@article {pmid40715029,
year = {2025},
author = {Jang, S and Yoon, S and Yang, H and Choi, N and Han, SH and Kim, LK and Kim, HP and Park, JH and Lee, D and Yoo, KH},
title = {Coordinated gene expression within sustained STAT3-associated chromatin conformations contributes to hepatocellular carcinoma progression.},
journal = {Cancer communications (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/cac2.70049},
pmid = {40715029},
issn = {2523-3548},
support = {//National Research Foundation of Korea/ ; 2022M3A9B6017424//Ministry of Science and ICT, Korea/ ; NRF-2021R1A6A1A03038890//Ministry of Science and ICT, Korea/ ; 2023R1A2C1005868//Ministry of Science and ICT, Korea/ ; 2022M3A9B6017654//Ministry of Science and ICT, Korea/ ; //Korea Basic Science Institute/ ; //National Research Facilities and Equipment Center/ ; RS-2024-00436674//Ministry of Education of Korea/ ; },
abstract = {BACKGROUND: Phosphorylated signal transducer and activator of transcription 3 (p-STAT3) has emerged as a critical modulator of hepatocellular carcinoma (HCC) progression. However, its role in three-dimensional (3D) chromatin conformation and the expression of genes linked to HCC aggressiveness remains largely unexplored. This study aimed to identify HCC 3D chromatin conformations that are regulated by sustained STAT3 activation and validate the molecular mechanisms underlying the aggressiveness of HCC.

METHODS: Comparative analyses were performed using HCC cell lines with varying levels of STAT3 activation. Chromatin immunoprecipitation-sequencing (ChIP-seq) for p-STAT3 and H3K27ac was conducted to map p-STAT3-associated genomic regions and assess its influence on chromatin states. Chromatin conformation sequencings (high-throughput chromosome conformation capture and high-throughput chromosome conformation capture followed by immunoprecipitation) were employed to investigate the 3D genome landscape and identify conformational changes linked to sustained p-STAT3 activation. RNA-sequencing was performed to assess transcriptional changes in response to these chromatin rearrangements. Functional assays, including invasion and tube formation assays, were carried out to validate the phenotypic impact of p-STAT3 activation on HCC progressiveness. Pharmacological inhibition of STAT3 was tested to explore potential therapeutic avenues and resistance mechanisms.

RESULTS: We found that sustained activation of p-STAT3 was significantly associated with poor prognostic outcomes in HCC patients. ChIP-seq demonstrated that p-STAT3 regulated chromatin interactions, leading to the formation of frequently interacting regions (FIREs), stable structural units within the 3D genome. Genes within these p-STAT3-associated FIREs exhibited coordinated expression, with many involved in aggressiveness HCC phenotypes like invasion and tube formation. Chromatin conformation data indicated that these FIREs altered topologically associating domains (TADs), potentially influencing broader chromatin organization. Despite STAT3 inhibition, p-STAT3-associated chromatin conformations remained intact, maintaining the expression of genes within FIREs and contributing to drug resistance.

CONCLUSIONS: Sustained p-STAT3 activation significantly alters the 3D chromatin conformation in HCC, particularly through the formation of FIREs. These p-STAT3-associated FIREs drive the expression of genes involved in HCC aggressiveness and remain active despite STAT3-targeted treatments, suggesting a mechanism of drug resistance. These findings highlight the potential of targeting 3D chromatin dynamics as a therapeutic strategy in HCC, especially in cases of STAT3 inhibitor resistance.},
}

@article {pmid40694328,
year = {2025},
author = {Frederick, J and Virk, RKA and Ye, IC and Almassalha, LM and Wodarcyk, GM and VanDerway, D and Gong, R and Dunton, CL and Kuo, T and Medina, KI and Loxas, M and Ahrendsen, JT and Gursel, DB and Gonzalez, PC and Nap, RJ and John, S and Agrawal, V and Anthony, NM and Carinato, J and Li, WS and Kakkaramadam, R and Jain, S and Shahabi, S and Ameer, GA and Szleifer, IG and Backman, V},
title = {Leveraging chromatin packing domains to target chemoevasion in vivo.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {30},
pages = {e2425319122},
doi = {10.1073/pnas.2425319122},
pmid = {40694328},
issn = {1091-6490},
support = {U54CA268084//HHS | NIH | National Cancer Institute (NCI)/ ; U54CA193419//HHS | NIH | National Cancer Institute (NCI)/ ; R01CA228272//HHS | NIH | National Cancer Institute (NCI)/ ; R01CA225002//HHS | NIH | National Cancer Institute (NCI)/ ; R01CA155284//HHS | NIH | National Cancer Institute (NCI)/ ; R01CA165309//HHS | NIH | National Cancer Institute (NCI)/ ; T32AI083216//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; EFMA-1830961//NSF | ENG | Division of Emerging Frontiers and Multidisciplinary Activities (EFMA)/ ; EFMA-1830968//NSF | ENG | Division of Emerging Frontiers and Multidisciplinary Activities (EFMA)/ ; CBET-1249311//NSF | ENG | Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET)/ ; EFRI-1240416//NSF | ENG | Division of Emerging Frontiers and Multidisciplinary Activities (EFMA)/ ; DGE-1842165//NSF | EDU | Division of Graduate Education (DGE)/ ; Innovation Award//Lefkofsky Family Foundation (LFF)/ ; Funded Lever Award//Chicago Biomedical Consortium (CBC)/ ; Searle Funds//Chicago Community Trust (CCT)/ ; },
mesh = {Humans ; *Chromatin/metabolism/chemistry/genetics ; Animals ; Mice ; Female ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology ; Xenograft Model Antitumor Assays ; *Drug Resistance, Neoplasm ; *Ovarian Neoplasms/drug therapy/genetics/pathology ; },
abstract = {Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains. However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based model that connects chromatin organization to cell fate decisions, such as survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional activity through macromolecular crowding. The model accurately predicts chemoevasion in vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. We conducted a proof-of-concept compound screen using live-cell chromatin imaging to identify several TPRs that synergistically enhanced chemotherapy-induced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a framework for enhancing cancer therapies, with broad potential across multiple cancer types.},
}

Humans
*Chromatin/metabolism/chemistry/genetics
Animals
Mice
Female
Cell Line, Tumor
*Antineoplastic Agents/pharmacology
Xenograft Model Antitumor Assays
*Drug Resistance, Neoplasm
*Ovarian Neoplasms/drug therapy/genetics/pathology

@article {pmid40685638,
year = {2025},
author = {Xu, T and Bush, SJ and Che, Y and Zhao, H and Wang, T and Jia, P and Wang, S and Sun, P and Zhang, P and Gao, S and Xu, Y and Wang, C and Dang, N and Zhang, YE and Yang, X and Ye, K},
title = {Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf061},
pmid = {40685638},
issn = {2210-3244},
abstract = {Long terminal repeat retrotransposons (LTR-RTs), a major type of class I transposable elements, are the most abundant repeat element in plants. The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs. However, for non-model species, this remains a challenge. To address this, we developed LTR_Stream for sub-lineage clustering of LTR-RTs in specific or closely related species, providing higher precision than current database-based lineage-level clustering. Using LTR_Stream, we analysed Retand LTR-RTs in three Papaver species. Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome. For instance, we found autonomous Retand elements could spread among the ancestors of different subgenomes, like retroviruses pandemics, enriching genetic diversity. Additionally, we identified that specific truncated fragments containing transcription factors motifs such as TCP and bZIP may contribute to generation of novel topologically associating domain like (TAD-like) boundaries. Notably, our pre-allopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization, suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs. We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.},
}

@article {pmid40684399,
year = {2025},
author = {Hilditch, C and Curtis, S and Cotton, S and LeBlanc, S and De Sousa, S},
title = {Non-penetrant Xq26.3 duplication involving the invariant TAD border: clinical evidence for the VGLL1 region as the GPR101 pituitary enhancer of X-linked acrogigantism.},
journal = {Pituitary},
volume = {28},
number = {4},
pages = {85},
pmid = {40684399},
issn = {1573-7403},
mesh = {Humans ; *Receptors, G-Protein-Coupled/genetics/metabolism ; Male ; *Gigantism/genetics ; Female ; *Chromosomes, Human, X/genetics ; *Transcription Factors/genetics ; *Genetic Diseases, X-Linked/genetics ; Pedigree ; Adult ; Pituitary Gland/metabolism ; DNA-Binding Proteins/genetics ; },
abstract = {INTRODUCTION: X-linked acrogigantism (X-LAG; OMIM: 300942) is a rare X-linked dominant, fully penetrant form of infancy-onset pituitary gigantism caused by Xq26.3 tandem duplications involving the GPR101 gene. All previously reported X-LAG-associated duplications disrupt the integrity of the resident topologically associating domain (TAD). This creates a neo-TAD, permitting ectopic chromatin interactions between GPR101 and centromeric pituitary enhancers postulated to lie between RBMX and VGLL1, and culminating in pituitary GPR101 misexpression and growth hormone excess. Conversely, none of the few previously reported cases of Xq26.3 duplications in unaffected individuals include the tissue-invariant TAD border that shields GPR101 from its centromeric enhancers. Preservation of this boundary has thus been considered synonymous with non-penetrance of X-LAG.

METHODS: We examined a series of four family members from the same kindred with an incidentally detected GPR101-containing Xq26.3 duplication involving the invariant TAD border.

RESULTS: Chromosome microarray demonstrated an interstitial chromosome Xq26.3 duplication: arr[GRCh37] Xq26.3(135,954,223 - 136,224,319)x2, including GPR101, the TAD invariant border and RBMX, but not VGLL1. None of the relatives with the Xq26.3 duplication exhibited evidence of growth hormone excess, making this the first unaffected family with a GPR101-containing Xq26.3 duplication involving the invariant TAD border. The predicted neo-TAD in this kindred excludes the VGLL1 region, which is present in all previously described X-LAG patients and absent in all previously described unaffected individuals with Xq26.3 duplications.

CONCLUSION: Our clinical findings suggest that TAD border involvement is not sufficient for X-LAG to develop, and implicates the VGLL1 region as likely the sole pituitary enhancer responsible for GPR101 misexpression and the X-LAG phenotype. Pending corroborative studies, this new insight into X-LAG pathogenesis may guide interpretation of future Xq26.3 duplications and counselling of families in whom such duplications are found.},
}

Humans
*Receptors, G-Protein-Coupled/genetics/metabolism
Male
*Gigantism/genetics
Female
*Chromosomes, Human, X/genetics
*Transcription Factors/genetics
*Genetic Diseases, X-Linked/genetics
Pedigree
Adult
Pituitary Gland/metabolism
DNA-Binding Proteins/genetics

@article {pmid40683887,
year = {2025},
author = {Beckwith, KS and Ødegård-Fougner, Ø and Morero, NR and Barton, C and Schueder, F and Tang, W and Alexander, S and Peters, JM and Jungmann, R and Birney, E and Ellenberg, J},
title = {Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6673},
pmid = {40683887},
issn = {2041-1723},
support = {U01 EB021223/EB/NIBIB NIH HHS/United States ; U01 DA047728/DA/NIDA NIH HHS/United States ; 101020558//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Cohesins ; *Chromosomal Proteins, Non-Histone/metabolism/genetics ; *Cell Cycle Proteins/metabolism/genetics ; *DNA/metabolism/chemistry/genetics ; Humans ; CCCTC-Binding Factor/metabolism ; Nucleic Acid Conformation ; Imaging, Three-Dimensional/methods ; Cell Nucleus/metabolism ; Single-Cell Analysis/methods ; },
abstract = {The spatial organization of the genome is essential for its functions, including gene expression and chromosome segregation. Phase separation and loop extrusion have been proposed to underlie compartments and topologically associating domains, however, whether the fold of genomic DNA inside the nucleus is consistent with such mechanisms has been difficult to establish in situ. Here, we present a 3D DNA-tracing workflow that resolves genome architecture in single structurally well-preserved cells with nanometre resolution. Our findings reveal that genomic DNA generally behaves as a flexible random coil at the 100-kb scale. At CTCF sites however, we find Cohesin-dependent loops in a subset of cells, in variable conformations from the kilobase to megabase scale. The 3D-folds we measured in hundreds of single cells allowed us to formulate a computational model that explains how sparse and dynamic loops in single cells underlie the appearance of compact topological domains measured in cell populations.},
}

Cohesins
*Chromosomal Proteins, Non-Histone/metabolism/genetics
*Cell Cycle Proteins/metabolism/genetics
*DNA/metabolism/chemistry/genetics
Humans
CCCTC-Binding Factor/metabolism
Nucleic Acid Conformation
Imaging, Three-Dimensional/methods
Cell Nucleus/metabolism
Single-Cell Analysis/methods

@article {pmid40683617,
year = {2025},
author = {Parida, P and Mukherjee, N and Singh, A and Lewis, S and Sharan, K and Mallya, S and Singh, A and Das, SS and Rao, M and Higginson, DS and Sabarinathan, R and Damerla, RR},
title = {Precise identification of viral-host integration events in HPV-positive cervical cancers by targeted long-read sequencing.},
journal = {Tumour virus research},
volume = {},
number = {},
pages = {200325},
doi = {10.1016/j.tvr.2025.200325},
pmid = {40683617},
issn = {2666-6790},
abstract = {Human papillomaviral (HPV) integrations into host human genome, a frequently observed event in HPV associated cervical cancer, are currently mapped through expensive Whole Genome sequencing (WGS) or RNA sequencing (RNA-seq) methodologies. This study aims to develop a targeted sequencing assay to determine HPV integrations in cervical tumors without the need for WGS or RNA-seq. We employed a library preparation strategy using tiled single primers that bind to HPV genome as a template and possibly extend HPV sequences into adjacent host human genomic sequences resulting in HPV and human chimeric sequences. Using this strategy, we sequenced known HPV integrations in HPV18 positive HeLa and HPV16 positive SiHa cell lines. We further used this method to detect HPV integration sites in four HPV-positive cervical cancer patients and confirmed these integration breakpoints by WGS and Sanger sequencing. Functional impact of HPV integrations was explored through differentially expressed genes within or near topologically associating domain (TAD) boundaries, possibly disrupted by respective integration events in these patients. We found ZFP36L1, CPA3, CPB1 and CXCL8 as some of the differentially expressed genes within disrupted TADs, which are known cancer associated genes. Our approach also reduced the cost of HPV integration detection by 90% compared to WGS while also minimizing sequencing data volume. We believe that this method captures HPV integrations at significantly reduced costs and lesser sequencing data volume leading to better understanding of disease progression and monitoring cancer treatment.},
}

@article {pmid40668555,
year = {2025},
author = {Shrestha, B and Wang, Z},
title = {HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf341},
pmid = {40668555},
issn = {1477-4054},
support = {1R35GM137974 to Z.W./GM/NIGMS NIH HHS/United States ; },
mesh = {*Chromatin/metabolism/chemistry/genetics ; Humans ; Chromatin Assembly and Disassembly ; *Deep Learning ; *Software ; },
abstract = {The 3D organization of chromatin is essential for the functioning of cellular processes, including transcriptional regulation, genome integrity, chromatin accessibility, and higher order nuclear architecture. However, detecting anomalous chromatin interactions in spatiotemporal Hi-C data remains a significant challenge. We present HiC4D-SPOT, an unsupervised deep-learning framework that models chromatin dynamics using a ConvLSTM-based autoencoder to identify structural anomalies. Benchmarking results demonstrate high reconstruction fidelity, with Pearson Correlation Coefficient and Spearman Correlation Coefficient values of 0.9, while accurately detecting deviations linked to temporal inconsistencies, topologically associating domain (TAD) and loop perturbations, and significant chromatin remodeling events. HiC4D-SPOT successfully identifies swapped time points in a time-swap experiment, captures simulated TAD and loop disruptions with high confidence scores and statistical significance of 0.01, and detects HERV-H boundary weakening during cardiomyocyte differentiation, as well as cohesin-mediated loop loss and recovery-aligning with experimentally observed chromatin remodeling events. These findings establish HiC4D-SPOT as an efficient tool for analyzing 3D chromatin dynamics, enabling the detection of biologically significant structural anomalies in spatiotemporal Hi-C data.},
}

*Chromatin/metabolism/chemistry/genetics
Humans
Chromatin Assembly and Disassembly
*Deep Learning
*Software

@article {pmid40666074,
year = {2025},
author = {Lyu, H and Li, Y and Chen, X and Liu, Y and Liu, E and Cheng, X},
title = {Topologically associating domains of chromatin on single-cell Hi-C data: a survey of bioinformatic tools and applications in the light of artificial intelligence.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1602234},
pmid = {40666074},
issn = {1664-8021},
abstract = {Topologically associating domains (TADs) uncovered on bulk Hi-C data are regarded as fundamental building blocks of a three-dimensional genome, and they are believed to effectively participate in the regulatory programs of gene expression. The computational analysis of TADs on single-cell Hi-C (scHi-C) data in the era of single-cell transcriptomics has received continuous attention since it may provide information beyond that on bulk Hi-C data. Unfortunately, the contact matrix for a single cell is ultra-sparse due to the low sequencing depth. Coupled with noises, artifacts, and dropout events from experiments, as well as cell heterogeneity caused by the cell cycle and transcription status, the computational analysis of TAD structures at the single-cell level has encountered some challenges not encountered at the bulk level. Herein, conduct a survey of bioinformatic tools and applications for TAD structures at the single-cell level in the light of artificial intelligence, including imputation of scHi-C data, identification of TAD boundaries and hierarchy, and differential analysis of TAD structures. The categories, characteristics, and evolutions of the latest available methods are summarized, especially the artificial intelligence strategies involved in these issues. This is followed by a discussion on why deep neural networks are attractive when discovering complex patterns from scHi-C data with an enormous number of cells and how it promotes the computational analysis of TADs at the single-cell level. Furthermore, the challenges that may be encountered in the analysis are outlined, and an outlook on the emerging trends in the near future is presented cautiously.},
}

@article {pmid40644525,
year = {2025},
author = {An, H and Fan, C and Kim, D and Bui, H and Park, Y},
title = {Discovery of oligodendrocyte enhancers that regulate Sox10 expression.},
journal = {PLoS genetics},
volume = {21},
number = {7},
pages = {e1011778},
doi = {10.1371/journal.pgen.1011778},
pmid = {40644525},
issn = {1553-7404},
abstract = {Oligodendrocytes (OLs) assemble myelin sheaths around axons in central nervous system (CNS). Myelin is essential for the saltatory conduction of action potentials and also performs other critical functions for the operation of the CNS. Sox10 (SRY-box containing gene 10) is a high-mobility group transcription factor that orchestrates the development of OLs. Despite its key role in OL biology, there is scant information on how the expression of Sox10 is regulated in OL lineage cells. Especially, OL enhancers that control its transcription remain elusive. We have recently developed an innovative method that rationally links OL enhancers to target genes. This study applied the new method to Sox10, uncovering two OL enhancers for it (termed Sox10-E1 and Sox10-E2). Epigenome editing analysis revealed that Sox10-E1 and Sox10-E2 regulate Sox10 expression non-redundantly. Luciferase assay and human and mouse brain multi-omics data show that, during the differentiation of OL precursor cells (OPCs) into OLs, the enhancer activity of Sox10-E1 does not change while that of Sox10-E2 decreases significantly. Chromatin interaction data indicate that the two Sox10 enhancers lie close to the border of the Sox10 topologically associating domain (TAD). Consistently, Pick1, a gene that is near the Sox10 TAD border, is also under the transcriptional control of Sox10-E1 and Sox10-E2. Hence, genomic deletions involving Sox10-E1 and Sox10-E2 would perturb not only SOX10, but also PICK1 and other genes, and may cause a pathology that is more complex than that of conventional Waardenburg-Shah syndrome that results from SOX10 coding mutations.},
}

@article {pmid40637236,
year = {2025},
author = {Ma, W and Wang, F and Fan, Y and Hao, G and Su, Y and Wong, KC and Li, X},
title = {DeepNanoHi-C: deep learning enables accurate single-cell nanopore long-read data analysis and 3D genome interpretation.},
journal = {Nucleic acids research},
volume = {53},
number = {13},
pages = {},
doi = {10.1093/nar/gkaf640},
pmid = {40637236},
issn = {1362-4962},
support = {62472195//China National Natural Science Foundation/ ; 62076109//China National Natural Science Foundation/ ; },
mesh = {*Deep Learning ; *Single-Cell Analysis/methods ; *Chromatin/genetics/chemistry ; Humans ; Nanopores ; *Nanopore Sequencing/methods ; *Genomics/methods ; Genome ; },
abstract = {Single-cell long-read concatemer sequencing (scNanoHi-C) technology provides unique insights into the higher-order chromatin structure across the genome in individual cells, crucial for understanding 3D genome organization. However, the lack of specialized analytical tools for scNanoHi-C data impedes progress, as existing methods, which primarily focus on scHi-C technologies, do not fully address the specific challenges of scNanoHi-C, such as sparsity, cell-specific variability, and complex chromatin interaction networks. Here, we introduce DeepNanoHi-C, a novel deep learning framework specifically designed for scNanoHi-C data, which leverages a multistep autoencoder and a Sparse Gated Mixture of Experts (SGMoE) to accurately predict chromatin interactions by imputing sparse contact maps, thereby capturing cell-specific structural features. DeepNanoHi-C effectively captures complex global chromatin contact patterns through the multistep autoencoder and dynamically selects the most appropriate expert from a pool of experts based on distinct chromatin contact patterns. Furthermore, DeepNanoHi-C integrates multiscale predictions through a dual-channel prediction net, refining complex interaction information and facilitating comprehensive downstream analyses of chromatin architecture. Experimental validation shows that DeepNanoHi-C outperforms existing methods in distinguishing cell types and demonstrates robust performance in data imputation tasks. Additionally, the framework identifies single-cell 3D genome features, such as cell-specific topologically associating domain (TAD) boundaries, further confirming its ability to accurately model chromatin interactions. Beyond single-cell analysis, DeepNanoHi-C also uncovers conserved genomic structures across species, providing insights into the evolutionary conservation of chromatin organization.},
}

*Deep Learning
*Single-Cell Analysis/methods
*Chromatin/genetics/chemistry
Humans
Nanopores
*Nanopore Sequencing/methods
*Genomics/methods
Genome

@article {pmid40630581,
year = {2025},
author = {Trivellin, G and Sánchez-Gaya, V and Grasso, A and Pasińska, M and Stratakis, CA and Milnes, D and Kirk, EP and Beckers, A and Lania, AG and Pétrossians, P and Rada-Iglesias, A and Franke, M and Daly, AF},
title = {Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1 -adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.25329768},
pmid = {40630581},
abstract = {BACKGROUND: Structural variants (SVs) that disrupt topologically associating domains (TADs) can cause disease by rewiring enhancer-promoter interactions. Duplications involving GPR101 are known to cause X-linked acrogigantism (X-LAG) by enabling aberrant expression of GPR101 through hijacking of enhancers at VGLL1 . However, not all GPR101 -containing duplications are pathogenic, presenting a diagnostic challenge, especially in the prenatal setting.

