020}, author = {Luo, Z and Hu, T and Jiang, H and Wang, R and Xu, Q and Zhang, S and Cao, J and Song, X}, title = {Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila.}, journal = {Genome research}, volume = {30}, number = {3}, pages = {406-414}, pmid = {32165395}, issn = {1549-5469}, mesh = {Centromere ; Chromatin/*chemistry ; Chromosomes/*chemistry ; Macronucleus/*genetics ; Meiosis/genetics ; Micronucleus, Germline/*genetics ; Tetrahymena thermophila/*genetics ; }, abstract = {The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila is still largely unknown. Here, we explored the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP methods. We found that the meiotic crescent MIC has a specific chromosome interaction pattern, with all the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which is also helpful to identify the midpoints of centromeres in the MIC. We revealed that the MAC chromosomes lack A/B compartments, topologically associating domains (TADs), and chromatin loops. The MIC chromosomes have TAD-like structures but not A/B compartments and chromatin loops. The boundaries of the TAD-like structures in the MIC are highly consistent with the chromatin breakage sequence (CBS) sites, suggesting that each TAD-like structure of the MIC chromosomes develops into one MAC chromosome during MAC development, which provides a mechanism of the formation of MAC chromosomes during conjugation. Overall, we demonstrated the distinct higher-order chromatin organization in the two nuclei of the T. thermophila and suggest that the higher-order chromatin structures may play important roles during the development of the MAC chromosomes.}, }
@article {pmid32160531, year = {2020}, author = {Santana, JF and Parida, M and Long, A and Wankum, J and Lilienthal, AJ and Nukala, KM and Manak, JR}, title = {The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains.}, journal = {Cell reports}, volume = {30}, number = {10}, pages = {3218-3228.e5}, pmid = {32160531}, issn = {2211-1247}, support = {T32 GM008629/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Cycle Proteins/*chemistry/*metabolism ; Drosophila Proteins/*chemistry/*metabolism ; Drosophila melanogaster/*metabolism ; Histones/*metabolism ; Insulator Elements/*genetics ; Lysine/*metabolism ; Methylation ; Oncogene Proteins/*metabolism ; Polycomb-Group Proteins/*chemistry ; Protein Binding ; Protein Domains ; Protein Stability ; Proto-Oncogene Proteins c-myb/*chemistry/*metabolism ; RNA Polymerase II/metabolism ; Transcription Initiation Site ; }, abstract = {Drosophila Myb (Dm-Myb) encodes a protein that plays a key role in regulation of mitotic phase genes. Here, we further refine its role in the context of a developing tissue as a potentiator of gene expression required for proper RNA polymerase II (RNA Pol II) function and efficient H3K4 methylation at promoters. In contrast to its role in gene activation, Myb is also required for repression of many genes, although no specific mechanism for this role has been proposed. We now reveal a critical role for Myb in contributing to insulator function, in part by promoting binding of insulator proteins BEAF-32 and CP190 and stabilizing H3K27me3 Polycomb-group (PcG) domains. In the absence of Myb, H3K27me3 is markedly reduced throughout the genome, leading to H3K4me3 spreading and gene derepression. Finally, Myb is enriched at boundaries that demarcate chromatin environments, including chromatin loop anchors. These results reveal functions of Myb that extend beyond transcriptional regulation.}, }
@article {pmid32116548, year = {2020}, author = {Van der Veen, DR and Laing, EE and Bae, SE and Johnston, JD and Dijk, DJ and Archer, SN}, title = {A Topological Cluster of Differentially Regulated Genes in Mice Lacking PER3.