METHODS: We evaluated POSTRE, a tool designed to predict the regulatory impact of SVs, to distinguish pathogenic from benign GPR101 duplications. We analyzed six non-pathogenic duplications, and 27 known X-LAG associated pathogenic duplications. Tissue-specific enhancer maps built using H3K27ac ChIP-seq and ATAC-seq data as well as gene expression data derived from human anterior pituitary samples were integrated into POSTRE to enable predictions in a X-LAG relevant tissue context.

RESULTS: POSTRE correctly classified all 33 duplications as benign or pathogenic. In addition, one X-LAG case with mild clinical features (e.g., severe GH hypersecretion in the absence of pituitary tumorigenesis) was found to include only 2/5 VGLL1 enhancers (also predicted to be the weakest enhancers), whereas all 26 typical X-LAG cases had 24 enhancers duplicated. This suggests that milder enhancer hijacking at VGLL1 could explain the different clinical features of X-LAG in this individual.

CONCLUSIONS: These findings support the utility of POSTRE to support diagnostic pipelines when interpreting SVs affecting chromatin architecture in pituitary disease. By accurately modelling enhancer adoption in a cell type-specific context, POSTRE could help to reduce uncertainty in genetic counselling and offers a rapid alternative to performing chromatin conformation capture experiments.},
}

@article {pmid40629848,
year = {2025},
author = {Wei, J and Xue, Y and Gao, YQ},
title = {Hierarchical Prediction and Perturbation of Chromatin Organization Reveal How Loop Domains Mediate Higher-Order Architectures.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04799},
doi = {10.1002/advs.202504799},
pmid = {40629848},
issn = {2198-3844},
support = {2022ZD0115001//National Science and Technology Major Project/ ; 92353304//National Natural Science Foundation of China/ ; T2495221//National Natural Science Foundation of China/ ; NCI202305//New Cornerstone Science Foundation/ ; },
abstract = {The genome is folded within the dense cell nucleus in a hierarchical manner, resulting in complex interactions between distinct folding strategies at various length scales. To elucidate how short-range loop domains regulate higher-order structures of the chromatin, such as topologically associating domains (TADs) and compartments, HiCGen is introduced as a hierarchical and cell-type-specific generator based on Swin-transformer architecture. HiCGen predicts genome organization across different spatial scales utilizing DNA sequence and genomic features as inputs. The model enables in silico screening through genetic or epigenetic perturbations on genome architecture, with resolution down to 1 kb. The analysis reveals unexpected linear correlations between loop properties and genome organization at various levels, including insulation degree, compartmentalization, and contact intensity over genomic distances exceeding 10 Mb. Regional or global perturbation conducted by HiCGen provides biological implications for such cross-scale correlations and their genome-function dependence. Notably, perturbation analysis of the human genome in sigmoid colon tissue demonstrates that modest activation of carcinogenesis-associated enhancers is sufficient to hijack nearby promoter, reshape TAD boundaries, and even flip compartment at mega-base scale.},
}

@article {pmid40628528,
year = {2025},
author = {Rahmaninejad, H and Xiao, Y and Tortora, MMC and Fudenberg, G},
title = {Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280108.124},
pmid = {40628528},
issn = {1549-5469},
abstract = {In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This process enriches cohesin at barriers, isolates neighboring topologically associating domains, and elevates contact frequency between convergent CTCF barriers across the genome. However, recent in vivo measurements present a puzzle: reported CTCF residence times on chromatin are in the range of a few minutes, whereas cohesin lifetimes are much longer. Can the observed features of genome folding result from relatively transient barriers? To address this question, we develop a dynamic barrier model, where CTCF sites switch between bound and unbound states. Using this model, we investigate how barrier dynamics would impact observables for a range of experimental genomic and imaging data sets, including ChIP-seq, Hi-C, and microscopy. We find the interplay of CTCF and cohesin binding timescales influence the strength of each of these features, leaving a signature of barrier dynamics even in the population-averaged snapshots offered by genomic data sets. First, in addition to barrier occupancy, barrier bound times are crucial for instructing features of genome folding. Second, the ratio of boundary to extruder lifetime greatly alters simulated ChIP-seq and simulated Hi-C. Third, large-scale changes in chromosome morphology observed experimentally after increasing extruder lifetime require dynamic barriers. By integrating multiple sources of experimental data, our biophysical model argues that CTCF barrier bound times effectively approach those of cohesin extruder lifetimes. Together, we demonstrate how models that are informed by biophysically measured protein dynamics broaden our understanding of genome folding.},
}

@article {pmid40626176,
year = {2025},
author = {Liehr, T and Cross, E and Kankel, S},
title = {Directional genomic hybridization (dGH™) identifies small inverted duplications in situ.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1604822},
pmid = {40626176},
issn = {1664-8021},
abstract = {Although fluorescence in situ hybridization (FISH) is a standard approach for characterizing the chromosomal structure involving a region of interest, FISH targeting single chromatids is not routinely performed. However, this latter approach seems principally well-suited to distinguish small, tandem inverted duplications from direct duplications in clinical cases. A commercially available single-chromatid FISH approach, called "directional genomic hybridization" (dGH™), was applied in this study to nine cases of small supernumerary marker chromosomes (sSMCs) known to contain inverted duplications. Successful detection of small inverted duplications has been demonstrated for the first time in this study using a custom KromaTiD dGH™ InSite Assay. In all five euchromatic sSMC cases, inversions were detected using the dGH single-chromatid molecular cytogenetic assay. Thus, the dGH method of FISH is a readily applicable, straightforward approach for identifying small inverted duplications that are undetectable by conventional (molecular) cytogenetic methods. This technique may be used to identify the presence of small inversions within regions presenting a copy number gain as detected by chromosome microarray. Distinguishing small inverted duplications from direct duplications may have an impact on topologically associating domains (TADs) and, thus, on clinical outcome.},
}

@article {pmid40598900,
year = {2025},
author = {Maestri, D and Caruso, LB and Cable, JM and Sklutuis, R and Preston-Alp, S and White, RE and Luftig, MA and Tempera, I},
title = {EBNA leader protein orchestrates chromatin architecture remodeling during Epstein-Barr virus-induced B cell transformation.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf629},
pmid = {40598900},
issn = {1362-4962},
support = {P30 CA010815/CA/NCI NIH HHS/United States ; R01AI130209/GF/NIH HHS/United States ; R01AI182056/GF/NIH HHS/United States ; R01AI153508/GF/NIH HHS/United States ; P01 CA269043/GF/NIH HHS/United States ; P30 CA010815/GF/NIH HHS/United States ; R01CA140337/GF/NIH HHS/United States ; T32CA09171/GF/NIH HHS/United States ; T32CA288356/GF/NIH HHS/United States ; },
mesh = {Humans ; *Herpesvirus 4, Human/genetics/pathogenicity ; *B-Lymphocytes/virology/metabolism/pathology ; *Chromatin Assembly and Disassembly/genetics ; Chromatin/metabolism/genetics ; *Epstein-Barr Virus Nuclear Antigens/metabolism/genetics ; *Cell Transformation, Viral/genetics ; *Viral Proteins/metabolism/genetics ; Enhancer Elements, Genetic ; CCCTC-Binding Factor/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Epstein-Barr Virus Infections/virology/genetics ; },
abstract = {Epstein-Barr virus Nuclear Antigen Leader Protein (EBNA-LP) plays a pivotal role in the transformation of B cells by Epstein-Barr virus (EBV), functioning independently of EBNA2 to regulate chromatin architecture and gene expression. Our study reveals that EBNA-LP binds to chromatin regions distinct from EBNA2 and facilitates the formation of long-distance chromatin loops by interacting with the cellular factor YY1. This interaction reconfigures the three-dimensional structure of the host genome, enhancing the integrity of topologically associating domains (TADs) and promoting the interaction between enhancers and promoters within these domains. In EBV-infected B cells, EBNA-LP strengthens YY1-mediated chromatin loops within TADs, which helps maintain stable regulatory programs essential for B cell transformation. Notably, EBNA-LP is crucial for establishing EBV-induced enhancers, yet it is not required for their maintenance once formed. Additionally, our data suggest a compensatory increase in CTCF binding in the absence of EBNA-LP, leading to more promiscuous chromatin interactions between TADs and a reduced TAD insulation at their boundaries. These findings provide new insights into the molecular mechanisms by which EBV reshapes the host genome chromatin architecture to support B cell transformation and highlight potential therapeutic targets for disrupting EBV-driven oncogenesis.},
}

Humans
*Herpesvirus 4, Human/genetics/pathogenicity
*B-Lymphocytes/virology/metabolism/pathology
*Chromatin Assembly and Disassembly/genetics
Chromatin/metabolism/genetics
*Epstein-Barr Virus Nuclear Antigens/metabolism/genetics
*Cell Transformation, Viral/genetics
*Viral Proteins/metabolism/genetics
Enhancer Elements, Genetic
CCCTC-Binding Factor/metabolism
Promoter Regions, Genetic
Protein Binding
Epstein-Barr Virus Infections/virology/genetics

@article {pmid40597210,
year = {2025},
author = {Bai, X and Tang, X and Wang, Y and Yue, S and Xu, X and Hu, P and Xu, J and Li, Y and Wang, J and Tao, H and Zheng, Y and Chen, B and Tian, M and Lin, L and Wang, R and Sun, Y and Ren, C and Bo, X and Li, H and Chen, H and Lu, M},
title = {The hierarchical folding dynamics of topologically associating domains during early embryo development.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {175},
pmid = {40597210},
issn = {1741-7007},
support = {62173338//National Natural Science Foundation of China/ ; 82001520//National Natural Science Foundation of China/ ; 20220484198//Beijing Nova Program of Science and Technology/ ; 20230484290//Beijing Nova Program of Science and Technology/ ; 62422318//National Natural Science Foundation of China/ ; 2024YFA1307700//National Key Research and Development Program of China/ ; 2023YFF0725500//National Key Research and Development Program of China/ ; },
mesh = {*Embryonic Development/genetics ; Animals ; *Chromatin/metabolism/chemistry ; *Gene Expression Regulation, Developmental ; Histones/metabolism ; Zygote/metabolism ; Mice ; },
abstract = {BACKGROUND: Recent research has indicated a close connection between the three-dimensional (3D) structure of chromatin and early embryo development, with precise higher-order chromatin folding playing a significant role in mediating gene expression. However, the specific role of 3D genomic hierarchical structure and its dynamics in early embryo development remains largely unknown.

RESULTS: In this study, we examined the hierarchical topological association domain (TAD) during early embryo development and its relationship with zygotic gene activation (ZGA), gene expression, and chromatin accessibility to gain a better understanding of the dynamics of TAD nesting levels during this developmental stage. Our findings show that ZGA precedes the establishment of hierarchical TAD, leading to widespread gene expression, an increase in the percentage of high-level TAD structures, and enhanced chromatin accessibility at higher hierarchical levels. Additionally, we utilized a deep neural network to investigate the formation of TAD boundaries and found that histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine trimethylation (H3K27me3) are key features in the establishment of TAD boundaries. Furthermore, we observed heterogeneous dynamics of hierarchical TAD among different species.

CONCLUSIONS: Overall, our study sheds light on the folding dynamics of hierarchical TADs during early embryo development and underscores their close relationship with transcriptional programs.},
}

*Embryonic Development/genetics
Animals
*Chromatin/metabolism/chemistry
*Gene Expression Regulation, Developmental
Histones/metabolism
Zygote/metabolism
Mice

@article {pmid40588575,
year = {2025},
author = {Sreenivasan, VKA and Yumiceba, V and Spielmann, M},
title = {Structural variants in the 3D genome as drivers of disease.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40588575},
issn = {1471-0064},
abstract = {The spatial organization of the genome within the nucleus - also known as genome architecture or 3D genome - is important to the regulation of gene expression. Disruption of the 3D genome, for example, by structural variation, can contribute to disease, including developmental disorders and cancer. Structural variants can rearrange higher-order chromatin structures, such as topologically associating domains, and disrupt interactions between cis-regulatory elements, which can lead to altered gene expression, a phenomenon known as position effects. New experimental and computational approaches are revealing the effect of structural variants on the 3D genome and gene expression and can help interpret their pathogenic potential, which has important implications for patients. Here, we review mechanisms of disease caused by position effects owing to disruptions of genome architecture, and more specifically topologically associating domains, as well as their consequences and clinical impact.},
}

@article {pmid40588507,
year = {2025},
author = {Wong, EWP and Sahin, M and Yang, R and Lee, U and Li, D and Zhan, YA and Misra, R and Tomas, F and Alomran, N and Polyzos, A and Lee, CJ and Trieu, T and Martinez-Fundichely, A and Wiesner, T and Rosowicz, A and Cheng, S and Liu, C and Lallo, M and Shoushtari, AN 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 = {Disruption of TAD hierarchy promotes LTR co-option in cancer.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40588507},
issn = {1546-1718},
abstract = {Transposable elements (TEs) are abundant in the human genome, and they provide the source for genetic and functional diversity. Previous studies have suggested that TEs are repressed by DNA methylation and chromatin modifications. Here through integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters (altPs) at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and the recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. Perturbation of hierarchical chromatin topology can lead to co-option of LTRs as functional altPs, driving aberrant transcriptional activation of oncogenes. These data uncovered a new layer of regulatory mechanisms of TE expression and posit TAD hierarchy dysregulation as a new mechanism for altP-mediated oncogene activation and transcriptional diversity in cancer.},
}

@article {pmid40586163,
year = {2025},
author = {Xu, K and Yu, Z and Sun, C and Gou, C and Zhu, J and Wang, J and Bo, X and Yu, G and Li, H and Chen, H},
title = {ChromInSight: Revealing DNA Double-Strand Breaks Through Chromatin Structural Insights With an Interpretable Graph Neural Network Framework.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04571},
doi = {10.1002/advs.202504571},
pmid = {40586163},
issn = {2198-3844},
support = {62422318//National Natural Science Foundation of China/ ; 62173338//National Natural Science Foundation of China/ ; 2024YFA1307700//National Key R&D Program of China/ ; 2023YFF0725500//National Key R&D Program of China/ ; },
abstract = {DNA double-strand breaks (DSBs) represent one of the most severe forms of genomic damage. Although substantial progress has been made in elucidating general patterns associated with DSBs, the influence of 3D chromatin structure on DSB formation remains underexplored, particularly concerning its spatial configuration. Here, the ChromInSight framework is introduced. Using standardized datasets,Hi-DSB is developed and deployed in ChromInSight, a genome-wide DSB prediction model based on graph contrastive learning (GCL), and applied advanced interpretability techniques to identify DSB-associated genomic patterns. The findings reveal that the spatial cluster-scene between hub nodes and DSB sites is predominantly shaped by the 3D conformation of chromatin, rather than by linear genomic distance. This phenomenon is validated at both the Loop and topologically associating domain (TAD) levels and proposed a "spatial isolation - damage containment" hypothesis, which illustrates the genome strategy for managing damage. These findings support the role of 3D genome architecture in genomic instability. Consequently, the framework provides a powerful tool for investigating the intricate relationship between chromatin structure and genomic stability.},
}

@article {pmid40579703,
year = {2025},
author = {Li, KY and Cao, Q and Chow, SH and Nicoletti, C and Puri, PL and Wang, H and Leung, D and Yip, KY},
title = {Regulatory roles of three-dimensional structures of chromatin domains.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {184},
pmid = {40579703},
issn = {1474-760X},
support = {U54AG079758/AG/NIA NIH HHS/United States ; U54AG079758/AG/NIA NIH HHS/United States ; General Research Fund 14107420//Research Grants Council, University Grants Committee/ ; General Research Fund 14107420//Research Grants Council, University Grants Committee/ ; General Research Fund 14107420//Research Grants Council, University Grants Committee/ ; General Research Fund 14107420//Research Grants Council, University Grants Committee/ ; 32100515//National Natural Science Foundation of China/ ; 2021.061//Chinese University of Hong Kong/ ; EDUC4-12813//California Institute for Regenerative Medicine/ ; P30CA030199/CA/NCI NIH HHS/United States ; },
mesh = {*Chromatin/chemistry/genetics/metabolism ; Humans ; *Gene Expression Regulation ; Enhancer Elements, Genetic ; Transcription Factors/metabolism ; Binding Sites ; Histones/metabolism ; },
abstract = {BACKGROUND: Transcriptional enhancers usually, but not always, regulate genes within the same topologically associating domain (TAD). We hypothesize that this incomplete insulation is partially due to three-dimensional structures of corresponding chromatin domains in individual cells: whereas enhancers and genes buried inside the core of a domain interact mostly with other regions in the same domain, those on the surface can more easily interact with the outside.

RESULTS: Here we show that a simple measure, the intra-TAD ratio, can quantify the coreness of a region with respect to the single-cell domains to which it belongs. We show that domain surfaces are permissive for high gene expression. Cell type-specific active cis-regulatory elements, active histone marks, and transcription factor binding sites are enriched on domain surfaces, most strongly in chromatin subcompartments typically considered inactive.

CONCLUSIONS: These findings suggest a model of gene regulation that involves positioning active cis-regulatory elements on domain surfaces. We also find that disease-associated non-coding variants are enriched on domain surfaces.},
}

*Chromatin/chemistry/genetics/metabolism
Humans
*Gene Expression Regulation
Enhancer Elements, Genetic
Transcription Factors/metabolism
Binding Sites
Histones/metabolism

@article {pmid40544603,
year = {2025},
author = {Liu, X and Tao, Y and Zhang, L and Liu, Y and Shi, D and Wang, J and Xue, P and Xu, B and Fang, W and Ran, Y},
title = {Caged-hypocrellin mediated photodynamic therapy induces chromatin remodeling and disrupts mitochondrial energy metabolism in multidrug-resistant Candida auris.},
journal = {Redox biology},
volume = {85},
number = {},
pages = {103708},
doi = {10.1016/j.redox.2025.103708},
pmid = {40544603},
issn = {2213-2317},
abstract = {Candida auris is a fungal pathogen with frequent development of multidrug-resistance or pan-drug resistance. Currently, the treatment options for Candida auris are limited. Therefore, there is an urgent need for alternative therapeutic strategies. Antimicrobial photodynamic therapy (aPDT), which generates reactive oxygen species (ROS) through light-activated photosensitizers, has shown promise against C. auris; however, its molecular mechanism remains unclear. To investigate COP1T-HA-mediated PDT-induced genomic alterations, we constructed a 3D genome map of Candida species, which uncovered the reorganization of chromatin architecture in response to PDT treatment. Our data showed that low-dose PDT causes subtle local adjustments in chromatin topology, whereas high-dose PDT leads to more pronounced changes in A/B compartmentalization, topologically associating domain (TAD) organization, and chromatin looping associated with key genes related to mitochondrial energy metabolism. Confocal imaging confirmed that high-dose COP1T-HA-mediated PDT induces localized ROS accumulation near the nucleus and a temporally ordered cellular stress response. Furthermore, functional validation through QCR10, NDUFA5, and MP knockouts confirmed the essential roles of these genes in mitochondrial integrity, ATP synthesis, ROS homeostasis, and biofilm formation. Mutants showed altered mitochondrial membrane potential, intracellular pH imbalance, and enhanced glycolytic compensation, highlighting the impact of electron transport disruption on energy metabolism. This study provides the first comprehensive insight into COP1T-HA-mediated PDT-induced chromatin reorganization in C. auris and establishes a direct connection between 3D genome remodeling and fungal energy metabolism, offering a foundation for chromatin-targeted antifungal strategies.},
}

@article {pmid40537528,
year = {2025},
author = {González-Almela, E and Castells-Garcia, A and Le Dily, F and Merino, MF and Carnevali, D and Cusco, P and Di Croce, L and Cosma, MP},
title = {Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5313},
pmid = {40537528},
issn = {2041-1723},
support = {31971177//National Science Foundation of China | International Cooperation and Exchange Programme/ ; },
abstract = {Herpes simplex virus type 1 (HSV-1) remodels the host chromatin structure and induces a host-to-virus transcriptional switch during lytic infection. We combine super-resolution imaging and chromosome-capture technologies to identify the mechanism of remodeling. We show that the host chromatin undergoes massive condensation caused by the hijacking of RNA polymerase II (RNAP II) and topoisomerase I (TOP1). In addition, HSV-1 infection results in the rearrangement of topologically associating domains and loops, although the A/B compartments are maintained in the host. The position of viral genomes and their association with RNAP II and cohesin is determined nanometrically. We reveal specific host-HSV-1 genome interactions and enrichment of upregulated human genes in the most contacting regions. Finally, TOP1 inhibition fully blocks HSV-1 infection, suggesting possible antiviral strategies. This viral mechanism of host chromatin rewiring sheds light on the role of transcription in chromatin architecture.},
}

@article {pmid40513402,
year = {2025},
author = {Cetin, S and Sefer, E},
title = {The significance of chromosome conformation capture in 3D genome architecture comprehension.},
journal = {Computational biology and chemistry},
volume = {119},
number = {},
pages = {108534},
doi = {10.1016/j.compbiolchem.2025.108534},
pmid = {40513402},
issn = {1476-928X},
abstract = {Chromosomes are intricate macromolecules composed of chromatin that create three-dimensional structures within cells. The arrangement and interactions of chromosomes play a crucial role in shaping the genome's structure, function, and gene expression regulation. To fully grasp the architecture and adaptability of the genome, it is essential to understand the complex relationship between chromosomal structure and nucleotide sequences. Advances in our understanding of genome topology have been significantly driven by next-generation sequencing technologies designed for capturing chromatin conformation. The exploration of 3D genome organization has led to the development of high-throughput chromatin conformation capture (Hi-C) techniques. Hi-C is essential for revealing new aspects of genome architecture and for mapping genome-wide chromosomal interactions, both within individual chromosomes and between them. These interactions include chromosomal territories, topologically associating domains (TADs), and chromatin or gene loops. This review provides a comprehensive overview of the historical development and current state of 'C' technologies, in-depth insights into various Hi-C techniques, and the analysis of 3D genome structures. It concludes with a discussion on computational tools for analyzing high-resolution Hi-C data, the challenges in modeling 3D genome structures, and potential future advancements in the field.},
}

@article {pmid40501564,
year = {2025},
author = {Xu, W and Cui, J and Zhang, S and Lu, L and Liu, X and Li, Y and Jin, F},
title = {Map functional insulators with cross-platform Hi-C meta-analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656183},
pmid = {40501564},
issn = {2692-8205},
abstract = {CTCF forms the boundaries of topologically associating domains (TADs) but their insulating function in transcription is controversial. Here we report that functional insulators (FINs) shall be determined not only by their ability to form static loops or boundaries, but also by the dynamic context if their flanking sequences form new loops upon boundary loss. We performed a meta-analysis of nine independent Hi-C and micro-C datasets upon acute CTCF- or cohesin protein-depletion and found that only at several hundred loci, newly gained enhancers-promoters (E-P) loops can be reproducibly observed upon CTCF depletion. The new E-P loops are cohesin-dependent and associated with recurrent gene activation. These findings allow us to map FINs and define their direct target genes genome-wide. FINs are mostly present in euchromatin, do not overlap with TAD boundaries, and can be perturbed by Wapl -depletion or CTCF-displacement. We therefore conclude that FINs, but not TAD boundaries, are bona fide insulators.},
}

@article {pmid40495214,
year = {2025},
author = {Li, J and Xu, L and Wang, J and Wang, X and Lin, Y and Zou, AY and Ren, F and Wang, Y and Li, J and Chang, Z},
title = {CREPT is required for the metastasis of triple-negative breast cancer through a co-operational-chromatin loop-based gene regulation.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {170},
pmid = {40495214},
issn = {1476-4598},
support = {81230044, 81872249 and 81830092//National Natural Science Foundation of China/ ; 81230044, 81872249 and 81830092//National Natural Science Foundation of China/ ; 2016YFA0500301//Chinese National Major Scientific Research Program/ ; 7172213//Beijing Scientific Projects/ ; JFLKYXM202303AZ-203//Jinfeng Lab/ ; },
mesh = {*Triple Negative Breast Neoplasms/genetics/pathology/metabolism ; Humans ; Animals ; Female ; *Gene Expression Regulation, Neoplastic ; Mice ; *Chromatin/genetics/metabolism ; Neoplasm Metastasis ; Cell Line, Tumor ; Promoter Regions, Genetic ; Prognosis ; },
abstract = {Triple-negative breast cancer (TNBC) is recognized for its aggressiveness, yet the mechanism underlying metastasis remains unclear. Here, we report that CREPT/RPRD1B, which exhibits somatic gene copy-number amplifications and elevated expression, correlates with poor patient survival and drives TNBC metastasis. We demonstrate that CREPT alters three-dimensional genome structures in topologically-associating domain (TAD) status and chromatin loops via occupying promoters and enhancers. Specifically, CREPT mediates 1082 co-operational chromatin loops configured by enhancer-promoter and promoter-termination loops, which are validated by HiChIP analyses and visualized by Tn5-FISH experiments. These loops orchestrate RNAPII loading and recycling to enhance the metastatic gene expression. Disruption of these co-operational loops using CRISPR-dCas9 suppresses TNBC metastasis in vivo. Furthermore, depletion of CREPT using an AAV-based shRNA blocks TNBC metastasis in both preventative and therapeutic mouse models. We propose that targeting CREPT to disrupt the co-operational chromatin loop structures represents a promising therapeutic strategy for metastatic TNBC.},
}

*Triple Negative Breast Neoplasms/genetics/pathology/metabolism
Humans
Animals
Female
*Gene Expression Regulation, Neoplastic
Mice
*Chromatin/genetics/metabolism
Neoplasm Metastasis
Cell Line, Tumor
Promoter Regions, Genetic
Prognosis

@article {pmid40456819,
year = {2025},
author = {Zhang, K and Chen, M and Chen, M and Wang, Y and Liu, H and Li, Y and Guan, X and Lei, L and Tao, L and Liu, X and He, D and Fei, X},
title = {The 3D genome of plasma cells in multiple myeloma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19331},
pmid = {40456819},
issn = {2045-2322},
support = {2020YJ0438//The Science and Technology Department of Sichuan Province/ ; },
mesh = {Humans ; *Multiple Myeloma/genetics/pathology ; *Plasma Cells/metabolism/pathology ; Transcriptome ; Male ; Female ; Gene Expression Profiling ; Polymorphism, Single Nucleotide ; Aged ; *Genome, Human ; Gene Expression Regulation, Neoplastic ; Middle Aged ; Genomics/methods ; },
abstract = {Multiple myeloma (MM) is a hematological malignancy characterized by expanding clonal plasma cells in the bone marrow (BM) that produce monoclonal immunoglobulin. It is an incurable disease, accounting for about 10% of blood malignancies and the second most common hematologic malignancy. Therefore, in-depth research into the molecular mechanisms and therapeutic targets of the disease is crucial. For the first time, we performed high-throughput chromosome conformation capture (Hi-C) analysis of plasma cells in five multiple myeloma patients, and integrated it with genome resequencing and transcriptomic associated with genomic variation and gene expression. As a result, 19 specific TAD (Topologically Associating Domain) boundaries in MM samples related to the immune response and Wnt signaling pathways were identified. Additionally, Loop structures were also analyzed, revealing that promoter-enhancer-associated loops were the most prevalent. Genomic characteristics of MM patients were explored, identifying SNPs, InDels, and CNVs, with variations in the CDS region potentially affecting gene function. Transcriptome analysis showed differentially expressed genes in MM patients, mainly involved in p53 signaling and cell adhesion. Multi-omics analysis identified overlapping genes related to MM, including those involved in MHC class II protein complex assembly and antigen presentation. The study provides insights into the complex genomic and transcriptomic changes in MM plasma cells, potentially aiding in identifying therapeutic targets.},
}

Humans
*Multiple Myeloma/genetics/pathology
*Plasma Cells/metabolism/pathology
Transcriptome
Male
Female
Gene Expression Profiling
Polymorphism, Single Nucleotide
Aged
*Genome, Human
Gene Expression Regulation, Neoplastic
Middle Aged
Genomics/methods

@article {pmid40448401,
year = {2025},
author = {Yamasaki, YY and Toyoda, A and Kadota, M and Kuraku, S and Kitano, J},
title = {3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17814},
doi = {10.1111/mec.17814},
pmid = {40448401},
issn = {1365-294X},
support = {JPMJCR20S2//Core Research for Evolutional Science and Technology/ ; 16H06279//Japan Society for the Promotion of Science/ ; 20J01503//Japan Society for the Promotion of Science/ ; 21H02542//Japan Society for the Promotion of Science/ ; 22H04983//Japan Society for the Promotion of Science/ ; 22KK0105//Japan Society for the Promotion of Science/ ; },
abstract = {DNA within the nucleus is organised into a well-regulated three-dimensional (3D) structure. However, how such 3D genome structures influence speciation processes remains largely elusive. Recent studies have shown that 3D genome structures influence mutation rates, including the occurrence of chromosomal rearrangement. For example, breakpoints of chromosomal rearrangements tend to be located at topologically associating domain (TAD) boundaries. Here, we hypothesised that TAD structures may constrain the location of chromosomal inversions and thereby shape the genomic landscape of divergence between species with ongoing gene flow, given that inversions can act as barriers to gene flow. To test this hypothesis, we used a pair of Japanese stickleback species, Gasterosteus nipponicus (Japan Sea stickleback) and G. aculeatus (three-spined stickleback). We first constructed chromosome-scale genome assemblies of both species using high fidelity long reads and high-resolution proximity ligation data and identified several chromosomal inversions. Second, via population genomic analyses, we revealed higher genetic differentiation in inverted regions than in colinear regions and no gene flow within inversions, which contrasts with the significant gene flow in colinear regions. Third, using Hi-C data, we revealed 3D genome structures of sticklebacks, delineated by A/B compartments and TADs. Finally, we found that inversion breakpoints tend to be located at TAD boundaries. Thus, our study demonstrates that the 3D genome constrains breakpoints of inversions that can act as barriers to gene flow in the stickleback. Further integration of 3D genome analyses with population genomics could provide novel insights into how the 3D genome influences speciation.},
}

@article {pmid40436628,
year = {2025},
author = {Williamson, I and Graham, KA and Woolf, M and Becher, H and Hill, RE and Bickmore, WA and Lettice, LA},
title = {Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function.},
journal = {Genes & development},
volume = {},
number = {},
pages = {},
doi = {10.1101/gad.352648.125},
pmid = {40436628},
issn = {1549-5477},
abstract = {Mammalian enhancers can regulate genes over large genomic distances, often skipping over other genes. Despite this, precise developmental regulation suggests that mechanisms exist to ensure enhancers only activate their correct targets. Sculpting of three-dimensional chromosome organization through cohesin-dependent loop extrusion is thought to be important for facilitating and constraining enhancer action. The boundaries of topologically associating domains (TADs) are thought to prevent enhancers acting on genes in adjacent TADs. However, there are examples where enhancers appear to act across TAD boundaries, but it has remained unclear whether a single enhancer can simultaneously activate genes in different TADs. Here we show that some Shh enhancers can activate transcription concurrently not only at Shh but also at Mnx1 located in an adjacent TAD. This occurs in the context of a chromatin conformation maintaining genes and enhancers in close proximity and is influenced by cohesin. To our knowledge, this is the first report of two endogenous mammalian genes transcribed concurrently under the control of the same enhancer and across a TAD boundary. These findings have implications for understanding the design rules of gene regulatory landscapes and are consistent with a transcription cluster model of enhancer-promoter communication.},
}

@article {pmid40405503,
year = {2025},
author = {Xu, Y and Wu, D and Zhao, M and Tang, W and Cheng, X and Hu, Q and Liu, Z and Gan, J and Hua, J and Zou, G and Lu, A and Yang, C and Zheng, Y and Li, W and Li, J and Wang, X and Ma, C},
title = {The rice AT-rich pincer-like element family of conserved noncoding sequences regulates chromatin loop formation.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf211},
pmid = {40405503},
issn = {1532-2548},
abstract = {The comprehensive annotation of regulatory elements in linear genomes is needed to elucidate the molecular mechanisms underlying chromatin loop formation in plants. Here, we characterized a novel family of conserved noncoding sequences (CNSs) in the rice (Oryza sativa) genome. These sequences, known as AT-rich pincer-like elements (APEs), are composed of 13-bp repeat unit arrays in a reverse-forward configuration. Our findings revealed that there are 611 APE copies across the japonica genome. Deletion of single APEs disrupted the long-range chromatin loops anchoring target APE regions and moderately remodeled the profile of A/B compartments, topologically associating domains (TADs), and chromatin loops, thereby rewiring the expression of looped gene(s) including those controlling important agronomic traits. Thus, APEs function as hub motifs directly mediating chromatin looping and maintaining 3D genome integrity and stability at the levels of compartments, TADs, and loops. Moreover, neighboring genomic regions harboring numerous paired non-APE (NA) CNSs were more likely to interact with each other. This finding suggests that NA CNS pairs might play a helper role in determining loop frequency in a dose-dependent manner, likely by ensuring the pairing selectivity of anchor sites. Our study highlights the importance of APEs and NA CNSs in maintaining 3D genome structure, thereby providing the framework required to link many noncoding repetitive elements to their molecular functions in plants.},
}

@article {pmid40391535,
year = {2025},
author = {Lee, H and Seo, PJ},
title = {Deciphering the 3D structures of plant genomes: Building blocks of hierarchically organized chromatin domains.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf218},
pmid = {40391535},
issn = {1460-2431},
abstract = {The spatial arrangement of chromatin within the nucleus is intricately regulated and acts as a key determinant of gene expression. Advanced high-resolution chromatin conformation capture techniques have revealed that plant genomes exhibit hierarchical organization within the nucleus, into large A and B compartments, intermediate topologically associating domain (TAD)-like domains, and fine gene-scale chromatin domains. In this review, we highlight recent findings demonstrating that TAD-like domains are closely associated with distinct epigenetic states, which are modulated by cohesin components. In addition, we underscore the significance of gene-scale chromatin domains, which are established by RNA polymerase II and accessible chromatin structures at gene borders. These fine-scale chromatin domains likely serve as the fundamental structural units for higher-order chromatin organization. Examining the chromatin structures at different levels of the hierarchy allows us to elucidate their epigenetic features and the molecular mechanisms for domain formation, providing insights into the three-dimensional organization of plant genomes.},
}

@article {pmid40390127,
year = {2025},
author = {Zhang, Y and Dali, R and Blanchette, M},
title = {RobusTAD: reference panel based annotation of nested topologically associating domains.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {129},
pmid = {40390127},
issn = {1474-760X},
abstract = {Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains challenging, both in terms of the precise identification of boundaries and the correct inference of hierarchies. While domain boundary is relatively well conserved across cells, few approaches have taken advantage of this fact. Here, we present RobusTAD to annotate TAD hierarchies. It incorporates additional Hi-C data to refine boundaries annotated from the study sample. RobusTAD outperforms existing tools at boundary and domain annotation across several benchmarking tasks.},
}

@article {pmid40390095,
year = {2025},
author = {Hou, C and Tian, GG and Hu, S and Chen, B and Li, X and Xu, B and Cao, Y and Le, W and Hu, R and Chen, H and Zhang, Y and Fang, Q and Zhang, M and Wang, Z and Zhang, Z and Zhang, J and Wei, Z and Yao, G and Wang, Y and Yin, P and Guo, Y and Tong, G and Teng, X and Sun, Y and Cao, Y and Wu, J},
title = {RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in human.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {57},
pmid = {40390095},
issn = {1756-994X},
support = {2022YFA0806301//National Key Research and Development Program of China/ ; 82201780//National Nature Science Foundation of China/ ; 23JC1402800//the Scientific and Technological Innovation Action program of Shanghai/ ; },
abstract = {BACKGROUND: Three-dimensional (3D) chromatin architecture undergoes dynamic reorganization during mammalian gametogenesis and early embryogenesis. While mouse studies have shown species-specific patterns as well as mechanisms underlying de novo organization, these remain poorly characterized in humans. Although RNA polymerases II and III have been shown to regulate chromatin structure, the potential role of RNA polymerase I (Pol I), which drives ribosomal RNA production, in shaping 3D genome organization during these developmental transitions has not been investigated.

METHODS: We employed a modified low-input in situ Hi-C approach to systematically compare 3D genome architecture dynamics from gametogenesis through early embryogenesis in human and mouse. Complementary Smart-seq2 for low-input transcriptomics, CUT&Tag for Pol I profiling, and Pol I functional inhibition assays were performed to elucidate the mechanisms governing chromatin organization.

RESULTS: Our study revealed an extensive reorganization of the 3D genome from human oogenesis to early embryogenesis, displaying significant differences with the mouse, including dramatically attenuated topologically associating domains (TADs) at germinal vesicle (GV) stage oocytes. The 3D genome reconstruction timing is a fundamental difference between species. In human, reconstruction initiates at the 4-cell stage embryo in human, while in mouse, it commences at the 2-cell stage embryo. We discovered that Pol I is crucial for establishing the chromatin structures during mouse embryogenesis, but not in human embryos. Intriguingly, the absence of Pol I transcription weakens TAD structure in mouse female germline stem cells, whereas it fortifies it in human counterparts.

CONCLUSIONS: These observed interspecies distinctions in chromatin organization dynamics provide novel insights into the evolutionary divergence of chromatin architecture regulation during early mammalian development. Our findings provide mechanistic insights into species-specific chromatin organization during germ cell and embryonic development and have potential implications for fertility preservation and birth defect prevention.},
}

@article {pmid40384625,
year = {2025},
author = {Kurbidaeva, A and Gupta, S and Zaidem, M and Castanera, R and Sato, Y and Joly-Lopez, Z and Casacuberta, JM and Purugganan, MD},
title = {Topologically associating domains and the evolution of three-dimensional genome architecture in rice.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {4},
pages = {e70139},
doi = {10.1111/tpj.70139},
pmid = {40384625},
issn = {1365-313X},
support = {//National Science Foundation/ ; //Tamkeen/NYU Abu Dhabi Research Institute/ ; //Zegar Family Foundation/ ; //European Social Fund Plus/ ; //Ministerio de Ciencia e Innovación/ ; //Severo Ochoa Center of Excellence/ ; },
mesh = {*Oryza/genetics ; *Genome, Plant/genetics ; *Evolution, Molecular ; Chromatin/genetics ; DNA Transposable Elements/genetics ; Chromosomes, Plant/genetics ; },
abstract = {We examined the nature and evolution of three-dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genus Oryza. These included three varieties from subspecies within domesticated Asian rice O. sativa as well as their closely related wild relatives O. rufipogon and O. meridionalis. We used the high-resolution chromosome conformation capture technique Micro-C, which we modified for use in rice. Our analysis of rice TADs shows that TAD boundaries have high transcriptional activity, low methylation levels, low transposable element (TE) content, and increased gene density. We also find a significant correlation of expression levels for genes within TADs, suggesting that they do function as genomic domains with shared regulatory features. Our findings indicate that animal and plant TADs may share more commonalities than were initially thought, as evidenced by similar genetic and epigenetic signatures associated with TADs and boundaries. To examine 3D genome divergence, we employed a computer vision-based algorithm for the comparison of chromatin contact maps and complemented this analysis by assessing the evolutionary conservation of individual TADs and their boundaries. We conclude that overall chromatin organization is conserved in rice, and 3D structural divergence correlates with evolutionary distance between genomes. We also note that individual TADs are not well conserved, even at short evolutionary timescales.},
}

*Oryza/genetics
*Genome, Plant/genetics
*Evolution, Molecular
Chromatin/genetics
DNA Transposable Elements/genetics
Chromosomes, Plant/genetics

@article {pmid40382218,
year = {2025},
author = {Li, X and Liu, N},
title = {Advances in understanding LINE-1 regulation and function in the human genome.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.04.011},
pmid = {40382218},
issn = {0168-9525},
abstract = {LINE-1 (long interspersed nuclear element 1, L1) retrotransposons constitute ~17% of human DNA (~0.5 million genomic L1 copies) and exhibit context-dependent expression in different cell lines. Recent studies reveal that L1 is under multilayered control by diverse factors that either collaborate or compete with each other to ensure precise L1 activity. Remarkably, L1s have been co-opted as various transcription-dependent regulatory elements, such as promoters, enhancers, and topologically associating domain (TAD) boundaries, that regulate gene expression in zygotic genome activation, aging, cancer, and other disorders. This review highlights the regulation of L1 and its regulatory functions that influence disease and development.},
}

@article {pmid40375066,
year = {2025},
author = {Yin, H and Zhao, Q and Yang, L and Yi, G and Yao, W and Fang, L and Bai, L},
title = {A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {484},
pmid = {40375066},
issn = {1471-2164},
support = {2021YFF1000600//National Key Research and Developmental Program of China/ ; 2021YFF1000600//National Key Research and Developmental Program of China/ ; 2021YFF1000600//National Key Research and Developmental Program of China/ ; 2021YFF1000600//National Key Research and Developmental Program of China/ ; 2021YFF1000600//National Key Research and Developmental Program of China/ ; 31972539//National Natural Science Foundation of China/ ; 31972539//National Natural Science Foundation of China/ ; 31501933//National Natural Science Foundation of China/ ; CJGJZD20210408092402006//Science and Technology Program of Shenzhen/ ; 2021YFD301201//National Key R&D Program of China/ ; 2021YFD301201//National Key R&D Program of China/ ; 2021YFD301201//National Key R&D Program of China/ ; 2021YFD301201//National Key R&D Program of China/ ; },
mesh = {Animals ; *Chromatin/chemistry/genetics ; Swine/genetics ; Quantitative Trait Loci ; *Gene Expression Regulation ; Organ Specificity ; Breeding ; },
abstract = {BACKGROUND: Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds.