}, journal = {Frontiers in molecular neuroscience}, volume = {13}, number = {}, pages = {15}, pmid = {32116548}, issn = {1662-5099}, support = {BB/E003672/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020309/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F022883/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Polymorphisms in the human circadian clock gene PERIOD3 (PER3) are associated with a wide variety of phenotypes such as diurnal preference, delayed sleep phase disorder, sleep homeostasis, cognitive performance, bipolar disorder, type 2 diabetes, cardiac regulation, cancer, light sensitivity, hormone and cytokine secretion, and addiction. However, the molecular mechanisms underlying these phenotypic associations remain unknown. Per3 knockout mice (Per3[-/-]) have phenotypes related to activity, sleep homeostasis, anhedonia, metabolism, and behavioral responses to light. Using a protocol that induces behavioral differences in response to light in wild type and Per3[-/-] mice, we compared genome-wide expression in the eye and hypothalamus in the two genotypes. Differentially expressed transcripts were related to inflammation, taste, olfactory and melatonin receptors, lipid metabolism, cell cycle, ubiquitination, and hormones, as well as receptors and channels related to sleep regulation. Differentially expressed transcripts in both tissues co-localized with Per3 on an ∼8Mbp region of distal chromosome 4. The most down-regulated transcript is Prdm16, which is involved in adipocyte differentiation and may mediate altered body mass accumulation in Per3[-/-] mice. eQTL analysis with BXD mouse strains showed that the expression of some of these transcripts and also others co-localized at distal chromosome 4, is correlated with brain tissue expression levels of Per3 with a highly significant linkage to genetic variation in that region. These data identify a cluster of transcripts on mouse distal chromosome 4 that are co-regulated with Per3 and whose expression levels correlate with those of Per3. This locus lies within a topologically associating domain island that contains many genes with functional links to several of the diverse non-circadian phenotypes associated with polymorphisms in human PER3.}, }
@article {pmid32113985, year = {2020}, author = {Ji, L and Huo, X and Zhang, Y and Yan, Z and Wang, Q and Wen, B}, title = {TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1863}, number = {5}, pages = {194518}, doi = {10.1016/j.bbagrm.2020.194518}, pmid = {32113985}, issn = {1876-4320}, mesh = {Animals ; Cell Line ; Chromatin/*chemistry/metabolism ; Chromatin Assembly and Disassembly ; Mice ; Nuclear Lamina/metabolism ; Promyelocytic Leukemia Protein/metabolism ; Protein Binding ; Transcriptome ; Ubiquitin-Protein Ligases/genetics/*metabolism ; }, abstract = {In the nucleus, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs). However, the molecular mechanisms underlying these 3D chromatin architectures remain incompletely understood. Here, we investigated the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. In mouse hepatocytes, chromatin interactions between A and B compartments increase and compartmentalization strength is reduced significantly upon Topors knockdown. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. In the absence of TOPORS, chromatin-lamina interactions decrease and the coverage of LADs reduces from 53.31% to 46.52%. Interestingly, these changes in 3D genome are associated with PML nuclear bodies and PML-associated domains (PADs). Moreover, chromatin accessibility is altered predominantly at intergenic regions upon Topors knockdown, including a subset of enhancers. These alterations of chromatin are concordant with transcriptome changes, which are associated with carcinogenesis. Collectively, our findings demonstrate that TOPORS functions as a regulator in chromatin structure, providing novel insight into the architectural roles of tumor suppressors in higher-order genome organization.}, }
@article {pmid32110488, year = {2020}, author = {Sjakste, T and Leonova, E and Petrovs, R and Trapina, I and Röder, MS and Sjakste, N}, title = {Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8569}, pmid = {32110488}, issn = {2167-8359}, abstract = {BACKGROUND: The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings.<br><br>METHODS: The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer.<br><br>RESULTS: Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3&#xa0;+&#xa0;1 structures.<br><br>DISCUSSION: The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.}, }