RESULTS: Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)-critical growth factors involved in bone and cartilage development.

CONCLUSION: Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.},
}

Animals
*Chromatin/chemistry/genetics
Swine/genetics
Quantitative Trait Loci
*Gene Expression Regulation
Organ Specificity
Breeding

@article {pmid40374602,
year = {2025},
author = {Sept, CE and Tak, YE and Goel, V and Bhakta, MS and Cerda-Smith, CG and Hutchinson, HM and Blanchette, M and Eyler, CE and Johnstone, SE and Joung, JK and Hansen, AS and Aryee, MJ},
title = {High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4506},
pmid = {40374602},
issn = {2041-1723},
support = {RM1HG009490//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R35GM118158//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; T32GM135117//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {*CCCTC-Binding Factor/metabolism/genetics ; Cohesins ; *Chromosomal Proteins, Non-Histone/metabolism/genetics ; *Cell Cycle Proteins/metabolism/genetics ; *Chromatin/metabolism/genetics/chemistry ; Humans ; Binding Sites ; Enhancer Elements, Genetic ; *DNA Footprinting/methods ; Promoter Regions, Genetic ; Protein Binding ; },
abstract = {Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.},
}

*CCCTC-Binding Factor/metabolism/genetics
Cohesins
*Chromosomal Proteins, Non-Histone/metabolism/genetics
*Cell Cycle Proteins/metabolism/genetics
*Chromatin/metabolism/genetics/chemistry
Humans
Binding Sites
Enhancer Elements, Genetic
*DNA Footprinting/methods
Promoter Regions, Genetic
Protein Binding

@article {pmid40340859,
year = {2025},
author = {Denaud, S and Sabarís, G and Di Stefano, M and Papadopoulos, GL and Schuettengruber, B and Cavalli, G},
title = {Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {116},
pmid = {40340859},
issn = {1474-760X},
mesh = {Animals ; *Chromatin/genetics/metabolism/chemistry ; *Epigenesis, Genetic ; Histones/metabolism ; Drosophila Proteins/genetics/metabolism ; *Drosophila melanogaster/genetics ; *Drosophila/genetics ; Histone Code ; Polycomb-Group Proteins/genetics ; },
abstract = {The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the epigenetic signature of Polycomb TADs, we show that the epigenome is not a major driving force for the establishment of TADs. On the other hand, physical domains have an important impact on the formation of epigenetic domains, as they can restrict the spreading of repressive histone marks and looping between cis-regulatory elements.},
}

Animals
*Chromatin/genetics/metabolism/chemistry
*Epigenesis, Genetic
Histones/metabolism
Drosophila Proteins/genetics/metabolism
*Drosophila melanogaster/genetics
*Drosophila/genetics
Histone Code
Polycomb-Group Proteins/genetics

@article {pmid40332394,
year = {2025},
author = {Blotas, C and Le Nabec, A and Collobert, M and Bulcaen, M and Carlon, MS and Férec, C and Moisan, S},
title = {Cis-Regulation of the CFTR Gene in Pancreatic Cells.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083788},
pmid = {40332394},
issn = {1422-0067},
support = {RF20210502832//Vaincre la mucoviscidose/ ; 2020-J1810150-E015//Mucovereniging Belgium/ ; US_172749169_6//Emily's Entourage/ ; 1SE8122N//FWO-SB/ ; },
mesh = {*Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism ; Humans ; *Pancreas/metabolism/cytology ; Promoter Regions, Genetic ; Chromatin/genetics/metabolism ; *Gene Expression Regulation ; Cell Line ; Transcription Factors/metabolism/genetics ; *Regulatory Sequences, Nucleic Acid ; Cystic Fibrosis/genetics ; },
abstract = {Genome organization is essential for precise spatial and temporal gene expression and relies on interactions between promoters and distal cis-regulatory elements (CREs), which constitute ~8% of the human genome. For the cystic fibrosis transmembrane conductance regulator (CFTR) gene, tissue-specific expression, especially in the pancreas, remains poorly understood. Unraveling its regulation could clarify the clinical heterogeneity observed in cystic fibrosis and CFTR-related disorders. To understand the role of 3D chromatin architecture in establishing tissue-specific expression of the CFTR gene, we mapped chromatin interactions and epigenomic regulation in Capan-1 pancreatic cells. Candidate CREs are validated by luciferase reporter assay and CRISPR knock-out. We identified active CREs not only around the CFTR gene but also outside the topologically associating domain (TAD). We demonstrate the involvement of multiple CREs upstream and downstream of the CFTR gene and reveal a cooperative effect of the -44 kb, -35 kb, +15.6 kb, and +37.7 kb regions, which share common predicted transcription factor (TF) motifs. We also extend our analysis to compare 3D chromatin conformation in intestinal and pancreatic cells, providing valuable insights into the tissue specificity of CREs in regulating CFTR gene expression.},
}

*Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism
Humans
*Pancreas/metabolism/cytology
Promoter Regions, Genetic
Chromatin/genetics/metabolism
*Gene Expression Regulation
Cell Line
Transcription Factors/metabolism/genetics
*Regulatory Sequences, Nucleic Acid
Cystic Fibrosis/genetics

@article {pmid40329044,
year = {2025},
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 = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40329044},
issn = {1744-4292},
support = {U54DK107977//HHS | National Institutes of Health (NIH)/ ; 1UM1HG011585-03//HHS | National Institutes of Health (NIH)/ ; 422841138//Deutsche Forschungsgemeinschaft (DFG)/ ; EXC-2049 - 390688087//Deutsche Forschungsgemeinschaft (DFG)/ ; PITN-GA-2007-214902//EC | Seventh Framework Programme (FP7)/ ; MC_U120061476//UKRI | Medical Research Council (MRC)/ ; MC_U120027516//UKRI | Medical Research Council (MRC)/ ; MC_UP_1605/12//UKRI | Medical Research Council (MRC)/ ; MRC Centenary grant//UKRI | Medical Research Council (MRC)/ ; Long-Term Fellowship//Federation of European Biochemical Societies (FEBS)/ ; 01IS18025A 01IS18037A//Helmholtz-Gemeinschaft/ ; M4C2 CN00000041 CUP E63C22000940007, MUR PRIN 2022 CUP E53D23001810006, MUR PRIN PNRR 2022 CUP E53D2//EC | NextGenerationEU (NGEU)/ ; },
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, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.},
}

@article {pmid40315272,
year = {2025},
author = {Han, J and Hu, G and Dai, Y and Zhang, X and Tian, J and Zhou, J and Xu, X and Chen, Q and Kou, X and Xu, L and Wu, X and Sun, Z and Geng, J and Li, L and Qiu, C and Mehari, TG and Wang, B and Zhang, H and Shen, X and Xu, Z and Wendel, JF and Wang, K},
title = {Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton.},
journal = {PLoS genetics},
volume = {21},
number = {5},
pages = {e1011689},
doi = {10.1371/journal.pgen.1011689},
pmid = {40315272},
issn = {1553-7404},
abstract = {Centromeres are pivotal for accurate chromosome segregation, yet their regulation and evolutionary dynamics remain poorly understood. Here, we investigate centromeres of the diploid species Gossypium anomalum (Ga, B-genome) that were transferred into tetraploid cotton G. hirsutum (Gh, AD-genome) as either an additional or integrated chromosome, as well as in synthetic allohexaploid (AABBDD) lines. We demonstrate consistent size reduction for all Ga centromeres in the Gh background. Histone modification profiling across 10 marks revealed heightened levels of both active and repressive chromatin marks within the Ga centromeres when transferred into the Gh background, particularly for H3K36me2. The centromeric histone modification perturbation extended into pericentromeric regions, with variable CENH3-binding domains consistently exhibiting a more pronounced increase in histone modification levels compared to stable centromere regions, highlighting the role of histone modification elevation in centromere dynamics. In addition, we observed enhanced chromatin accessibility and the presence of non-B-form DNA motifs, such as A-phased DNA repeats within stable centromere domains that are correlated with centromere stability. Hi-C analysis reveals a reorganized 3D chromatin architecture within the introgression line centromeres, including the formation of new topologically associating domains linked to H3K36me2 dynamics, emphasizing the importance of H3K36me2 in centromere organization. Together, these findings elucidate epigenetic mechanisms underlying centromere composition following intergenomic hybridization and allopolyploid formation, offering insights into centromere evolution in plants and its myriad epigenetic and potentially functional dimensions.},
}

@article {pmid40308064,
year = {2025},
author = {Yang, Q and Wu, T and Liu, M and Zhang, X and Sun, X and Feng, D and Lu, Y and Chen, X and Hong, Y and Ma, W and Zhao, J},
title = {An integrative 3D-genome database for plants.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101346},
doi = {10.1016/j.xplc.2025.101346},
pmid = {40308064},
issn = {2590-3462},
abstract = {High-throughput sequencing technologies have revolutionized studies of 3D-genome structures, revealing unprecedented insights into the complexity of genome-wide gene regulation in eukaryotes. To analyze and compare 3D-genome structures, we developed the 3D-genome database for plants, 3D-GDP, for interspecies comparative functional genomics (http://www.3d-gdp.com/). 3D-GDP encompasses all publicly available plant 3D-genome sequences. It offers detailed analyses and comparisons of 3D-genome structures among 26 plant species, with comprehensive information on topologically associating domains (TADs), loops and compartments, as well as gene annotations. 3D-GDP also provides a range of bioinformatic tools such as genome browser, TAD function prediction, and specialized modules for predicting and systematically comparing chromatin structures across species to identify conserved TADs and loop structures. Taken together, the 3D-genome database for plants (3D-GDP) represents a resourceful integrating database and innovative platform that can be used to reveal evolutionary conservation of 3D-genome structures and their relevance to genome-wide gene regulation in plants and beyond.},
}

@article {pmid40278067,
year = {2025},
author = {Wu, C and Fan, J and Hu, D and Sun, H and Lu, G and Wang, Y and Yang, Y},
title = {The Three-Dimensional Structure of the Genome of the Dark Septate Endophyte Exophiala tremulae and Its Symbiosis Effect on Alpine Meadow Plant Growth.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040246},
pmid = {40278067},
issn = {2309-608X},
support = {U23A2043//the National Natural Science Foundation of China/ ; },
abstract = {The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai-Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, Exophiala tremulae CICC2537, was sequenced and assembled at the chromosome level using the PacBio sequencing platform, with the assistance of the Hi-C technique for scaffolding, and its 3D genome structures were investigated. The genome size of E. tremulae is 51.903848 Mb, and it contains eight chromosomes. A total of 12,277 protein-coding genes were predicted, and 11,932 genes (97.19%) were annotated. As for the distribution of exon and intron number and the distribution of gene GC and CDS GC, E. tremulae showed similar distribution patterns to the other investigated members of the genus Exophiala. The analysis of carbohydrate-active enzymes showed that E. tremulae possesses the greatest number of enzymes with auxiliary activities and the lowest number of enzymes with carbohydrate-binding modules among the investigated fungi. The total number of candidate effector proteins was 3337, out of which cytoplasmic and apoplastic effector proteins made up 3100 and 163, respectively. The whole genome of E. tremulae contained 40 compartment As and 76 compartment Bs, and there was no significant difference in GC content in its compartment As and Bs. The whole genome of E. tremulae was predicted to contain 155 topologically associating domains (TADs), and their average length was 250,000 bp, but there were no significant differences in the numbers of genes and the GC content per bin localized within the boundaries and interiors of TADs. Comparative genome analysis showed that E. tremulae diverged from Exophiala mesophila about 34.1 (30.0-39.1) Myr ago, and from Exophiala calicioides about 85.6 (76.1-90.6) Myr ago. Compared with all the investigated fungi, the numbers of contraction and expansion gene families in the E. tremulae genome were 13 and 89, respectively, and the numbers of contraction and expansion genes were 14 and 670, respectively. Our work provides a basis for the use of the dark septate fungus in alpine artificial grassland and further research into its symbiosis mechanisms, which may improve the growth of plant species used in the Qinghai-Tibet Plateau.},
}

@article {pmid40269984,
year = {2025},
author = {Sandås, K and Spindola, L and Løkhammer, S and Stavrum, AK and Andreassen, O and Tesfaye, M and Hellard, SL},
title = {Using LDpred2 to adapt polygenic risk score techniques for methylation score creation.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {190},
pmid = {40269984},
issn = {1756-0500},
mesh = {Humans ; *DNA Methylation/genetics ; *Genome-Wide Association Study/methods ; *Schizophrenia/genetics ; *Multifactorial Inheritance/genetics ; *Genetic Predisposition to Disease ; *Software ; Models, Genetic ; Genetic Risk Score ; },
abstract = {OBJECTIVE: This study sought to determine if the R package LDpred2, designed for polygenic risk score creation for genome-wide association studies using summary statistics, could be adapted for deriving DNA methylation scores from methylome-wide association studies. Recognizing that linkage disequilibrium, used as prior in LDpred2, does not apply to methylation, we explored co-methylated regions and topologically associating domains as alternative structural priors for correlation between methylation sites. A genomic sliding-window approach was also tested. The performance of the LDpred2-based models was evaluated on methylation data from schizophrenia and control samples (N = 1,227).

RESULTS: LDpred2 models employing topologically associating domains and sliding window clusters as priors performed similarly to existing methods, explaining approximately 3.6% of schizophrenia phenotypic variance. The co-methylated regions model underperformed due to insufficient clustering of probes. The similarity in performance between the model using topologically associating domains and a null model consisting of random clusters suggests that the structural information provided by these domains enhances performance only marginally. In conclusion, while LDpred2 can be adapted for methylation data, it does not substantially enhance methylation score performance over existing methods, and the choice of structural prior may not be a critical factor.},
}

Humans
*DNA Methylation/genetics
*Genome-Wide Association Study/methods
*Schizophrenia/genetics
*Multifactorial Inheritance/genetics
*Genetic Predisposition to Disease
*Software
Models, Genetic
Genetic Risk Score

@article {pmid40268951,
year = {2025},
author = {Xu, H and Chi, Y and Yin, C and Li, C and Chen, Y and Liu, Z and Liu, X and Xie, H and Chen, ZJ and Zhao, H and Wu, K and Zhao, S and Xing, D},
title = {Three-dimensional genome structures of single mammalian sperm.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3805},
pmid = {40268951},
issn = {2041-1723},
support = {32430061//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is challenging to study with traditional imaging or sequencing approaches. In this study, we develop an enhanced chromosome conformation capture assay, and resolve the 3D whole-genome structures of single mammalian sperm. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discover that sperm genomes are divided into chromosomal territories and A/B compartments, similarly to somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells. The discoveries and methods established in this work will be valuable for future studies of sperm related infertility.},
}

@article {pmid40007120,
year = {2025},
author = {Lee, S and Liu, X and Ziabkin, I and Zidovska, A},
title = {Image-based analysis of the genome's fractality during the cell cycle.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2025.02.014},
pmid = {40007120},
issn = {1542-0086},
support = {R01 GM145924/GM/NIGMS NIH HHS/United States ; },
abstract = {The human genome consists of about 2 m of DNA packed inside the cell nucleus barely 10 μm in diameter. DNA is complexed with histones, forming chromatin fiber, which folds inside the nucleus into loops, topologically associating domains, A/B compartments, and chromosome territories. This organization is knot-free and self-similar across length scales, leading to a hypothesis that the genome presents a fractal globule, which was corroborated by chromosome conformation capture experiments. In addition, many microscopy techniques have been used to obtain the fractal dimension of the genome's spatial distribution from its images. However, different techniques often required that different definitions of fractal dimension be adapted, making the comparison of these results not trivial. In this study, we use spinning disk confocal microscopy to collect high-resolution images of nuclei in live human cells during the cell cycle. We then systematically compare existing image-based fractal analyses-including mass-scaling, box-counting, lacunarity, and multifractal spectrum-by applying them to images of human cell nuclei and investigate changes in the genome's spatial organization during the cell cycle. Our data reveal that different image-based fractal measurements offer distinct metrics, highlighting different features of the genome's spatial organization. Yet, all these metrics consistently indicate the following trend for the changes in the genome's organization during the cell cycle: the genome being compactly packed in early G1 phase, followed by a decondensation throughout the G1 phase, and a subsequent condensation in the S and G2 phases. Our comprehensive comparison of image-based fractal analyses reconciles the perceived discrepancies between different methods. Moreover, our results offer new insights into the physical principles underlying the genome's organization and its changes during the cell cycle.},
}

@article {pmid40250193,
year = {2025},
author = {Vargas, LCZ and Ortíz-Ortíz, J and Martínez, YA and Viguri, GEC and Rojas, FIT and Ávila-López, PA},
title = {Identification of ZNF384 as a regulator of epigenome in leukemia.},
journal = {Leukemia research},
volume = {153},
number = {},
pages = {107691},
doi = {10.1016/j.leukres.2025.107691},
pmid = {40250193},
issn = {1873-5835},
abstract = {Leukemia is a complex hematologic cancer driven by genetic and epigenetic changes that impact gene expression. Understanding these molecular mechanisms is essential for improving leukemia diagnosis and prognosis. This study examines the role of the zinc finger protein ZNF384 in the epigenome and its influence on gene regulation in leukemia. We analyzed next-generation sequencing data from The Encyclopedia of DNA Elements (ENCODE), integrating datasets such as chromatin immunoprecipitation sequencing (ChIP-seq) of ZNF384 and regulatory histone marks, RNA sequencing (RNA-seq), and Hi-C data from K562 and GM12878 cells. Additionally, we used RNA-seq from K562 ZNF384 knock-down (KD) cells generated via CRISPR interference (CRISPRi) to validate our findings. This enabled us to explore the chromatin interaction patterns of ZNF384 and its regulatory impact. Our results demonstrate that ZNF384 associates with promoters and enhancers in K562 and GM12878 cells, facilitating increased transcription levels. We also found ZNF384 enriched at topologically associating domain (TAD) boundaries and chromatin loops, suggesting a role in three-dimensional (3D) chromatin organization. Furthermore, we identified a significant binding of ZNF384 at SINE-Alu elements in both K562 and GM12878 cells. In summary, this study highlights the regulatory role of ZNF384 in the leukemia epigenome and its impact on gene expression. Understanding the oncogenic implications of ZNF384 may improve leukemia diagnosis and prognosis.},
}

@article {pmid40247362,
year = {2025},
author = {Zhou, H and Liu, Y and Tian, GG and Wu, J},
title = {Nicotinamide mononucleotide promotes female germline stem cell proliferation by activating the H4K16ac-Hmgb1-Fyn-PLD signaling pathway through epigenetic remodeling.},
journal = {Cell & bioscience},
volume = {15},
number = {1},
pages = {48},
pmid = {40247362},
issn = {2045-3701},
support = {2022YFA0806301//the National Key Research and Development Program of China/ ; 23JC1402800//the Scientific and Technological Innovation Action Program of Shanghai/ ; },
abstract = {BACKGROUND: Nicotinamide mononucleotide (NMN), an endogenous nucleotide essential for various physiological processes, has an unclear role and regulatory mechanisms in female germline stem cell (FGSC) development.

RESULTS: We demonstrate that NMN significantly enhances FGSC viability and proliferation. Quantitative acetylation proteomics revealed that NMN markedly increases the acetylation of histone H4 at lysine 16 (H4K16ac). Subsequent chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) identified high mobility group box 1 (Hmgb1) as a downstream target of H4K16ac, a finding further validated by ChIP-qPCR. Knockdown of Hmgb1 reduced FGSC proliferation by disrupting cell cycle progression, inducing apoptosis, and decreasing chromatin accessibility. High-throughput chromosome conformation capture (Hi-C) analysis showed that Hmgb1 knockdown induced A/B compartment switching, increased the number of topologically associating domains (TADs), and decreased chromatin loop formation in FGSCs. Notably, the chromatin loop at the promoter region of Fyn proto-oncogene (Fyn) disappeared following Hmgb1 knockdown. ChIP-qPCR and dual-luciferase reporter assays further confirmed the interaction between Hmgb1 and the Fyn promoter. Importantly, Fyn overexpression reversed the inhibitory effects of Hmgb1 knockdown on FGSC proliferation. Proteomic analysis suggested this rescue was mediated through the phospholipase D (PLD) signaling pathway, as Fyn overexpression selectively enhanced the phosphorylation of PLD1 at threonine 147 without affecting serine 561. Furthermore, treatment with 5-fluoro-2-indolyldechlorohaloamide, a PLD inhibitor, nullified the pro-proliferative effects of Fyn overexpression.

CONCLUSIONS: Our findings reveal that NMN promotes FGSC proliferation by activating the H4K16ac-Hmgb1-Fyn-PLD signaling pathway through epigenetic remodeling. These results deepen our understanding of FGSC proliferation and highlight potential therapeutic avenues for advancing FGSC applications in reproductive medicine.},
}

@article {pmid40236218,
year = {2025},
author = {Li, C and Mowlaei, ME and , and Carnevale, V and Kumar, S and Shi, X},
title = {TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.29.646133},
pmid = {40236218},
issn = {2692-8205},
abstract = {High-throughput chromosome conformation capture sequencing (Hi-C) is a key technology for studying the three-dimensional (3D) structure of genomes and chromatin folding. Hi-C data reveals important patterns of genome organization such as topologically associating domains (TADs) and chromatin loops with critical roles in transcriptional regulation and disease etiology and progression. However, the relatively low resolution of existing Hi-C data often hinders robust and reliable inference of 3D structures. Hence, we propose TRUHiC, a new computational method that leverages recent state-of-the-art deep generative modeling to augment low-resolution Hi-C data for the characterization of 3D chromatin structures. Applying TRUHiC to publically available Hi-C data for human and mice, we demonstrate that the augmented data significantly improves the characterization of TADs and loops across diverse cell lines and species. We further present a pre-trained TRUHiC on human lymphoblastoid cell lines that can be adaptable and transferable to improve chromatin characterization of various cell lines, tissues, and species.},
}

@article {pmid40235997,
year = {2025},
author = {Liang, H and Berger, B and Singh, R},
title = {Tracing the Shared Foundations of Gene Expression and Chromatin Structure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.31.646349},
pmid = {40235997},
issn = {2692-8205},
abstract = {UNLABELLED: The three-dimensional organization of chromatin into topologically associating domains (TADs) may impact gene regulation by bringing distant genes into contact. However, many questions about TADs' function and their influence on transcription remain unresolved due to technical limitations in defining TAD boundaries and measuring the direct effect that TADs have on gene expression. Here, we develop consensus TAD maps for human and mouse with a novel "bag-of-genes" approach for defining the gene composition within TADs. This approach enables new functional interpretations of TADs by providing a way to capture species-level differences in chromatin organization. We also leverage a generative AI foundation model computed from 33 million transcriptomes to define contextual similarity, an embedding-based metric that is more powerful than co-expression at representing functional gene relationships. Our analytical framework directly leads to testable hypotheses about chromatin organization across cellular states. We find that TADs play an active role in facilitating gene co-regulation, possibly through a mechanism involving transcriptional condensates. We also discover that the TAD-linked enhancement of transcriptional context is strongest in early developmental stages and systematically declines with aging. Investigation of cancer cells show distinct patterns of TAD usage that shift with chemotherapy treatment, suggesting specific roles for TAD-mediated regulation in cellular development and plasticity. Finally, we develop "TAD signatures" to improve statistical analysis of single-cell transcriptomic data sets in predicting cancer cell-line drug response. These findings reshape our understanding of cellular plasticity in development and disease, indicating that chromatin organization acts through probabilistic mechanisms rather than deterministic rules.

SOFTWARE AVAILABILITY: https://singhlab.net/tadmap.},
}

@article {pmid40210441,
year = {2025},
author = {Kim, J and Wang, H and Ercan, S},
title = {Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279365.124},
pmid = {40210441},
issn = {1549-5469},
abstract = {In mammals, cohesin and CTCF organize the 3D genome into topologically associating domains (TADs) to regulate communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called "fountains," which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20-40 kb in C. elegans Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded at sites bound by the C. elegans ortholog of NIPBL and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly owing to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers, and fountain strength is associated with transcription. Compared with mammals, the average processivity of C. elegans cohesin is about 10-fold shorter, and the binding of NIPBL ortholog does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.},
}

@article {pmid40200588,
year = {2025},
author = {Hu, A and Zhou, W and Luo, X and Qiu, R and Li, J},
title = {Correlation Between DNA Double-Strand Break Distribution in 3D Genome and Ionizing Radiation-Induced Cell Death.},
journal = {Radiation research},
volume = {},
number = {},
pages = {},
doi = {10.1667/RADE-24-00277.1},
pmid = {40200588},
issn = {1938-5404},
abstract = {The target theory is the most classical hypothesis explaining radiation-induced cell death, yet the physical or biological nature of the "target" remains ambiguous. This study hypothesizes that the distribution of DNA double-strand breaks (DSBs) within the 3D genome is a pivotal factor affecting the probability of radiation-induced cell death. We propose that clustered DSBs in DNA segments with high-interaction frequencies are more susceptible to leading to cell death than isolated DSBs. Topologically associating domains (TAD) can be regarded as the reference unit for evaluating the impact of DSB clustering in the 3D genome. To quantify this correlation between the DSB distribution in 3D genome and radiation-induced effect, we developed a simplified model considering the DSB distribution across TADs. Utilizing track-structure Monte Carlo codes to simulate the electron and carbon ion irradiation, and we calculated the incidence of each DSB case across a variety of radiation doses and linear energy transfers (LETs). Our simulation results indicate that DSBs in TADs with frequent interactions (case 3) are significantly more likely to induce cell death than clustered DSBs within a single TAD (case 2). Moreover, case 2 is significantly more likely to induce cell death than isolated DSBs (case 1). The curves of the incidence of cases 2 and 3 compared with LETs have a similar shape to the radiation quality factor (Q) used in radiation protection. This indicates that these two cases are also associated with the stochastic effects induced by high-LET radiation. Our study underscores the crucial significance of the 3D genome structure in the fundamental mechanisms of radiobiological effects. The hypothesis in our research offers novel perspectives on the mechanisms that regulate radiobiological effects. Moreover, it serves as a valuable reference for the establishment of mechanistic models that can predict cell survival under different doses and LETs.},
}

@article {pmid40196636,
year = {2025},
author = {Qiu, J and Jadali, A and Martinez, E and Song, Z and Ni, JZ and Kwan, KY},
title = {CHD7 binds to insulators during neuronal differentiation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.28.646031},
pmid = {40196636},
issn = {2692-8205},
abstract = {Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in neuronal differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrated that CHD7 knockdown impaired neuronal differentiation. Genome-wide analysis revealed CHD7 binding at diverse cis -regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2 . Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR-9 transcription, irrespective of the method. Blocking the CHD7 and CTCF marked sites suggested that the elements function as insulators to regulate gene expression. The study highlights CHD7 activity at insulators and underscores an unreported mechanism for promoting neuronal differentiation.},
}

@article {pmid40131313,
year = {2025},
author = {Wang, X and Luo, J and Wu, L and Luo, H and Guo, F},
title = {deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf127},
pmid = {40131313},
issn = {1477-4054},
support = {62372156//National Natural Science Foundation of China/ ; 232102211046//Henan Provincial Department of Science and Technology Research Project/ ; },
mesh = {*Neural Networks, Computer ; Humans ; Computational Biology/methods ; Algorithms ; Chromatin/chemistry/genetics ; Software ; Genomics/methods ; },
abstract = {MOTIVATION: Topologically associated domains (TADs) play a key role in the 3D organization and function of genomes, and accurate detection of TADs is essential for revealing the relationship between genomic structure and function. Most current methods are developed to extract features in Hi-C interaction matrix to identify TADs. However, due to complexities in Hi-C contact matrices, it is difficult to directly extract features associated with TADs, which prevents current methods from identifying accurate TADs.

RESULTS: In this paper, a novel method is proposed, deepTAD, which is developed based on a convolutional neural network (CNN) and transformer model. First, based on Hi-C contact matrix, deepTAD utilizes CNN to directly extract features associated with TAD boundaries. Next, deepTAD takes advantage of the transformer model to analyze the variation features around TAD boundaries and determines the TAD boundaries. Second, deepTAD uses the Wilcoxon rank-sum test to further identify false-positive boundaries. Finally, deepTAD computes cosine similarity among identified TAD boundaries and assembles TAD boundaries to obtain hierarchical TADs. The experimental results show that TAD boundaries identified by deepTAD have a significant enrichment of biological features, including structural proteins, histone modifications, and transcription start site loci. Additionally, when evaluating the completeness and accuracy of identified TADs, deepTAD has a good performance compared with other methods. The source code of deepTAD is available at https://github.com/xiaoyan-wang99/deepTAD.},
}

*Neural Networks, Computer
Humans
Computational Biology/methods
Algorithms
Chromatin/chemistry/genetics
Software
Genomics/methods

@article {pmid40117347,
year = {2025},
author = {Li, SH and Liang, YC and Jiang, TX and Jea, WC and Chih-Kuan Chen, and Lu, J and Núñez-León, D and Yu, Z and Lai, YC and Widelitz, RB and Andersson, L and Wu, P and Chuong, CM},
title = {Skin regional specification and higher-order HoxC regulation.},
journal = {Science advances},
volume = {11},
number = {12},
pages = {eado2223},
doi = {10.1126/sciadv.ado2223},
pmid = {40117347},
issn = {2375-2548},
mesh = {Animals ; *Homeodomain Proteins/genetics/metabolism ; *Feathers ; *Chickens/genetics ; *Skin/metabolism ; Gene Expression Regulation, Developmental ; },
abstract = {The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195-base pair (bp) duplication in HoxC10 intron. Micro-C analyses show that HoxC-containing topologically associating domain (TAD) is normally closed in the scalp but open in the dorsal and tail regions, allowing multiple long-distance contacts. In the PC scalp, the TAD is open, resulting in high HoxC expression. CRISPR-Cas9 deletion of the 195-bp duplication reduces crest feather formation, and HoxC misexpression alters feather shapes. The 195-bp sequence is found only in Archelosauria (crocodilians and birds) and not in mammals. These findings suggest that higher-order regulation of the HoxC cluster modulates gene expression, driving the evolution of adaptive integumentary appendages in birds.},
}

Animals
*Homeodomain Proteins/genetics/metabolism
*Feathers
*Chickens/genetics
*Skin/metabolism
Gene Expression Regulation, Developmental

@article {pmid40098664,
year = {2025},
author = {Xu, S and Shan, L and Tian, R and Yu, Z and Sun, D and Zhang, Z and Seim, I and Zhou, M and Sun, L and Liang, N and Zhang, Q and Chai, S and Yin, D and Deme, L and Wu, T and Chen, Y and Xu, Z and Zheng, Y and Ren, W and Yang, G},
title = {Multi-level genomic convergence of secondary aquatic adaptation in marine mammals.},
journal = {Innovation (Cambridge (Mass.))},
volume = {6},
number = {3},
pages = {100798},
pmid = {40098664},
issn = {2666-6758},
abstract = {Marine mammals provide a valuable model for studying the molecular basis of convergent evolution during secondary aquatic adaptation. Using multi-omics data and functional experiments, including CRISPR-Cas9 mouse models and luciferase reporter assays, this study explored the molecular mechanisms driving this transition across coding regions, regulatory elements, and genomic architecture. Convergent amino acid substitutions in APPL1 [P378L] and NEIL1 [E71G] were found to promote lipid accumulation and suppress cancer cell proliferation, likely contributing to the evolution of extensive blubber layers and cancer resistance. Convergently evolved conserved non-exonic elements (CNEs) and lineage-specific regulatory variations were shown to influence the activity of nearby genes (e.g., NKX3-2, SOX9, HAND2), shaping cetacean limb phenotypes. Additionally, convergent shifts in topologically associating domains (TADs) across cetaceans and pinnipeds were implicated in the regulation of ASXL3 and FAM43B expression, playing a role in the formation of thickened blubber layers and mitigating cancer susceptibility. Structural variations within conserved TADs were associated with the expression of neuronal genes, including NUP153 and ID4, potentially driving cognitive and social adaptations. These findings provide novel insights into the molecular foundations of the convergent evolution of secondary aquatic adaptations in mammals.},
}

@article {pmid40092712,
year = {2025},
author = {Ning, D and Deng, Y and Tian, SZ},
title = {Chromatin structure and gene transcription of recombinant p53 adenovirus vector within host.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1562357},
pmid = {40092712},
issn = {2296-889X},
abstract = {INTRODUCTION: The recombinant human p53 adenovirus (Ad-p53) offers a promising approach for cancer therapy, yet its chromatin structure and effects on host chromatin organization and gene expression are not fully understood.

METHODS: In this study, we employed in situ ChIA-PET to investigate the colorectal cancer cell line HCT116 with p53 knockout, comparing them to cells infected with the adenovirus-vector expressing p53. We examined alterations in chromatin interactions and gene expression following treatment with the anti-cancer drug 5-fluorouracil (5-FU).

RESULTS: Our results indicate that Ad-p53 forms a specific chromatin architecture within the vector and mainly interacts with repressive or inactive regions of host chromatin, without significantly affecting the expression of associated genes. Additionally, Ad-p53 does not affect topologically associating domains (TADs) or A/B compartments in the host genome.

DISCUSSION: These findings suggest that while Ad-p53 boosts p53 expression, enhancing drug sensitivity without substantially altering host HCT116 chromatin architecture.},
}

@article {pmid40063813,
year = {2025},
author = {Papale, A and Segueni, J and El Maroufi, H and Noordermeer, D and Holcman, D},
title = {Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {11},
pages = {e2413112122},
doi = {10.1073/pnas.2413112122},
pmid = {40063813},
issn = {1091-6490},
support = {882673//ERC/ ; 19CS145-00//plan cancer/ ; AnalysisSpectralEEG//Agence national recherche/ ; ANR-21-CE12-0034//Agence national recherche/ ; ANR-22-CE12-0016//Agence national recherche/ ; ANR-22-CE14-0021//Agence national recherche/ ; },
mesh = {*CCCTC-Binding Factor/metabolism/genetics ; *Chromatin/metabolism/genetics ; Animals ; Binding Sites ; Humans ; Enhancer Elements, Genetic ; Promoter Regions, Genetic ; Cohesins ; Cell Cycle Proteins/metabolism/genetics ; Chromosomal Proteins, Non-Histone/metabolism/genetics ; Insulator Elements/genetics ; Genome ; },
abstract = {Topologically associating domains (TADs) are sub-Megabase regions in vertebrate genomes with enriched intradomain interactions that restrict enhancer-promoter contacts across their boundaries. However, the mechanisms that separate TADs remain incompletely understood. Most boundaries between TADs contain CTCF binding sites (CBSs), which individually contribute to the blocking of Cohesin-mediated loop extrusion. Using genome-wide classification, here we show that the width of TAD boundaries forms a continuum from narrow to highly extended and correlates with CBSs distribution, chromatin features, and gene regulatory elements. To investigate how these boundary widths emerge, we modified the random crosslinker polymer model to incorporate specific boundary configurations, enabling us to evaluate the differential impact of boundary composition on TAD insulation. Our analysis, using three generic boundary categories, identifies differential influence on TAD insulation, with varying local and distal effects on neighboring domains. Notably, we find that increasing boundary width reduces long-range inter-TAD contacts, as confirmed by Hi-C data. While blocking loop extrusion at boundaries indirectly promotes spurious intermingling of neighboring TADs, extended boundaries counteract this effect, emphasizing their role in establishing genome organization. In conclusion, TAD boundary width not only enhances the efficiency of loop extrusion blocking but may also modulate enhancer-promoter contacts over long distances across TAD boundaries, providing a further mechanism for transcriptional regulation.},
}

*CCCTC-Binding Factor/metabolism/genetics
*Chromatin/metabolism/genetics
Animals
Binding Sites
Humans
Enhancer Elements, Genetic
Promoter Regions, Genetic
Cohesins
Cell Cycle Proteins/metabolism/genetics
Chromosomal Proteins, Non-Histone/metabolism/genetics
Insulator Elements/genetics
Genome

@article {pmid40060486,
year = {2025},
author = {Tastemel, M and Jussila, A and Saravanan, B and Huang, H and Xie, Y and Zhu, Q and Jiang, Y and Armand, E and Ren, B},
title = {Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.21.639596},
pmid = {40060486},
issn = {2692-8205},
abstract = {Loop-extrusion machinery, comprising the cohesin complex and CCCTC-binding factor CTCF, organizes the interphase chromosomes into topologically associating domains (TADs) and loops, but acute depletion of components of this machinery results in variable transcriptional changes in different cell types, highlighting the complex relationship between chromatin organization and gene regulation. Here, we systematically investigated the role of 3D genome architecture in gene regulation in mouse embryonic stem cells under various perturbation conditions. We found that acute depletion of cohesin or CTCF disrupts the formation of TADs, but affects gene regulation in a gene-specific and context-dependent manner. Furthermore, the loop extrusion machinery was dispensable for transcription from most genes in steady state, consistent with prior results, but became critical for a large number of genes during transition of cellular states. Through a genome-wide CRISPR screen, we uncovered multiple factors that can modulate the role of loop extrusion machinery in gene regulation in a gene-specific manner. Among them were the MORF acetyltransferase complex members (Kat6b, Ing5, Brpf1), which could antagonize the transcriptional insulation mediated by CTCF and cohesin complex at developmental genes. Interestingly, inhibition of Kat6b partially rescues the insulator defects in cells lacking the cohesin loader Nipbl, mutations of which are responsible for the developmental disorder Cornelia de Lange syndrome. Taken together, our findings uncovered interplays between the loop extrusion machinery and histone modifying complex that underscore the context-dependent and gene-specific role of the 3D genome.},
}

@article {pmid40058875,
year = {2025},
author = {Lee, J and Mo, HL and Ha, Y and Nam, DY and Lim, G and Park, JW and Park, S and Choi, WY and Lee, HJ and Rhee, JK},
title = {Unraveling the three-dimensional genome structure using machine learning.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {40058875},
issn = {1976-670X},
abstract = {The study of chromatin interactions has advanced considerably with technologies such as high-throughput chromosome conformation capture (Hi-C) sequencing, providing a genome-wide view of physical interactions within the nucleus. These techniques have revealed the existence of hierarchical chromatin structures such as compartments, topologically associating domains (TADs), and chromatin loops, which are crucial in genome organization and regulation. However, identifying and analyzing these structural features require advanced computational methods. In recent years, machine learning approaches, particularly deep learning, have emerged as powerful tools for detecting and analyzing structural information. In this review, we present an overview of various machine learning-based techniques for determining chromosomal organization. Starting with the progress in predicting interactions from DNA sequences, we describe methods for identifying various hierarchical structures from Hi-C data. Additionally, we present advances in enhancing the chromosome contact frequency map resolution to overcome the limitations of Hi-C data. Finally, we identify the remaining challenges and propose potential solutions and future directions.},
}

@article {pmid40053568,
year = {2025},
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 = {PloS one},
volume = {20},
number = {3},
pages = {e0308896},
doi = {10.1371/journal.pone.0308896},
pmid = {40053568},
issn = {1932-6203},
mesh = {*Proto-Oncogene Protein c-ets-1/genetics/metabolism ; Animals ; *B-Lymphocytes/metabolism/immunology ; Mice ; *T-Lymphocytes/metabolism/immunology ; Gene Expression Regulation ; Chromatin/metabolism/genetics ; Humans ; Enhancer Elements, Genetic ; },
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.},
}

*Proto-Oncogene Protein c-ets-1/genetics/metabolism
Animals
*B-Lymphocytes/metabolism/immunology
Mice
*T-Lymphocytes/metabolism/immunology
Gene Expression Regulation
Chromatin/metabolism/genetics
Humans
Enhancer Elements, Genetic

@article {pmid40022213,
year = {2025},
author = {Yang, X and Cheng, L and Xin, Y and Zhang, J and Chen, X and Xu, J and Zhang, M and Feng, R and Hyle, J and Qi, W and Rosikiewicz, W and Xu, B and Li, C and Xu, P},
title = {CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {44},
pmid = {40022213},
issn = {1474-760X},
support = {82170119//National Natural Science Foundation of China/ ; BK20210714//Jiangsu Province National Science and Technology grant/ ; ZXL2022443//Suzhou Municipality Gusu Leading Talents grant/ ; },
mesh = {Humans ; *CCCTC-Binding Factor/metabolism/genetics ; *Erythropoiesis/genetics ; *Chromatin/metabolism ; Cell Line ; Gene Expression Regulation ; Erythroid Precursor Cells/metabolism/cytology ; },
abstract = {BACKGROUND: CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, genome-wide impact of CTCF on erythropoiesis has not been extensively investigated.

RESULTS: Using a state-of-the-art human erythroid progenitor cell model (HUDEP-2 and HEL cell lines), we systematically investigate the effects of acute CTCF loss by an auxin-inducible degron system on transcriptional programs, chromatin accessibility, CTCF genome occupancy, and genome architecture. By integrating multi-omics datasets, we reveal that acute CTCF loss notably disrupts genome-wide chromatin accessibility and the transcription network. We detect over thousands of decreased chromatin accessibility regions but only a few hundred increased regions after CTCF depletion in HUDEP-2 and HEL lines, suggesting the role of CTCF in maintaining proper chromatin openness in the erythroid lineage. CTCF depletion in the erythroid context notably disrupts the boundary integrity of topologically associating domains and chromatin loops but does not affect nuclear compartmentalization. We find erythroid lineage-specific genes, including some metabolism-related genes, are suppressed at immature and mature stages. Notably, we find a subset of genes whose transcriptional levels increase upon CTCF depletion, accompanied by decreased chromatin accessibility regions enriched with the GATA motif. We further decipher the molecular mechanism underlying the CTCF/GATA2 repression axis through distal non-coding chromatin regions. These results suggest a suppressive role of CTCF in gene expression during erythroid lineage specification.