@article {pmid32109364, year = {2020}, author = {Yokoshi, M and Segawa, K and Fukaya, T}, title = {Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication.}, journal = {Molecular cell}, volume = {78}, number = {2}, pages = {224-235.e5}, doi = {10.1016/j.molcel.2020.02.007}, pmid = {32109364}, issn = {1097-4164}, mesh = {Animals ; Chromosomes/genetics ; Drosophila/genetics/growth &amp; development ; Embryo, Nonmammalian ; Embryonic Development/*genetics ; *Enhancer Elements, Genetic ; *Promoter Regions, Genetic ; *Transcription, Genetic ; }, abstract = {Formation of self-associating loop domains is a fundamental organizational feature of metazoan genomes. Here, we employed quantitative live-imaging methods to visualize impacts of higher-order chromosome topology on enhancer-promoter communication in developing Drosophila embryos. Evidence is provided that distal enhancers effectively produce transcriptional bursting from target promoters over distances when they are flanked with boundary elements. Importantly, neither inversion nor deletion of a boundary element abrogates this "enhancer-assisting activity," suggesting that they can facilitate intra-domain enhancer-promoter interaction and production of transcriptional bursting independently of topologically associating domain (TAD) formation. In contrast, domain-skipping activity of distal enhancers was lost after disruption of topological domains. This observation raises a possibility that intra-domain and inter-domain enhancer-promoter interactions are differentially regulated by chromosome topology.}, }
@article {pmid32101721, year = {2020}, author = {Lazaris, C and Aifantis, I and Tsirigos, A}, title = {On Epigenetic Plasticity and Genome Topology.}, journal = {Trends in cancer}, volume = {6}, number = {3}, pages = {177-180}, doi = {10.1016/j.trecan.2020.01.006}, pmid = {32101721}, issn = {2405-8025}, mesh = {Cell Transformation, Neoplastic/genetics ; Chromatin/genetics/ultrastructure ; *Epigenomics ; *Gene Expression Regulation, Neoplastic/genetics ; *Genome, Human ; Humans ; Models, Genetic ; Neoplasms/*genetics ; Oncogenes ; Transcription, Genetic ; }, abstract = {Mounting evidence links genetic lesions with genome topology alterations and aberrant gene activation. However, the role of epigenetic plasticity remains elusive. Emerging studies implicate DNA methylation, transcriptional elongation, long noncoding RNAs (lncRNAs), and CCCTC-binding factor (CTCF)-RNA interactions, but systematic approaches are needed to fully decipher the role of epigenetic plasticity in genome integrity and function.}, }
@article {pmid32086528, year = {2020}, author = {Li, Y and Liao, Z and Luo, H and Benyoucef, A and Kang, Y and Lai, Q and Dovat, S and Miller, B and Chepelev, I and Li, Y and Zhao, K and Brand, M and Huang, S}, title = {Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis.}, journal = {Nucleic acids research}, volume = {48}, number = {6}, pages = {3119-3133}, pmid = {32086528}, issn = {1362-4962}, support = {R01 CA204044/CA/NCI NIH HHS/United States ; R01 DK110108/DK/NIDDK NIH HHS/United States ; MOP-343603//CIHR/Canada ; }, mesh = {Binding Sites/genetics ; CCCTC-Binding Factor/*genetics ; Carcinogenesis/*genetics ; Chromatin/genetics ; DNA-Binding Proteins/genetics ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation, Neoplastic ; Genome, Human/genetics ; Histone Code/genetics ; Humans ; Jurkat Cells ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/*genetics/pathology ; Protein Binding/genetics ; T-Cell Acute Lymphocytic Leukemia Protein 1/*genetics ; Transcription, Genetic/genetics ; }, abstract = {Aberrant activation of the TAL1 is associated with up to 60% of T-ALL cases and is involved in CTCF-mediated genome organization within the TAL1 locus, suggesting that CTCF boundary plays a pathogenic role in T-ALL. Here, we show that -31-Kb CTCF binding site (-31CBS) serves as chromatin boundary that defines topologically associating domain (TAD) and enhancer/promoter interaction required for TAL1 activation. Deleted or inverted -31CBS impairs TAL1 expression in a context-dependent manner. Deletion of -31CBS reduces chromatin accessibility and blocks long-range interaction between the +51 erythroid enhancer and TAL1 promoter-1 leading to inhibition of TAL1 expression in erythroid cells, but not T-ALL cells. However, in