CONCLUSIONS: Our study reveals a novel role of CTCF in regulating erythroid differentiation by maintaining its proper chromatin openness and gene expression network, which extends our understanding of CTCF biology.},
}

Humans
*CCCTC-Binding Factor/metabolism/genetics
*Erythropoiesis/genetics
*Chromatin/metabolism
Cell Line
Gene Expression Regulation
Erythroid Precursor Cells/metabolism/cytology

@article {pmid40017784,
year = {2025},
author = {Zhang, S and Xie, X and Zhang, H and Zhao, Z and Xia, K and Song, H and Li, Q and Li, M and Ge, Z},
title = {Visualizing Reactive Oxygen Species-Induced DNA Damage Process in Higher-Ordered Origami Nanostructures.},
journal = {JACS Au},
volume = {5},
number = {2},
pages = {965-974},
pmid = {40017784},
issn = {2691-3704},
abstract = {The genetic information on organisms is stored in the cell nucleus in the form of higher-ordered DNA structures. Here, we use DNA framework nanostructures (DFNs) to simulate the compaction and stacking density of nucleosome DNA for precise conformational and structure determination, particularly the dynamic structural changes, preferential reaction regions, and sites of DFNs during the reactive oxygen species (ROS) reaction process. By developing an atomic force microscopy-based single-particle analysis (SPA) data reconstruction method to collect and reanalyze imaging information, we demonstrate that the geometric morphology of DFNs constrains their reaction kinetics with ROS, where local mechanical stress and regional base distribution are two key factors affecting their kinetics. Furthermore, we plot the reaction process diagram for ROS and DFNs, showing the reaction process and intermediate products with individual activation energies. This SPA method offers new research tools and insights for studying the dynamic changes of highly folded and organized DNA structural domains within the nucleus and helps to reveal the key mechanisms behind their functional differences in topologically associating domains.},
}

@article {pmid40011778,
year = {2025},
author = {Zhao, H and Shu, L and Qin, S and Lyu, F and Liu, F and Lin, E and Xia, S and Wang, B and Wang, M and Shan, F and Lin, Y and Zhang, L and Gu, Y and Blobel, GA and Huang, K and Zhang, H},
title = {Extensive mutual influences of SMC complexes shape 3D genome folding.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40011778},
issn = {1476-4687},
abstract = {Mammalian genomes are folded through the distinct actions of structural maintenance of chromosome (SMC) complexes, which include the chromatin loop-extruding cohesin (extrusive cohesin), the sister chromatid cohesive cohesin and the mitotic chromosome-associated condensins[1-3]. Although these complexes function at different stages of the cell cycle, they exist together on chromatin during the G2-to-M phase transition, when the genome structure undergoes substantial reorganization[1,2]. Yet, how the different SMC complexes affect each other and how their interactions orchestrate the dynamic folding of the three-dimensional genome remain unclear. Here we engineered all possible cohesin and condensin configurations on mitotic chromosomes to delineate the concerted, mutually influential action of SMC complexes. We show that condensin disrupts the binding of extrusive cohesin at CCCTC-binding factor (CTCF) sites, thereby promoting the disassembly of interphase topologically associating domains (TADs) and loops during mitotic progression. Conversely, extrusive cohesin impedes condensin-mediated mitotic chromosome spiralization. Condensin reduces peaks of cohesive cohesin, whereas cohesive cohesin antagonizes condensin-mediated longitudinal shortening of mitotic chromosomes. The presence of both extrusive and cohesive cohesin synergizes these effects and inhibits mitotic chromosome condensation. Extrusive cohesin positions cohesive cohesin at CTCF-binding sites. However, cohesive cohesin by itself cannot be arrested by CTCF molecules and is insufficient to establish TADs or loops. Moreover, it lacks loop-extrusion capacity, which indicates that cohesive cohesin has nonoverlapping functions with extrusive cohesin. Finally, cohesive cohesin restricts chromatin loop expansion mediated by extrusive cohesin. Collectively, our data describe a three-way interaction among major SMC complexes that dynamically modulates chromatin architecture during cell cycle progression.},
}

@article {pmid39999165,
year = {2025},
author = {Meng, L and Sheong, FK and Luo, Q},
title = {Linking DNA-packing density distribution and TAD boundary locations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {9},
pages = {e2418456122},
doi = {10.1073/pnas.2418456122},
pmid = {39999165},
issn = {1091-6490},
support = {2022M721203//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; No. 20173326//The Construction Plan of Guangdong Province High-level Universities and the Research Start-up Funds for the High-level Talent Introduction Project of South China Agricultural University/ ; 22403033//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Humans ; *DNA/chemistry/metabolism ; *Chromatin/metabolism/chemistry/genetics ; Genome, Human ; Chromatin Assembly and Disassembly ; },
abstract = {DNA is heterogeneously packaged into chromatin, which is further organized into topologically associating domains (TADs) with sharp boundaries. These boundary locations are critical for genome regulation. Here, we explore how the distribution of DNA-packing density across chromatin affects the TAD boundary locations. We develop a polymer-physics-based model that utilizes DNA accessibility data to parameterize DNA-packing density along chromosomes, treating them as heteropolymers, and simulates the stochastic folding of these heteropolymers within a nucleus to yield a conformation ensemble. Such an ensemble reproduces a subset (over 60%) of TAD boundaries across the human genome, as confirmed by Hi-C data. Additionally, it reproduces the spatial distance matrices of 2-Mb genomic regions provided by FISH experiments. Furthermore, our model suggests that utilizing DNA accessibility data alone as input is sufficient to predict the emergence and disappearance of key TADs during early T cell differentiation. We show that stochastic folding of heteropolymers in a confined space can replicate both the prevalence of chromatin domain structures and the cell-to-cell variation in domain boundary positions observed in single-cell experiments. Furthermore, regions of lower DNA-packing density preferentially form domain boundaries, and this preference drives the emergence of TAD boundaries observed in ensemble-averaged Hi-C maps. The enrichment of TAD boundaries at CTCF binding sites can be attributed to the influence of CTCF binding on local DNA-packing density in our model. Collectively, our findings establish a strong link between TAD boundaries and regions of lower DNA-packing density, providing insights into the mechanisms underlying TAD formation.},
}

Humans
*DNA/chemistry/metabolism
*Chromatin/metabolism/chemistry/genetics
Genome, Human
Chromatin Assembly and Disassembly

@article {pmid39983729,
year = {2025},
author = {Sakata, T and Tei, S and Izumi, K and Krantz, ID and Bando, M and Shirahige, K},
title = {A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.01.044},
pmid = {39983729},
issn = {1879-0445},
abstract = {The cohesin protein complex is essential for the formation of topologically associating domains (TADs) and chromatin loops on interphase chromosomes.[1,2,3,4,5] For the loading onto chromosomes, cohesin requires the cohesin loader complex formed by NIPBL[6,7,8] and MAU2.[9] Cohesin localizes at enhancers and gene promoters with NIPBL in mammalian cells[10,11,12,13,14] and forms enhancer-promoter loops.[15,16] Cornelia de Lange syndrome (CdLS) is a rare, genetically heterogeneous disorder affecting multiple organs and systems during development,[17,18] caused by mutations in the cohesin loader NIPBL gene (>60% of patients),[19,20,21,22,23] as well as in genes encoding cohesin, a chromatin regulator, BRD4, and cohesin-related factors.[24,25,26,27] We also reported CHOPS syndrome that phenotypically overlaps with CdLS[28,29] and is caused by gene mutations of a super elongation complex (SEC) core component, AFF4. Although these syndromes are associated with transcriptional dysregulation,[24,28,30,31,32] the underlying mechanism remains unclear. In this study, we provide the first comprehensive analysis of chromosome architectural changes caused by these mutations using cell lines derived from CdLS and CHOPS syndrome patients. In both patient cells, we found a decrease in cohesin, NIPBL, BRD4, and acetylation of lysine 27 on histone H3 (H3K27ac)[33,34,35] in most enhancers with enhancer-promoter loop attenuation. By contrast, TADs were maintained in both patient cells. These findings reveal a shared molecular mechanism in these syndromes and highlight unexpected roles for cohesin, cohesin loaders, and the SEC in maintaining the enhancer complexes. These complexes are crucial for recruiting transcriptional regulators, sustaining active histone modifications, and facilitating enhancer-promoter looping.},
}

@article {pmid39972127,
year = {2025},
author = {Sebastian, R and Sun, EG and Fedkenheuer, M and Fu, H and Jung, S and Thakur, BL and Redon, CE and Pegoraro, G and Tran, AD and Gross, JM and Mosavarpour, S and Kusi, NA and Ray, A and Dhall, A and Pongor, LS and Casellas, R and Aladjem, MI},
title = {Mechanism for local attenuation of DNA replication at double-strand breaks.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39972127},
issn = {1476-4687},
abstract = {DNA double-strand breaks (DSBs) disrupt the continuity of the genome, with consequences for malignant transformation. Massive DNA damage can elicit a cellular checkpoint response that prevents cell proliferation[1,2]. However, how highly aggressive cancer cells, which can tolerate widespread DNA damage, respond to DSBs alongside continuous chromosome duplication is unknown. Here we show that DSBs induce a local genome maintenance mechanism that inhibits replication initiation in DSB-containing topologically associating domains (TADs) without affecting DNA synthesis at other genomic locations. This process is facilitated by mediators of replication and DSBs (MRDs). In normal and cancer cells, MRDs include the TIMELESS-TIPIN complex and the WEE1 kinase, which actively dislodges the TIMELESS-TIPIN complex from replication origins adjacent to DSBs and prevents initiation of DNA synthesis at DSB-containing TADs. Dysregulation of MRDs, or disruption of 3D chromatin architecture by dissolving TADs, results in inadvertent replication in damaged chromatin and increased DNA damage in cancer cells. We propose that the intact MRD cascade precedes DSB repair to prevent genomic instability, which is otherwise observed when replication is forced, or when genome architecture is challenged, in the presence of DSBs[3-5]. These observations reveal a previously unknown vulnerability in the DNA replication machinery that may be exploited to therapeutically target cancer cells.},
}

@article {pmid39971902,
year = {2025},
author = {Yamaura, K and Takemata, N and Kariya, M and Osaka, A and Ishino, S and Yamauchi, M and Tamura, T and Hamachi, I and Takada, S and Ishino, Y and Atomi, H},
title = {Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1312},
pmid = {39971902},
issn = {2041-1723},
support = {JP21K20636, JP23H04281//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20H05934//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K22289//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJPR20K7, JPMJFR224V//MEXT | Japan Science and Technology Agency (JST)/ ; JPMJFS2123, JPMJSP2110//MEXT | Japan Science and Technology Agency (JST)/ ; },
mesh = {*Archaeal Proteins/metabolism/genetics/chemistry ; *Thermococcus/genetics/metabolism ; *DNA, Archaeal/genetics/metabolism ; *Chromosomes, Archaeal/genetics ; Nucleic Acid Conformation ; Genome, Archaeal ; Cell Cycle Proteins/metabolism/genetics/chemistry ; },
abstract = {In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.},
}

*Archaeal Proteins/metabolism/genetics/chemistry
*Thermococcus/genetics/metabolism
*DNA, Archaeal/genetics/metabolism
*Chromosomes, Archaeal/genetics
Nucleic Acid Conformation
Genome, Archaeal
Cell Cycle Proteins/metabolism/genetics/chemistry

@article {pmid39946792,
year = {2025},
author = {Gómora-García, JC and Furlan-Magaril, M},
title = {Pioneer factors outline chromatin architecture.},
journal = {Current opinion in cell biology},
volume = {93},
number = {},
pages = {102480},
doi = {10.1016/j.ceb.2025.102480},
pmid = {39946792},
issn = {1879-0410},
abstract = {Pioneer factors are transcription factors capable of binding to nucleosomal DNA, initiating chromatin opening, and facilitating gene expression. By overcoming nucleosomes, pioneer factors enable cellular reprogramming, tissue-specific gene expression, and genome response to external stimuli. Here we discuss the recent literature on how pioneer factors modulate chromatin architecture at multiple levels, from local chromatin accessibility to large-scale genome organization, including chromatin compartments, topologically associating domains, and enhancer-promoter looping. Understanding the mechanisms by which pioneer factors modulate chromatin organization dynamics is key to understand their broader impact on gene expression regulation.},
}

@article {pmid39910043,
year = {2025},
author = {Kaya, VO and Adebali, O},
title = {UV-induced reorganization of 3D genome mediates DNA damage response.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1376},
pmid = {39910043},
issn = {2041-1723},
mesh = {*Ultraviolet Rays/adverse effects ; *DNA Damage/radiation effects ; *DNA Repair/radiation effects ; Humans ; Genome, Human/radiation effects ; Genome ; Gene Expression Regulation/radiation effects ; Chromatin/radiation effects/metabolism/genetics ; },
abstract = {While it is well-established that UV radiation threatens genomic integrity, the precise mechanisms by which cells orchestrate DNA damage response and repair within the context of 3D genome architecture remain unclear. Here, we address this gap by investigating the UV-induced reorganization of the 3D genome and its critical role in mediating damage response. Employing temporal maps of contact matrices and transcriptional profiles, we illustrate the immediate and holistic changes in genome architecture post-irradiation, emphasizing the significance of this reconfiguration for effective DNA repair processes. We demonstrate that UV radiation triggers a comprehensive restructuring of the 3D genome organization at all levels, including loops, topologically associating domains and compartments. Through the analysis of DNA damage and excision repair maps, we uncover a correlation between genome folding, gene regulation, damage formation probability, and repair efficacy. We show that adaptive reorganization of the 3D genome is a key mediator of the damage response, providing new insights into the complex interplay of genomic structure and cellular defense mechanisms against UV-induced damage, thereby advancing our understanding of cellular resilience.},
}

*Ultraviolet Rays/adverse effects
*DNA Damage/radiation effects
*DNA Repair/radiation effects
Humans
Genome, Human/radiation effects
Genome
Gene Expression Regulation/radiation effects
Chromatin/radiation effects/metabolism/genetics

@article {pmid39887949,
year = {2025},
author = {Dautle, MA and Chen, Y},
title = {Single-Cell Hi-C Technologies and Computational Data Analysis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2412232},
doi = {10.1002/advs.202412232},
pmid = {39887949},
issn = {2198-3844},
support = {DBI-2239350//National Science Foundation/ ; },
abstract = {Single-cell chromatin conformation capture (scHi-C) techniques have evolved to provide significant insights into the structural organization and regulatory mechanisms in individual cells. Although many scHi-C protocols have been developed, they often involve intricate procedures and the resulting data are sparse, leading to computational challenges for systematic data analysis and limited applicability. This review provides a comprehensive overview, quantitative evaluation of thirteen protocols and practical guidance on computational topics. It is first assessed the efficiency of these protocols based on the total number of contacts recovered per cell and the cis/trans ratio. It is then provided systematic considerations for scHi-C quality control and data imputation. Additionally, the capabilities and implementations of various analysis methods, covering cell clustering, A/B compartment calling, topologically associating domain (TAD) calling, loop calling, 3D reconstruction, scHi-C data simulation and differential interaction analysis is summarized. It is further highlighted key computational challenges associated with the specific complexities of scHi-C data and propose potential solutions.},
}

@article {pmid39863579,
year = {2025},
author = {Zhao, M and Jankovic, D and Link, VM and Souza, COS and Hornick, KM and Oyesola, O and Belkaid, Y and Lack, J and Loke, P},
title = {Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1030},
pmid = {39863579},
issn = {2041-1723},
mesh = {Animals ; *Lipopolysaccharides/pharmacology ; *Interleukin-4/pharmacology/genetics/metabolism ; Male ; *Mice, Inbred C57BL ; *Epigenesis, Genetic ; Mice ; *Mice, Inbred BALB C ; *Genetic Variation ; Macrophages/metabolism/drug effects ; Macrophage Activation/genetics/drug effects ; Species Specificity ; NF-kappa B/metabolism ; Macrophages, Peritoneal/metabolism/drug effects ; },
abstract = {How macrophages in the tissue environment integrate multiple stimuli depends on the genetic background of the host, but this is still poorly understood. We investigate IL-4 activation of male C57BL/6 and BALB/c strain specific in vivo tissue-resident macrophages (TRMs) from the peritoneal cavity. C57BL/6 TRMs are more transcriptionally responsive to IL-4 stimulation, with induced genes associated with more super enhancers, induced enhancers, and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling reveals C57BL/6 specific enrichment of NF-κB, IRF, and STAT motifs. Additionally, IL-4-activated C57BL/6 TRMs demonstrate an augmented synergistic response upon in vitro lipopolysaccharide (LPS) exposure, despite naïve BALB/c TRMs displaying a more robust transcriptional response to LPS. Single-cell RNA sequencing (scRNA-seq) analysis of mixed bone marrow chimeras indicates that transcriptional differences and synergy 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.},
}

Animals
*Lipopolysaccharides/pharmacology
*Interleukin-4/pharmacology/genetics/metabolism
Male
*Mice, Inbred C57BL
*Epigenesis, Genetic
Mice
*Mice, Inbred BALB C
*Genetic Variation
Macrophages/metabolism/drug effects
Macrophage Activation/genetics/drug effects
Species Specificity
NF-kappa B/metabolism
Macrophages, Peritoneal/metabolism/drug effects

@article {pmid39849544,
year = {2025},
author = {Li, H and Xing, C and Li, J and Zhan, Y and Luo, M and Wang, P and Sheng, Y and Peng, H},
title = {Aberrant c-AMP signalling in richter syndrome revealed by single-cell transcriptome and 3D chromatin analysis.},
journal = {Biomarker research},
volume = {13},
number = {1},
pages = {15},
pmid = {39849544},
issn = {2050-7771},
support = {2024JJ6549//Natural Science Foundation of Hunan Province/ ; 2024JJ6566//Natural Science Foundation of Hunan Province/ ; 2023JJ60427//Natural Science Foundation of Hunan Province/ ; 32270791//National Natural Science Foundation of China/ ; 82070175//National Natural Science Foundation of China/ ; 2022RC1205//Huxiang Youth Talent Support Program/ ; CRP/CHN22-03_EC//International Centre for Genetic Engineering and Biotechnology/ ; C202303046332//the Scientific Research Project of Hunan Provincial Health Commission/ ; 23A0018//the Scientific Research Project of Hunan Provincial Department of Education/ ; },
abstract = {Richter syndrome (RS), characterized by aggressive lymphoma arising from chronic lymphocytic leukaemia (CLL), presents a poor response to treatment and grim prognosis. To elucidate RS mechanisms, paired samples from a patient with DLBCL-RS were subjected to single-cell RNA sequencing (scRNA-seq) and high-throughput chromosome conformation capture (Hi-C) sequencing. Over 10,000 cells were profiled via scRNA-seq, revealing the comprehensive B cell transformation in RS. Hi-C sequencing exposed a unique chromatin architecture in RS, with increased proximal and decreased distal interactions. At the compartment scale, the interaction between B compartments was strengthened in DLBCL cells, while topologically associating domains (TADs) in DLBCL had elevated intra-TAD and reduced inter-TAD contacts. Differentially expressed genes at TAD borders between CLL and DLBCL cells highlighted an enrichment of cAMP-mediated signalling. To substantiate the functional relevance of ATF1 and CAP1, the genes involve in cAMP-mediated signalling, in the context of cell proliferation, we have performed gain- and loss-of-function experiments in relevant cell lines. Collectively, integrated scRNA-seq and Hi-C data suggest that chromatin reorganization and altered cAMP signalling drive RS transformation.},
}

@article {pmid39827577,
year = {2025},
author = {Qi, S and Shi, Z and Yu, H},
title = {Genome folding by cohesion.},
journal = {Current opinion in genetics & development},
volume = {91},
number = {},
pages = {102310},
doi = {10.1016/j.gde.2025.102310},
pmid = {39827577},
issn = {1879-0380},
abstract = {Chromosomes in eukaryotic cells undergo compaction at multiple levels and are folded into hierarchical structures to fit into the nucleus with limited dimensions. Three-dimensional genome organization needs to be coordinated with chromosome-templated processes, including DNA replication and gene transcription. As an ATPase molecular machine, the cohesin complex is a major driver of genome folding, which regulates transcription by modulating promoter-enhancer contacts. Here, we review our current understanding of genome folding by cohesin. We summarize the available evidence supporting a role of loop extrusion by cohesin in forming chromatin loops and topologically associating domains. We describe different conformations of cohesin and discuss the regulation of loop extrusion by cohesin-binding factors and loop-extrusion barriers. Finally, we propose a dimeric inchworm model for cohesin-mediated loop extrusion.},
}

@article {pmid39820353,
year = {2025},
author = {Wei, K and Li, R and Zhao, X and Xie, B and Xie, T and Sun, Q and Chen, Y and Wei, P and Xu, W and Guo, X and Zhao, Z and Feng, H and Ni, L and Dong, C},
title = {TRIM28 is an essential regulator of three-dimensional chromatin state underpinning CD8[+] T cell activation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {750},
pmid = {39820353},
issn = {2041-1723},
mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; *Tripartite Motif-Containing Protein 28/metabolism/genetics ; Animals ; *Chromatin/metabolism ; Mice ; *Lymphocyte Activation ; *Chromosomal Proteins, Non-Histone/metabolism/genetics ; Cell Cycle Proteins/metabolism/genetics ; CCCTC-Binding Factor/metabolism/genetics ; RNA Polymerase II/metabolism ; Interleukin-2/metabolism/genetics ; Cohesins ; Mice, Knockout ; Mice, Inbred C57BL ; },
abstract = {T cell activation is accompanied by extensive changes in epigenome. However, the high-ordered chromatin organization underpinning CD8[+] T cell activation is not fully known. Here, we show extensive changes in the three-dimensional genome during CD8[+] T cell activation, associated with changes in gene transcription. We show that CD8[+] T-cell-specific deletion of Trim28 in mice disrupts autocrine IL-2 production and leads to impaired CD8[+] T cell activation in vitro and in vivo. Mechanistically, TRIM28 binds to regulatory regions of genes associated with the formation of chromosomal loops during activation. At the loop anchor regions, TRIM28-occupancy overlaps with that of CTCF, a factor known for defining the boundaries of topologically associating domains and for forming of the loop anchors. In the absence of Trim28, RNA Pol II and cohesin binding to these regions diminishes, and the chromosomal structure required for the active state is disrupted. These results thus identify a critical role for TRIM28-dependent chromatin topology in gene transcription in activated CD8[+] T cells.},
}

*CD8-Positive T-Lymphocytes/immunology/metabolism
*Tripartite Motif-Containing Protein 28/metabolism/genetics
Animals
*Chromatin/metabolism
Mice
*Lymphocyte Activation
*Chromosomal Proteins, Non-Histone/metabolism/genetics
Cell Cycle Proteins/metabolism/genetics
CCCTC-Binding Factor/metabolism/genetics
RNA Polymerase II/metabolism
Interleukin-2/metabolism/genetics
Cohesins
Mice, Knockout
Mice, Inbred C57BL

@article {pmid39777468,
year = {2025},
author = {Sun, Q and Zhou, Q and Qiao, Y and Chen, X and Sun, H and Wang, H},
title = {Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization.},
journal = {Nucleic acids research},
volume = {53},
number = {1},
pages = {},
doi = {10.1093/nar/gkae1271},
pmid = {39777468},
issn = {1362-4962},
support = {82172436//National Natural Science Foundation of China/ ; 2022YFA0806003//National Key R&D Program of China/ ; 14103522//Research Grants Council (RGC) of the Hong Kong Special Administrative Region, China/ ; 10210906//Health Bureau of the Hong Kong Special Administrative Region, China/ ; //Government of the Hong Kong SAR, China/ ; //Chinese University of Hong Kong/ ; //Strategic Seed Funding for Collaborative Research Scheme/ ; 2024A1515030291//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Humans ; K562 Cells ; *RNA-Binding Proteins/metabolism/genetics ; *RNA Splicing Factors/metabolism/genetics ; *Promoter Regions, Genetic ; Hep G2 Cells ; Protein Binding ; CCCTC-Binding Factor/metabolism/genetics ; Animals ; Cell Differentiation/genetics ; Mice ; Chromatin/metabolism ; Myoblasts/metabolism ; Transcription, Genetic ; Repressor Proteins ; },
abstract = {Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA-binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary-associated RBPs (baRBPs). We found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF-independent manner. Moreover, baRBP binding is associated with nascent promoter transcription. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown of RBFox2 in K562 cells causes mild TAD reorganization. Moreover, RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is downregulated and its bound boundaries are remodeled during MB differentiation into myotubes. Finally, transcriptional inhibition indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play an active role in modulating TAD organization through co-transcriptional association and synergistic actions with nascent promoter transcripts.},
}

Humans
K562 Cells
*RNA-Binding Proteins/metabolism/genetics
*RNA Splicing Factors/metabolism/genetics
*Promoter Regions, Genetic
Hep G2 Cells
Protein Binding
CCCTC-Binding Factor/metabolism/genetics
Animals
Cell Differentiation/genetics
Mice
Chromatin/metabolism
Myoblasts/metabolism
Transcription, Genetic
Repressor Proteins

@article {pmid39778075,
year = {2025},
author = {Li, M and Yang, Y and Wu, R and Gong, H and Yuan, Z and Wang, J and Long, E and Zhang, X and Chen, Y},
title = {SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2406413},
doi = {10.1002/advs.202406413},
pmid = {39778075},
issn = {2198-3844},
support = {2022YFC2504003//National Key R&D Program of China/ ; 2022YFC2504002//National Key R&D Program of China/ ; 2021-I2M-1-020//CAMS Innovation Fund for Medical Sciences/ ; 2022-I2M-1-020//CAMS Innovation Fund for Medical Sciences/ ; 2021-RC310-007//CAMS Innovation Fund for Medical Sciences/ ; },
abstract = {The dynamics of chromatin conformation involve continuous and reversible changes within the nucleus of a cell, which participate in regulating processes such as gene expression, DNA replication, and damage repair. Here, SEE is introduced, an artificial intelligence (AI) method that utilizes autoencoder and transformer techniques to analyze chromatin dynamics using single-cell RNA sequencing data and a limited number of single-cell Hi-C maps. SEE is employed to investigate chromatin dynamics across different scales, enabling the detection of (i) rearrangements in topologically associating domains (TADs), and (ii) oscillations in chromatin interactions at gene loci. Additionally, SEE facilitates the interpretation of disease-associated single-nucleotide polymorphisms (SNPs) by leveraging the dynamic features of chromatin conformation. Overall, SEE offers a single-cell, high-resolution approach to analyzing chromatin dynamics in both developmental and disease contexts.},
}

@article {pmid39757126,
year = {2025},
author = {Ren, X and Shi, Y and Xiao, B and Su, X and Shi, H and He, G and Chen, P and Wu, D and Shi, Y},
title = {Gene Doping Detection From the Perspective of 3D Genome.},
journal = {Drug testing and analysis},
volume = {},
number = {},
pages = {},
doi = {10.1002/dta.3850},
pmid = {39757126},
issn = {1942-7611},
support = {2022YFE0125300//Key Research and Development Plan of the Ministry of Science and Technology/ ; YG2023ZD26//Shanghai Jiao Tong University STAR/ ; YG2022ZD024//Shanghai Jiao Tong University STAR/ ; YG2022QN111//Shanghai Jiao Tong University STAR/ ; //Shanghai Gaofeng and Gaoyuan Project for the University Academic Program Development/ ; },
abstract = {Since the early 20th century, the concept of doping was first introduced. To achieve better athletic performance, chemical substances were used. By the mid-20th century, it became gradually recognized that the illegal use of doping substances can seriously endangered athletes' health and compromised the fairness of sports competitions. Over the past 30 years, the World Anti-Doping Agency (WADA) has established corresponding rules and regulations to prohibit athletes from using doping substances or restrict the use of certain drugs, and isotope, chromatography, and mass spectrometry techniques were accredited to detect doping substances. With the development of gene editing technology, many genetic diseases have been effectively treated, but enabled by the same technology, doping has also the potential to pose a threat to sports in the form of gene doping. WADA has explicitly indicated gene doping in the Prohibited List as a prohibited method (M3) and approved qPCR detection. However, gene doping can easily evade detection, if the target genes' upstream regulatory elements are considered, the task became more challenging. Hi-C experiment driven 3D genome technology, through perspectives such as topologically associating domain (TAD) and chromatin loop, provides a more comprehensive and in-depth understanding of gene regulation and expression, thereby better preventing the potential use of 3D genome level gene doping. In this work, we will explore gene doping from a different perspective by analyzing recent studies on gene doping and explore related genes under 3D genome.},
}

@article {pmid39741350,
year = {2024},
author = {Wang, D and Xiao, S and Shu, J and Luo, L and Yang, M and Calonje, M and He, H and Song, B and Zhou, Y},
title = {Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {324},
pmid = {39741350},
issn = {1474-760X},
mesh = {*Arabidopsis/genetics ; *Promoter Regions, Genetic ; *Arabidopsis Proteins/genetics/metabolism ; *Chromatin/metabolism/genetics ; *Gene Expression Regulation, Plant ; Cohesins ; Histones/metabolism ; Cell Cycle Proteins/metabolism/genetics ; Chromosomal Proteins, Non-Histone/metabolism/genetics ; Enhancer Elements, Genetic ; },
abstract = {BACKGROUND: Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete.

RESULTS: Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes.

CONCLUSIONS: We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.},
}

*Arabidopsis/genetics
*Promoter Regions, Genetic
*Arabidopsis Proteins/genetics/metabolism
*Chromatin/metabolism/genetics
*Gene Expression Regulation, Plant
Cohesins
Histones/metabolism
Cell Cycle Proteins/metabolism/genetics
Chromosomal Proteins, Non-Histone/metabolism/genetics
Enhancer Elements, Genetic

@article {pmid39731323,
year = {2024},
author = {Ma, N and Li, X and Ci, D and Zeng, HY and Zhang, C and Xie, X and Zhong, C and Deng, XW and Li, D and He, H},
title = {Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2408861},
doi = {10.1002/advs.202408861},
pmid = {39731323},
issn = {2198-3844},
support = {ZR202211070163//Key R&D Program of Shandong Province/ ; 32230006//National Natural Science Foundation of China/ ; 2021hszd017//Hubei Hongshan Laboratory/ ; 2023AFA075//Hubei Province Natural Science Fund Project for Outstanding Youth/ ; },
abstract = {In eukaryotes, chromatin is compacted within nuclei under the principle of compartmentalization. On top of that, condensin II establishes eukaryotic chromosome territories, while cohesin organizes the vertebrate genome by extruding chromatin loops and forming topologically associating domains (TADs). Thus far, the formation and roles of these chromatin structures in plants remain poorly understood. This study integrates Hi-C data from diverse plant species, demonstrating that nuclear DNA content influences large-scale chromosome conformation and affects the finer details of compartmental patterns. These contrasting compartmental patterns are distinguished by gene-to-gene loops and validated through cytological observations. Additionally, a novel chromatin domain type associated with tandem duplicate gene clusters is identified. These domains are independent of H3K27me3-mediated chromatin compartmentalization and exhibit evolutionary conservation across species. Gene pairs within TAD-like domains are younger and show higher levels of coexpression. These domains potentially promote the formation of tandem duplicates, a property appears unique to the Actinidia family. Overall, this study reveals functional chromatin domains in plants and provides evidence for the role of three-dimensional chromatin architecture in gene regulation and genome evolution.},
}

@article {pmid39727192,
year = {2024},
author = {Dang, D and Zhang, SW and Dong, K and Duan, R and Zhang, S},
title = {Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1267},
pmid = {39727192},
issn = {1362-4962},
support = {2019YFA0709501//National Key Research and Development Program of China/ ; 62173271//National Natural Science Foundation of China/ ; 2023K0602//R&D project of Pazhou Lab/ ; YSBR-034//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {Topologically associating domains (TADs) are essential components of three-dimensional (3D) genome organization and significantly influence gene transcription regulation. However, accurately identifying TADs from sparse chromatin contact maps and exploring the structural and functional elements within TADs remain challenging. To this end, we develop TADGATE, a graph attention auto-encoder that can generate imputed maps from sparse Hi-C contact maps while adaptively preserving or enhancing the underlying topological structures, thereby facilitating TAD identification. TADGATE captures specific attention patterns with two types of units within TADs and demonstrates TAD organization relates to chromatin compartmentalization with diverse biological properties. We identify many structural and functional elements within TADs, with their abundance reflecting the overall properties of these domains. We applied TADGATE to sparse and noisy Hi-C contact maps from 21 human tissues or cell lines. That improved the clarity of TAD structures, allowing us to investigate conserved and cell-type-specific boundaries and uncover cell-type-specific transcriptional regulatory mechanisms associated with topological domains. We also demonstrated TADGATE's capability to fill in sparse single-cell Hi-C contact maps and identify TAD-like domains within them, revealing the specific domain boundaries with distinct heterogeneity and the shared backbone boundaries characterized by strong CTCF enrichment and high gene expression levels.},
}

@article {pmid39682078,
year = {2024},
author = {Ren, H and Zhong, H and Zhang, J and Lu, Y and Hu, G and Duan, W and Ma, N and Yao, H},
title = {CTCF Point Mutation at R567 Disrupts Mouse Heart Development via 3D Genome Rearrangement and Transcription Dysregulation.},
journal = {Cell proliferation},
volume = {},
number = {},
pages = {e13783},
doi = {10.1111/cpr.13783},
pmid = {39682078},
issn = {1365-2184},
support = {31925009//National Natural Science Foundation of China/ ; U21A20195//National Natural Science Foundation of China/ ; 32300477//National Natural Science Foundation of China/ ; 32430016//National Natural Science Foundation of China/ ; 2021YFA1100300//National Key R&D Program of China/ ; 2023B03J1230//Guangzhou Key R&D Program/ ; 2022ZDLSF02-01//Key R&D Program of Shaanxi Province/ ; 2023JC-XJ-11//Special Support Project for Basic Research of Shaanxi Province/ ; },
abstract = {CTCF plays a vital role in shaping chromatin structure and regulating gene expression. Clinical studies have associated CTCF mutations with congenital developmental abnormalities, including congenital cardiomyopathy. In this study, we investigated the impact of the homozygous CTCF-R567W (Ctcf[R567W/R567W]) mutation on cardiac tissue morphogenesis during mouse embryonic development. Our results reveal significant impairments in heart development, characterised by ventricular muscle trabecular hyperplasia and reduced ventricular cavity sizes. We also observe a marked downregulation of genes involved in sarcomere assembly, calcium ion transport, and mitochondrial function in heart tissues from homozygous mice. Furthermore, the Ctcf[R567W/R567W] mutation disrupts CTCF's interaction with chromatin, resulting in alterations to topologically associating domain (TAD) structure within specific genomic regions and diminishing crucial promoter-enhancer interactions necessary for cardiac development. Additionally, we find that the heterozygous CTCF-R567W (Ctcf[+/R567W]) mutation significantly compromises cardiac contractility in 8-week-old mice. This study elucidates the mechanism by which the CTCF-R567W mutation hampers cardiac development, underscoring the essential role of CTCF-R567 in embryonic heart development and maturation.},
}

@article {pmid39669613,
year = {2024},
author = {Wolujewicz, P and Aguiar-Pulido, V and Thareja, G and Suhre, K and Elemento, O and Finnell, RH and Ross, ME},
title = {Integrative computational analyses implicate regulatory genomic elements contributing to spina bifida.},
journal = {Genetics in medicine open},
volume = {2},
number = {},
pages = {101894},
pmid = {39669613},
issn = {2949-7744},
abstract = {PURPOSE: Spina bifida (SB) arises from complex genetic interactions that converge to interfere with neural tube closure. Understanding the precise patterns conferring SB risk requires a deep exploration of the genomic networks and molecular pathways that govern neurulation. This study aims to delineate genome-wide regulatory signatures underlying SB pathophysiology.

METHODS: An untargeted, genome-wide approach was used to interrogate regulatory regions for rare single-nucleotide and copy-number variants (rSNVs and rCNVs, respectively) predicted to affect gene expression, comparing results from SB patients with healthy controls. Qualifying variants were subjected to a deep learning prioritization framework to identify the most functionally relevant variants, as well as the likely target genes affected by these rare regulatory variants.

RESULTS: This ensemble of computational tools identified rSNVs in specific transcription factor binding sites (TFBSs) that distinguish SB cases from controls. rSNV enrichment was found in specific TFBSs, especially CCCTC-binding factor binding sites. These TFBSs were subjected to a deep learning prioritization framework to identify the most functionally relevant variants, as well as the likely target genes affected by these rSNVs. The functional pathways or modules implicated by these regulated genes serve protein transport, cilia assembly, and central nervous system development. Moreover, the detected rare copy-number variants in SB cases are positioned to disrupt gene regulatory networks and alter 3-dimensional genomic architectures, including brain-specific enhancers and topologically associated domain boundaries of relevant cell types.

CONCLUSION: Our study provides a resource for identifying and interpreting genomic regulatory DNA variant contributions to human SB genetic predisposition.},
}

@article {pmid39638559,
year = {2024},
author = {Li, C and Bonder, MJ and Syed, S and Jensen, M and , and , and Gerstein, MB and Zody, MC and Chaisson, MJP and Talkowski, ME and Marschall, T and Korbel, JO and Eichler, EE and Lee, C and Shi, X},
title = {An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279419.124},
pmid = {39638559},
issn = {1549-5469},
abstract = {The human genome is packaged within a three-dimensional (3D) nucleus and organized into structural units known as compartments, topologically associating domains (TADs), and loops. TAD boundaries, separating adjacent TADs, have been found to be well conserved across mammalian species and more evolutionarily constrained than TADs themselves. Recent studies show that structural variants (SVs) can modify 3D genomes through the disruption of TADs, which play an essential role in insulating genes from outside regulatory elements' aberrant regulation. However, how SV affects the 3D genome structure and their association among different aspects of gene regulation and candidate cis-regulatory elements (cCREs) have rarely been studied systematically. Here, we assess the impact of SVs intersecting with TAD boundaries by developing an integrative Hi-C analysis pipeline, which enables the generation of an in-depth catalog of TADs and TAD boundaries in human lymphoblastoid cell lines (LCLs) to fill the gap of limited resources. Our catalog contains 18,865 TADs, including 4596 sub-TADs, with 185 SVs (TAD-SVs) that alter chromatin architecture. By leveraging the ENCODE registry of cCREs in humans, we determine that 34 of 185 TAD-SVs intersect with cCREs and observe significant enrichment of TAD-SVs within cCREs. This study provides a database of TADs and TAD-SVs in the human genome that will facilitate future investigations of the impact of SVs on chromatin structure and gene regulation in health and disease.},
}

@article {pmid39634272,
year = {2024},
author = {Mao, R and Cai, Z and Wang, T and Li, Y and Tian, S and Li, D and Li, P},
title = {Comparative study of the three-dimensional genomes of granulosa cells in germinal vesicle and metaphase II follicles.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1480153},
pmid = {39634272},
issn = {1664-8021},
abstract = {INTRODUCTION: Follicle development is a critical process in the female reproductive system, with significant implications for fertility and reproductive health. Germinal vesicle (GV) oocytes are primary oocytes that are arrested in the dictyate stage, also known as the diplotene stage of meiotic prophase I. Metaphase II (MII) is the stage at which the oocyte is typically retrieved for assisted reproductive technologies such as in vitro fertilization (IVF). The granulosa cells play a pivotal role in follicle development processes. 3D chromatin organization is a fundamental aspect of cellular biology that has significant implications for gene regulation and cellular function.

METHODS: In this study, we investigated 3D chromatin organization in granulosacells from GV and MII follicles, which is essential for understanding the regulatory mechanisms governing oocyte development.

RESULTS: The results revealed distinct compartmentalization patterns,including stable genomic regions and transitions during oocyte maturation. Notably, there was a significant shift in functional gene activation, particularly in processes related to hormone metabolic pathways. Furthermore, alterations in topologically associating domains (TADs) were observed, with differential expression observed in genes that are involved in crucial biological processes. The analysis also identified a subset of genes with altered promoter-enhancer interactions (PEIs), reflecting a regulatory shift in gene expression related to reproductive processes.

DISCUSSION: These findings provide valuable insights into 3D genome organization in granulosa cells with implications for reproductive health and the development of assisted reproductive technologies. Understanding spatial genome organization at different stages of follicular development may help realize novel strategies for enhancing success rates in assisted reproductive technologies.},
}

@article {pmid39617879,
year = {2024},
author = {Shen, W and Zhang, P and Jiang, Y and Tao, H and Zi, Z and Li, L},
title = {HTAD: a human-in-the-loop framework for supervised chromatin domain detection.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {302},
pmid = {39617879},
issn = {1474-760X},
mesh = {Humans ; *Chromatin ; Genome, Human ; Supervised Machine Learning ; Machine Learning ; Software ; },
abstract = {Topologically associating domains (TADs) are essential units of genome architecture, influencing transcriptional regulation and diseases. Despite numerous methods proposed for TAD identification, it remains challenging due to complex background and nested TAD structures. We introduce HTAD, a human-in-the-loop TAD caller that combines machine learning with human supervision to achieve high accuracy. HTAD begins with feature extraction for potential TAD border pairs, followed by an interactive labeling process through active learning. Performance assessments using public curation and synthetic datasets demonstrate HTAD's superiority over other state-of-the-art methods and reveal highly hierarchical TAD structures, offering a human-in-the-loop solution for detecting complex genomic patterns.},
}

Humans
*Chromatin
Genome, Human
Supervised Machine Learning
Machine Learning
Software

@article {pmid39614448,
year = {2024},
author = {Popenko, V and Spirin, P and Prassolov, V and Leonova, O},
title = {Chromomeres, Topologically Associating Domains and Structural Organization of Chromatin Bodies in Somatic Nuclei (Macronuclei) of Ciliates.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {29},
number = {11},
pages = {378},
doi = {10.31083/j.fbl2911378},
pmid = {39614448},
issn = {2768-6698},
support = {22-14-00353//Russian Science Foundation/ ; 075-15-2019-1660//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Chromatin/ultrastructure/metabolism/genetics ; *Ciliophora/genetics/ultrastructure ; Macronucleus/genetics/metabolism/ultrastructure ; Cell Nucleus/ultrastructure/metabolism ; Chromosomes/ultrastructure/genetics ; },
abstract = {BACKGROUND: In the twentieth century, the textbook idea of packaging genomic material in the cell nucleus and metaphase chromosomes was the presence of a hierarchy of structural levels of chromatin organization: nucleosomes - nucleosomal fibrils -30 nm fibrils - chromomeres - chromonemata - mitotic chromosomes. Chromomeres were observed in partially decondensed chromosomes and interphase chromatin as ~100 nm globular structures. They were thought to consist of loops of chromatin fibres attached at their bases to a central protein core. However, Hi-C and other related methods led to a new concept of chromatin organization in the nuclei of higher eukaryotes, according to which nucleosomal fibrils themselves determine the spatial configuration of chromatin in the form of topologically associating domains (TADs), which are formed by a loop extrusion process and are regions whose DNA sequences preferentially contact each other. Somatic macronuclei of ciliates are transcriptionally active, highly polyploid nuclei. A feature of macronuclei is that their genome is represented by a large number of "gene-sized" (~1-25 kb) or of "subchromosomal" (~50-1700 kb) size minichromosomes. The inactive macronuclear chromatin of "subchromosomal" ciliates usually looks like bodies 100-200 nm in size. The aim of this work was to find out which of the models (chromomeres or TADs) is more consistent with the confocal and electron microscopic data on structural organization of chromatin bodies.

METHODS: Macronuclear chromatin of four "subchromosomal" ciliate species (Bursaria truncatella, Paramecium multimicronucleatum, Didinium nasutum, Climacostomum virens) was examined using electron microscopy and confocal microscopy during regular growth, starvation and encystment.

RESULTS: Chromatin bodies ~70-200 nm in size observed in the interphase macronuclei consisted of tightly packed nucleosomes. Some of them were interconnected by one or more chromatin fibrils. Under hypotonic conditions in vitro, chromatin bodies decompacted, forming rosette-shaped structures of chromatin fibrils around an electron-dense centre. When the activity of the macronucleus decreased during starvation or encystment, chromatin bodies assembled into chromonema-like fibrils 100-300 nm thick. This data allows us to consider chromatin bodies as analogues of chromomeres. On the other hand, most likely, the formation of DNA loops in chromatin bodies occurs by the loop extrusion as in TADs.