TAL1-expressing T-ALL cells, the leukemia-prone TAL1 promoter-IV specifically interacts with the +19 stem cell enhancer located 19 Kb downstream of TAL1 and this interaction is disrupted by the -31CBS inversion in T-ALL cells. Inversion of -31CBS in Jurkat cells alters chromatin accessibility, histone modifications and CTCF-mediated TAD leading to inhibition of TAL1 expression and TAL1-driven leukemogenesis. Thus, our data reveal that -31CBS acts as critical regulator to define +19-enhancer and the leukemic prone promoter IV interaction for TAL1 activation in T-ALL. Manipulation of CTCF boundary can alter TAL1 TAD and oncogenic transcription networks in leukemogenesis.}, }
@article {pmid32083658, year = {2020}, author = {Soler-Vila, P and Cuscó, P and Farabella, I and Di Stefano, M and Marti-Renom, MA}, title = {Hierarchical chromatin organization detected by TADpole.}, journal = {Nucleic acids research}, volume = {48}, number = {7}, pages = {e39}, pmid = {32083658}, issn = {1362-4962}, mesh = {Algorithms ; Animals ; Chromatin/*chemistry ; Mice ; *Software ; }, abstract = {The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.}, }
@article {pmid32060283, year = {2020}, author = {Arzate-Mejía, RG and Josué Cerecedo-Castillo, A and Guerrero, G and Furlan-Magaril, M and Recillas-Targa, F}, title = {In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {894}, pmid = {32060283}, issn = {2041-1723}, mesh = {Animals ; Chromatin/genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/metabolism ; *Genome, Insect ; RNA Polymerase II/genetics/metabolism ; *Transcription, Genetic ; }, abstract = {Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. The molecular mechanisms responsible for TAD formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by architectural proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.}, }
@article {pmid32036200, year = {2020}, author = {Ibrahim, DM and Mundlos, S}, title = {Three-dimensional chromatin in disease: What holds us together and what drives us apart?.}, journal = {Current opinion in cell biology}, volume = {64}, number = {}, pages = {1-9}, doi = {10.1016/j.ceb.2020.01.003}, pmid = {32036200}, issn = {1879-0410}, mesh = {Animals ; Chromatin/*chemistry ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation ; Genome ; Humans ; *Imaging, Three-Dimensional ; Promoter Regions, Genetic ; }, abstract = {Recent advances in understanding spatial genome organization inside the nucleus have shown that chromatin is compartmentalized into megabase-scale units known as topologically associating domains (TADs). In further studies, TADs were linked to differing transcriptional activity, suggesting that they might provide a scaffold for gene regulation by promoting enhancer-promoter interaction and by insulating regulatory activities. One strong argument for this hypothesis was provided by the effects of disease-causing structural variations in congenital disease and cancer. By rearranging TADs, these mutations result in a rewiring of enhancer-promoter contacts, consecutive gene misexpression, and ultimately disease. However, not all rearrangements are equally effective in creating these effects. Here, we review several recent studies aiming to understand the mechanisms by which disease-causing mutations achieve gene misregulation. We will discuss which regulatory effects are to be expected by different disease mutations and how this new knowledge can be used for diagnostics in the clinic.}, }
@article {pmid32024999, year = {2020}, author = {Akdemir, KC and Le, VT and Chandran, S and Li, Y and Verhaak, RG and Beroukhim, R and Campbell, PJ and Chin, L and Dixon, JR and Futreal, PA and ,  and , }, title = {Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.}, journal = {Nature genetics}, volume = {52}, number = {3}, pages = {294-305}, pmid = {32024999}, issn = {1546-1718}, support = {DP5 OD023071/OD/NIH HHS/United States ; R01 CA095175/CA/NCI NIH HHS/United States ; R01 CA217991/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R35 GM127029/GM/NIGMS NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Chromatin/*genetics ; Gene Expression Regulation, Neoplastic ; Gene Rearrangement/*genetics ; Genome, Human/*genetics ; *Genomic Structural Variation ; Humans ; Neoplasms/*genetics ; }, abstract = {Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these features. Indeed, domain disruptions in human cancers can lead to misregulation of gene expression. However, the frequency of domain disruptions in human cancers remains unclear. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we analyzed 288,457 somatic structural variations (SVs) to understand the distributions and effects of SVs across TADs. Notably, SVs can lead to the fusion of discrete TADs, and complex rearrangements markedly change chromatin folding maps in the cancer genomes. Notably, only 14% of the boundary deletions resulted in a change in expression in nearby genes of more than twofold.}, }
@article {pmid32014867, year = {2020}, author = {Bolt, CC and Duboule, D}, title = {The regulatory landscapes of developmental genes.}, journal = {Development (Cambridge, England)}, volume = {147}, number = {3}, pages = {}, pmid = {32014867}, issn = {1477-9129}, support = {F32 HD093555/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Chromatin/genetics/metabolism ; DNA/genetics/metabolism ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; *Genes, Developmental ; Genetic Loci ; Humans ; Mice ; Promoter Regions, Genetic ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic ; }, abstract = {Regulatory landscapes have been defined in vertebrates as large DNA segments containing diverse enhancer sequences that produce coherent gene transcription. These genomic platforms integrate multiple cellular signals and hence can trigger pleiotropic expression of developmental genes. Identifying and evaluating how these chromatin regions operate may be difficult as the underlying regulatory mechanisms can be as unique as the genes they control. In this brief article and accompanying poster, we discuss some of the ways in which regulatory landscapes operate, illustrating these mechanisms using genes important for vertebrate development as examples. We also highlight some of the techniques available to researchers for analysing regulatory landscapes.}, }
@article {pmid32009153, year = {2020}, author = {Kumar, V and Leclerc, S and Taniguchi, Y}, title = {BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes.}, journal = {Nucleic acids research}, volume = {48}, number = {5}, pages = {e26}, pmid = {32009153}, issn = {1362-4962}, mesh = {*Algorithms ; Cell Line ; Chromatin Assembly and Disassembly ; Chromosome Mapping ; Chromosomes, Human/*chemistry/ultrastructure ; DNA/*genetics/metabolism ; Fibroblasts/cytology/metabolism ; Genetic Loci ; Humans ; Multigene Family ; }, abstract = {High-throughput chromosome conformation capture (Hi-C) technology enables the investigation of genome-wide interactions among chromosome loci. Current algorithms focus on topologically associating domains (TADs), that are contiguous clusters along the genome coordinate, to describe the hierarchical structure of chromosomes. However, high resolution Hi-C displays a variety of interaction patterns beyond what current TAD detection methods can capture. Here, we present BHi-Cect, a novel top-down algorithm that finds clusters by considering every locus with no assumption of genomic contiguity using spectral clustering. Our results reveal that the hierarchical structure of chromosome is organized as 'enclaves', which are complex interwoven clusters at both local and global scales. We show that the nesting of local clusters within global clusters characterizing enclaves, is associated with the epigenomic activity found on the underlying DNA. Furthermore, we show that the hierarchical nesting that links different enclaves integrates their respective function. BHi-Cect provides means to uncover the general principles guiding chromatin architecture.}, }
@article {pmid31971237, year = {2020}, author = {Brackley, CA and Marenduzzo, D}, title = {Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions.}, journal = {Briefings in functional genomics}, volume = {19}, number = {2}, pages = {111-118}, doi = {10.1093/bfgp/elz032}, pmid = {31971237}, issn = {2041-2657}, mesh = {Chromatin/*chemistry/*metabolism ; *Photobleaching ; Protein Processing, Post-Translational ; }, abstract = {We review the mechanism and consequences of the 'bridging-induced attraction', a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains that conform well with the observation of A/B compartments in HiC experiments.}, }
@article {pmid31968256, year = {2020}, author = {Rhodes, JDP and Feldmann, A and Hernández-Rodríguez, B and Díaz, N and Brown, JM and Fursova, NA and Blackledge, NP and Prathapan, P and Dobrinic, P and Huseyin, MK and Szczurek, A and Kruse, K and Nasmyth, KA and Buckle, VJ and Vaquerizas, JM and Klose, RJ}, title = {Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells.}, journal = {Cell reports}, volume = {30}, number = {3}, pages = {820-835.e10}, pmid = {31968256}, issn = {2211-1247}, support = {294401/ERC_/European Research Council/International ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_00016/1/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 209400/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UP_1605/10/MRC_/Medical Research Council/United Kingdom ; 26747/CRUK_/Cancer Research UK/United Kingdom ; 107935/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; CCCTC-Binding Factor/metabolism ; Cell Cycle Proteins/*metabolism ; Cell Line ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/*metabolism ; Chromosomes/*metabolism ; Embryonic Stem Cells/*metabolism ; Gene Expression Regulation ; Male ; Mice ; Polycomb-Group Proteins/*metabolism ; }, abstract = {How chromosome organization is related to genome function remains poorly understood. Cohesin, loop extrusion, and CCCTC-binding factor (CTCF) have been proposed to create topologically associating domains (TADs) to regulate gene expression. Here, we examine chromosome conformation in embryonic stem cells lacking cohesin and find, as in other cell types, that cohesin is required to create TADs and regulate A/B compartmentalization. However, in the absence of cohesin, we identify a series of long-range chromosomal interactions that persist. These correspond to regions of the genome occupied by the polycomb repressive system and are dependent on PRC1. Importantly, we discover that cohesin counteracts these polycomb-dependent interactions, but not interactions between super-enhancers. This disruptive activity is independent of CTCF and insulation and appears to modulate gene repression by the polycomb system. Therefore, we discover that cohesin disrupts polycomb-dependent chromosome interactions to modulate gene expression in embryonic stem cells.}, }
@article {pmid31960372, year = {2020}, author = {Hu, G}, title = {Evaluation of 3D Chromatin Interactions Using Hi-C.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2117}, number = {}, pages = {65-78}, pmid = {31960372}, issn = {1940-6029}, support = {U54 GM104942/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Chromatin/*chemistry/*metabolism ; Computational Biology/*methods ; Epigenomics ; High-Throughput Nucleotide Sequencing ; Mice ; Molecular Conformation ; Mouse Embryonic Stem Cells/*chemistry ; Software ; }, abstract = {The invention of Hi-C has greatly facilitated 3D genome research through an unbiased probing of 3D chromatin interactions. It produces enormous amount of sequencing data that capture multiscale chromatin conformation structures. In the last decade, numerous computational methods have been developed to analyze Hi-C data and predict A/B compartments, topologically associating domains (TADs), and significant chromatin contacts. This chapter introduced the iHiC package that provides several utilities to facilitate Hi-C data analysis with public software and demonstrated its application to a Hi-C dataset generated for mouse embryonic stem (ES) cells.}, }
@article {pmid31956095, year = {2020}, author = {Yang, K and Xue, Z and Lv, X}, title = {Molecular mechanism of the 3D genome structure and function regulation during cell terminal differentiation.}, journal = {Yi chuan = Hereditas}, volume = {42}, number = {1}, pages = {32-44}, doi = {10.16288/j.yczz.19-270}, pmid = {31956095}, issn = {0253-9772}, mesh = {*Cell Differentiation ; Chromatin/*chemistry ; *Chromatin Assembly and Disassembly ; *Genome ; Genomics ; }, abstract = {The eukaryotic chromatin is folded into highly complex three-dimensional (3D) structures, which plays an im