CONCLUSIONS: The data obtained is well explained by the model, according to which the chromatin bodies of ciliate macronuclei combine features inherent in both chromomeres and TADs; that is, they can be considered as chromomeres with loops packed in the same way as the loops in TADs.},
}

*Chromatin/ultrastructure/metabolism/genetics
*Ciliophora/genetics/ultrastructure
Macronucleus/genetics/metabolism/ultrastructure
Cell Nucleus/ultrastructure/metabolism
Chromosomes/ultrastructure/genetics

@article {pmid39605346,
year = {2024},
author = {Hanafiah, A and Geng, Z and Liu, T and Tai, YT and Cai, W and Wang, Q and Christensen, N and Liu, Y and Yue, F and Gao, Z},
title = {PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.13.623456},
pmid = {39605346},
issn = {2692-8205},
abstract = {Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.},
}

@article {pmid39605341,
year = {2024},
author = {Frederick, J and Virk, RKA and Ye, IC and Almassalha, LM and Wodarcyk, GM and VanDerway, D and Carrillo Gonzalez, P and Nap, RJ and Agrawal, V and Anthony, NM and Carinato, J and Li, WS and Dunton, CL and Medina, KI and Kakkaramadam, R and Jain, S and Shahabi, S and Ameer, G and Szleifer, IG and Backman, V},
title = {Leveraging chromatin packing domains to target chemoevasion in vivo.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.14.623612},
pmid = {39605341},
issn = {2692-8205},
abstract = {Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains (TADs). However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based mechanistic model that connects chromatin organization to cell fate decisions, specifically survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional efficiency through macromolecular crowding. The model accurately predicts chemoevasion in vitro , suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. Using live-cell chromatin imaging, we conducted a compound screen that identified several TPRs which synergistically enhanced chemotherapyinduced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft (PDX) model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a novel framework for enhancing cancer therapies, with broad potential across multiple cancer types.},
}

@article {pmid39574698,
year = {2024},
author = {Gjoni, K and Ren, X and Everitt, A and Shen, Y and Pollard, KS},
title = {De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.06.621353},
pmid = {39574698},
issn = {2692-8205},
abstract = {Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.},
}

@article {pmid39572529,
year = {2024},
author = {de Luca, KL and Rullens, PMJ and Karpinska, MA and de Vries, SS and Gacek-Matthews, A and Pongor, LS and Legube, G and Jachowicz, JW and Oudelaar, AM and Kind, J},
title = {Genome-wide profiling of DNA repair proteins in single cells.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9918},
pmid = {39572529},
issn = {2041-1723},
mesh = {Humans ; *DNA Repair ; *Single-Cell Analysis/methods ; *DNA Breaks, Double-Stranded ; *Chromatin/metabolism ; Genome, Human ; Genomic Instability ; Protein Binding ; DNA Damage ; DNA-Binding Proteins/metabolism/genetics ; },
abstract = {Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular viability. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present a comprehensive analysis of repair protein localization in single human cells using DamID and ChIC sequencing techniques. This study reports genome-wide binding profiles in response to DNA double-strand breaks induced by AsiSI, and explores variability in genomic damage locations and associated repair features in the context of spatial genome organization. By unbiasedly detecting repair factor localization, we find that repair proteins often occupy entire topologically associating domains, mimicking variability in chromatin loop anchoring. Moreover, we demonstrate the formation of multi-way chromatin hubs in response to DNA damage. Notably, larger hubs show increased coordination of repair protein binding, suggesting a preference for cooperative repair mechanisms. Together, our work offers insights into the heterogeneous processes underlying genome stability in single cells.},
}

Humans
*DNA Repair
*Single-Cell Analysis/methods
*DNA Breaks, Double-Stranded
*Chromatin/metabolism
Genome, Human
Genomic Instability
Protein Binding
DNA Damage
DNA-Binding Proteins/metabolism/genetics

@article {pmid39545685,
year = {2024},
author = {Lee, D and Kang, J and Kim, A},
title = {TAD-dependent sub-TAD is required for enhancer-promoter interaction enabling the β-globin transcription.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {38},
number = {22},
pages = {e70181},
doi = {10.1096/fj.202401526RR},
pmid = {39545685},
issn = {1530-6860},
support = {NRF-2020R1I1A3054808//National Research Foundation of Korea (NRF)/ ; 2022R1C1C2006355//National Research Foundation of Korea (NRF)/ ; },
abstract = {Topologically associating domains (TADs) are chromatin domains in the eukaryotic genome. TADs often comprise several sub-TADs. The boundaries of TADs and sub-TADs are enriched in CTCF, an architectural protein. Deletion of CTCF-binding motifs at one boundary disrupts the domains, often resulting in a transcriptional decrease in genes inside the domains. However, it is not clear how TAD and sub-TAD affect each other in the domain formation. Unaffected gene transcription was observed in the β-globin locus when one boundary of TAD or sub-TAD was destroyed. Here, we disrupted β-globin TAD and sub-TAD by deleting CTCF motifs at both boundaries in MEL/ch11 cells. Disruption of TAD impaired sub-TAD, but sub-TAD disruption did not affect TAD. Both TAD and sub-TAD disruption compromised the β-globin transcription, accompanied by the loss of enhancer-promoter interactions. However, histone H3 occupancy and H3K27ac were largely maintained across the β-globin locus. Genome-wide analysis showed that putative enhancer-promoter interactions and gene transcription were decreased by the disruption of CTCF-mediated topological domains in neural progenitor cells. Collectively, our results indicate that there is unequal relationship between TAD and sub-TAD formation. TAD is likely not sufficient for gene transcription, and, therefore, sub-TAD appears to be required. TAD-dependently formed sub-TADs are considered to provide chromatin environments for enhancer-promoter interactions enabling gene transcription.},
}

@article {pmid39543681,
year = {2024},
author = {Yuan, T and Yan, H and Li, KC and Surovtsev, I and King, MC and Mochrie, SGJ},
title = {Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {293},
pmid = {39543681},
issn = {1474-760X},
support = {1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 1830904//Division of Emerging Frontiers and Multidisciplinary Activities/ ; 2412859//Division of Physics/ ; 2412859//Division of Physics/ ; 2412859//Division of Physics/ ; 2412859//Division of Physics/ ; 2412859//Division of Physics/ ; },
abstract = {BACKGROUND: Inhomogeneous patterns of chromatin-chromatin contacts within 10-100-kb-sized regions of the genome are a generic feature of chromatin spatial organization. These features, termed topologically associating domains (TADs), have led to the loop extrusion factor (LEF) model. Currently, our ability to model TADs relies on the observation that in vertebrates TAD boundaries are correlated with DNA sequences that bind CTCF, which therefore is inferred to block loop extrusion. However, although TADs feature prominently in their Hi-C maps, non-vertebrate eukaryotes either do not express CTCF or show few TAD boundaries that correlate with CTCF sites. In all of these organisms, the counterparts of CTCF remain unknown, frustrating comparisons between Hi-C data and simulations.

RESULTS: To extend the LEF model across the tree of life, here, we propose the conserved-current loop extrusion (CCLE) model that interprets loop-extruding cohesin as a nearly conserved probability current. From cohesin ChIP-seq data alone, we derive a position-dependent loop extrusion rate, allowing for a modified paradigm for loop extrusion, that goes beyond solely localized barriers to also include loop extrusion rates that vary continuously. We show that CCLE accurately predicts the TAD-scale Hi-C maps of interphase Schizosaccharomyces pombe, as well as those of meiotic and mitotic Saccharomyces cerevisiae, demonstrating its utility in organisms lacking CTCF.

CONCLUSIONS: The success of CCLE in yeasts suggests that loop extrusion by cohesin is indeed the primary mechanism underlying TADs in these systems. CCLE allows us to obtain loop extrusion parameters such as the LEF density and processivity, which compare well to independent estimates.},
}

@article {pmid39537822,
year = {2024},
author = {Zhang, R and Sun, J and Liu, S and Ding, J and Xiang, M},
title = {Multiscale 3D genome rewiring during PTF1A-mediated somatic cell reprogramming into neural stem cells.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1505},
pmid = {39537822},
issn = {2399-3642},
support = {2021ZD0202603//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 81970794, 81721003//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023B1212060018//Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province)/ ; },
mesh = {*Neural Stem Cells/metabolism/cytology ; *Transcription Factors/metabolism/genetics ; Animals ; *Cellular Reprogramming/genetics ; Mice ; Genome ; Chromatin/metabolism/genetics ; Cell Transdifferentiation/genetics ; Fibroblasts/metabolism/cytology ; },
abstract = {The genome is intricately folded into chromatin compartments, topologically associating domains (TADs) and loops unique to each cell type. How this higher-order genome organization regulates cell fate transition remains elusive. Here we show how a single non-neural progenitor transcription factor, PTF1A, reorchestrates the 3D genome during fibroblast transdifferentiation into neural stem cells (NSCs). Multiomics analyses integrating Hi-C data, PTF1A and CTCF DNA-binding profiles, H3K27ac modification, and gene expression, demonstrate that PTF1A binds to subTAD boundaries subsequently associated with elevated CTCF binding and enhanced boundary insulation, and reorganizes chromatin loops, leading to gene expression changes that drive transdifferentiation into NSCs. Moreover, PTF1A activates enhancers and super-enhancers near low-insulation boundaries and modulates H3K27ac deposition, promoting cell fate transitions. Together, our data implicate an involvement of 3D genome in transcriptional and cell fate alterations, and highlight an essential role for PTF1A in gene expression control and multiscale 3D genome remodeling during cell reprogramming.},
}

*Neural Stem Cells/metabolism/cytology
*Transcription Factors/metabolism/genetics
Animals
*Cellular Reprogramming/genetics
Mice
Genome
Chromatin/metabolism/genetics
Cell Transdifferentiation/genetics
Fibroblasts/metabolism/cytology

@article {pmid39507620,
year = {2024},
author = {de Bruijn, SE and Panneman, DM and Weisschuh, N and Cadena, EL and Boonen, EGM and Holtes, LK and Astuti, GDN and Cremers, FPM and Leijsten, N and Corominas, J and Gilissen, C and Skowronska, A and Woodley, J and Beggs, AD and Toulis, V and Chen, D and Cheetham, ME and Hardcastle, AJ and McLaren, TL and Lamey, TM and Thompson, JA and Chen, FK and de Roach, JN and Urwin, IR and Sullivan, LS and Roosing, S},
title = {Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1469686},
doi = {10.3389/fgene.2024.1469686},
pmid = {39507620},
issn = {1664-8021},
abstract = {INTRODUCTION: Autosomal dominant retinitis pigmentosa type 17 (adRP, type RP17) is caused by complex structural variants (SVs) affecting a locus on chromosome 17 (chr17q22). The SVs disrupt the 3D regulatory landscape by altering the topologically associating domain (TAD) structure of the locus, creating novel TAD structures (neo-TADs) and ectopic enhancer-gene contacts. Currently, screening for RP17-associated SVs is not included in routine diagnostics given the complexity of the variants and a lack of cost-effective detection methods. The aim of this study was to accurately detect novel RP17-SVs by establishing a systematic and efficient workflow.

METHODS: Genetically unexplained probands diagnosed with adRP (n = 509) from an international cohort were screened using a smMIPs or genomic qPCR-based approach tailored for the RP17 locus. Suspected copy number changes were validated using high-density SNP-array genotyping, and SV breakpoint characterization was performed by mutation-specific breakpoint PCR, genome sequencing and, if required, optical genome mapping. In silico modeling of novel SVs was performed to predict the formation of neo-TADs and whether ectopic contacts between the retinal enhancers and the GDPD1-promoter could be formed.

RESULTS: Using this workflow, potential RP17-SVs were detected in eight probands of which seven were confirmed. Two novel SVs were identified that are predicted to cause TAD rearrangement and retinal enhancer-GDPD1 contact, one from Germany (DE-SV9) and three with the same SV from the United States (US-SV10). Previously reported RP17-SVs were also identified in three Australian probands, one with UK-SV2 and two with SA-SV3.

DISCUSSION: In summary, we describe a validated multi-step pipeline for reliable and efficient RP17-SV discovery and expand the range of disease-associated SVs. Based on these data, RP17-SVs can be considered a frequent cause of adRP which warrants the inclusion of RP17-screening as a standard diagnostic test for this disease.},
}

@article {pmid39481374,
year = {2024},
author = {Lee, JJY and Johnston, MJ and Farooq, H and Chen, HM and Younes, ST and Suarez, R and Zwaig, M and Juretic, N and Weiss, WA and Ragoussis, J and Jabado, N and Taylor, MD and Gallo, M},
title = {3D genome topology distinguishes molecular subgroups of medulloblastoma.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2024.10.003},
pmid = {39481374},
issn = {1537-6605},
abstract = {Four main medulloblastoma (MB) molecular subtypes have been identified based on transcriptional, DNA methylation, and genetic profiles. However, it is currently not known whether 3D genome architecture differs between MB subtypes. To address this question, we performed in situ Hi-C to reconstruct the 3D genome architecture of MB subtypes. In total, we generated Hi-C and matching transcriptome data for 28 surgical specimens and Hi-C data for one patient-derived xenograft. The average resolution of the Hi-C maps was 6,833 bp. Using these data, we found that insulation scores of topologically associating domains (TADs) were effective at distinguishing MB molecular subgroups. TAD insulation score differences between subtypes were globally not associated with differential gene expression, although we identified few exceptions near genes expressed in the lineages of origin of specific MB subtypes. Our study therefore supports the notion that TAD insulation scores can distinguish MB subtypes independently of their transcriptional differences.},
}

@article {pmid39468060,
year = {2024},
author = {Göbel, AM and Zhou, S and Wang, Z and Tzourtzou, S and Himmelbach, A and Zheng, S and Pradillo, M and Liu, C and Jiang, H},
title = {Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9308},
pmid = {39468060},
issn = {2041-1723},
support = {JI347/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; LI 2862/8-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 100489995//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 757600//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Arabidopsis/genetics ; *Arabidopsis Proteins/genetics/metabolism ; *Mutation ; *Gene Expression Regulation, Plant ; *Chromatin/metabolism/genetics ; *Genome, Plant ; Chromatin Assembly and Disassembly/genetics ; },
abstract = {In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana. Here, we demonstrate that Arabidopsis PDS5 proteins play a negative role in TAD-like domain formation. Through Hi-C analysis, we show that mutations in PDS5 genes lead to the widespread emergence of enhanced TAD-like domains throughout the Arabidopsis genome, excluding pericentromeric regions. These domains exhibit increased chromatin insulation and enhanced chromatin interactions, without significant changes in gene expression or histone modifications. Our results suggest that PDS5 proteins are key regulators of genome architecture, influencing 3D chromatin organization independently of transcriptional activity. This study provides insights into the unique chromatin structure of Arabidopsis and the broader mechanisms governing plant genome folding.},
}

*Arabidopsis/genetics
*Arabidopsis Proteins/genetics/metabolism
*Mutation
*Gene Expression Regulation, Plant
*Chromatin/metabolism/genetics
*Genome, Plant
Chromatin Assembly and Disassembly/genetics

@article {pmid39457417,
year = {2024},
author = {Houchens, D and Chowdhury, HMAM and Oluwadare, O},
title = {coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data.},
journal = {Genes},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/genes15101293},
pmid = {39457417},
issn = {2073-4425},
support = {R35GM150402/NH/NIH HHS/United States ; },
mesh = {*Algorithms ; Humans ; Chromatin/genetics ; Cluster Analysis ; Computational Biology/methods ; Chromatin Assembly and Disassembly ; },
abstract = {BACKGROUND/OBJECTIVES: Topologically associating domains (TADs) are key structural units of the genome, playing a crucial role in gene regulation. TAD boundaries are enriched with specific biological markers and have been linked to genetic diseases, making consistent TAD detection essential. However, accurately identifying TADs remains challenging due to the lack of a definitive validation method. This study aims to develop a novel algorithm, termed coiTAD, which introduces an innovative approach for preprocessing Hi-C data to improve TAD prediction. This method employs a proposed "circle of influence" (COI) approach derived from Hi-C contact matrices.

METHODS: The coiTAD algorithm is based on the creation of novel features derived from the circle of influence in input contact matrices, which are subsequently clustered using the HDBSCAN clustering algorithm. The TADs are extracted from the clustered features based on intra-cluster interactions, thereby providing a more accurate method for identifying TADs.

RESULTS: Rigorous tests were conducted using both simulated and real Hi-C datasets. The algorithm's validation included analysis of boundary proteins such as H3K4me1, RNAPII, and CTCF. coiTAD consistently matched other TAD prediction methods.

CONCLUSIONS: The coiTAD algorithm represents a novel approach for detecting TADs. At its core, the circle-of-influence methodology introduces an innovative strategy for preparing Hi-C data, enabling the assessment of interaction strengths between genomic regions. This approach facilitates a nuanced analysis that effectively captures structural variations within chromatin. Ultimately, the coiTAD algorithm enhances our understanding of chromatin organization and offers a robust tool for genomic research. The source code for coiTAD is publicly available, and the URL can be found in the Data Availability Statement section.},
}

*Algorithms
Humans
Chromatin/genetics
Cluster Analysis
Computational Biology/methods
Chromatin Assembly and Disassembly

@article {pmid39416077,
year = {2024},
author = {Rahmaninejad, H and Xiao, Y and Tortora, MMC and Fudenberg, G},
title = {Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617113},
pmid = {39416077},
issn = {2692-8205},
abstract = {In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between neighboring topologically associating domains, and elevated contact frequency between convergent CTCF barriers across the genome. However, recent in vivo measurements present a puzzle: reported residence times for CTCF on chromatin are in the range of a few minutes, while lifetimes for cohesin are much longer. Can the observed features of genome folding result from the action of relatively transient barriers? To address this question, we developed a dynamic barrier model, where CTCF sites switch between bound and unbound states with rates that can be directly compared with biophysical measurements. Using this model, we investigated how barrier dynamics would impact observables for a range of experimental genomic and imaging datasets, including ChIP-seq, Hi-C, and microscopy. We found the interplay of CTCF and cohesin binding timescales influence the strength of each of these features, leaving a signature of barrier dynamics even in the population-averaged snapshots offered by genomic datasets. First, in addition to barrier occupancy, barrier bound times are crucial for instructing features of genome folding. Second, the ratio of boundary to extruder lifetime greatly alters simulated ChIP-seq and simulated Hi-C. Third, large-scale changes in chromosome morphology observed experimentally after increasing extruder lifetime require dynamic barriers. By integrating multiple sources of experimental data, our biophysical model argues that CTCF barrier bound times effectively approach those of cohesin extruder lifetimes. Together, we demonstrate how models that are informed by biophysically measured protein dynamics broaden our understanding of genome folding.},
}

@article {pmid39394698,
year = {2024},
author = {Ding, T and Fu, S and Zhang, X and Yang, F and Zhang, J and Xu, H and Yang, J and Chen, C and Shi, Y and Bai, Y and Li, W and Chang, X and Wang, S and Zhang, C and Liu, Q and Zhang, H},
title = {Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.},
journal = {Genomics, proteomics & bioinformatics},
volume = {22},
number = {3},
pages = {},
doi = {10.1093/gpbjnl/qzae034},
pmid = {39394698},
issn = {2210-3244},
mesh = {Humans ; *Transcription, Genetic/genetics ; Chromatin Assembly and Disassembly/genetics ; },
abstract = {Topologically associating domain (TAD) reorganization commonly occurs in the cell nucleus and contributes to gene activation and inhibition through the separation or fusion of adjacent TADs. However, functional genes impacted by TAD alteration and the underlying mechanism of TAD reorganization regulating gene transcription remain to be fully elucidated. Here, we first developed a novel approach termed Inter3D to specifically identify genes regulated by TAD reorganization. Our study revealed that the segregation of TADs led to the disruption of intrachromosomal looping at the myosin light chain 12B (MYL12B) locus, via the meticulous reorganization of TADs mediating epigenomic landscapes within tumor cells, thereby exhibiting a significant correlation with the down-regulation of its transcriptional activity. Conversely, the fusion of TADs facilitated intrachromosomal interactions, suggesting a potential association with the activation of cytochrome P450 family 27 subfamily B member 1 (CYP27B1). Our study provides comprehensive insight into the capture of TAD rearrangement-mediated gene loci and moves toward understanding the functional role of TAD reorganization in gene transcription. The Inter3D pipeline developed in this study is freely available at https://github.com/bm2-lab/inter3D and https://ngdc.cncb.ac.cn/biocode/tool/BT7399.},
}

Humans
*Transcription, Genetic/genetics
Chromatin Assembly and Disassembly/genetics

@article {pmid39392751,
year = {2024},
author = {Tsaytler, P and Blaess, G and Scholze-Wittler, M and Meierhofer, D and Wittler, L and Koch, F and Herrmann, BG},
title = {SRF promotes long-range chromatin loop formation and stem cell pluripotency.},
journal = {Cell reports},
volume = {43},
number = {10},
pages = {114846},
doi = {10.1016/j.celrep.2024.114846},
pmid = {39392751},
issn = {2211-1247},
abstract = {Serum response factor (SRF) is a transcription factor essential for cell proliferation, differentiation, and migration and is required for primitive streak and mesoderm formation in the embryo. The canonical roles of SRF are mediated by a diverse set of context-dependent cofactors. Here, we show that SRF physically interacts with CTCF and cohesin subunits at topologically associating domain (TAD) boundaries and loop anchors. SRF promotes long-range chromatin loop formation and contributes to TAD insulation. In embryonic stem cells (ESCs), SRF associates with SOX2 and NANOG and contributes to the formation of three-dimensional (3D) pluripotency hubs. Our findings reveal additional roles of SRF in higher-order chromatin organization.},
}