@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.},
}

@article {pmid39383545,
year = {2024},
author = {Bondarieva, A and Tachibana, K},
title = {Genome folding and zygotic genome activation in mammalian preimplantation embryos.},
journal = {Current opinion in genetics & development},
volume = {89},
number = {},
pages = {102268},
doi = {10.1016/j.gde.2024.102268},
pmid = {39383545},
issn = {1879-0380},
abstract = {The totipotent one-cell embryo, or zygote, gives rise to all germ layers and extraembryonic tissues that culminate in the development of a new organism. A zygote is produced at fertilisation by the fusion of differentiated germ cells, egg and sperm. The chromatin of parental genomes is reprogrammed and spatially reorganised in the early embryo. The 3D chromatin organisation is established de novo after fertilisation by a cohesin-dependent mechanism of loop extrusion that forms chromatin loops and topologically associating domains (TADs). Strengthening of TAD insulation is concomitant with the transcriptional 'awakening' of the embryo known as zygotic genome activation (ZGA). Whether and how these processes are causally linked remains poorly understood. In this review, we discuss recent findings of 3D chromatin organisation in mammalian gametes and embryos and how these are potentially related to ZGA.},
}

@article {pmid39322849,
year = {2024},
author = {Lee, Y and Park, SH and Lee, H},
title = {Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {39322849},
issn = {1744-4292},
support = {2019-0-00567//Institute of Information & communications technology planning & evaluation/ ; 2019-0-01842//Institute of Information & communications technology planning & evaluation/ ; },
abstract = {The 3D genome prediction in cancer is crucial for uncovering the impact of structural variations (SVs) on tumorigenesis, especially when they are present in noncoding regions. We present InfoHiC, a systemic framework for predicting the 3D cancer genome directly from whole-genome sequencing (WGS). InfoHiC utilizes contig-specific copy number encoding on the SV contig assembly, and performs a contig-to-total Hi-C conversion for the cancer Hi-C prediction from multiple SV contigs. We showed that InfoHiC can predict 3D genome folding from all types of SVs using breast cancer cell line data. We applied it to WGS data of patients with breast cancer and pediatric patients with medulloblastoma, and identified neo topologically associating domains. For breast cancer, we discovered super-enhancer hijacking events associated with oncogenic overexpression and poor survival outcomes. For medulloblastoma, we found SVs in noncoding regions that caused super-enhancer hijacking events of medulloblastoma driver genes (GFI1, GFI1B, and PRDM6). In addition, we provide trained models for cancer Hi-C prediction from WGS at https://github.com/dmcb-gist/InfoHiC , uncovering the impacts of SVs in cancer patients and revealing novel therapeutic targets.},
}

@article {pmid39322282,
year = {2024},
author = {Hristov, BH and Noble, WS and Bertero, A},
title = {Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278327.123},
pmid = {39322282},
issn = {1549-5469},
abstract = {Most studies of genome organization have focused on intrachromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Interchromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework that uses Hi-C data to identify sets of loci that jointly interact in trans This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes coregulated by the same trans-acting element (i.e., a transcription or splicing factor) colocalize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same DNA binding proteins interact with one another in trans, especially those bound by factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA-binding proteins correlates with trans interaction of the encoding loci. Intriguingly, we observe that these trans-interacting loci are close to nuclear speckles. Our findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.},
}

@article {pmid39293448,
year = {2024},
author = {Erjavec, E and Angée, C and Hadjadj, D and Passet, B and David, P and Kostic, C and Dodé, E and Zanlonghi, X and Cagnard, N and Nedelec, B and Crippa, SV and Bole-Feysot, C and Zarhrate, M and Creuzet, S and Castille, J and Vilotte, JL and Calvas, P and Plaisancié, J and Chassaing, N and Kaplan, J and Rozet, JM and Taie, LF},
title = {Congenital microcoria deletion in mouse links Sox21 dysregulation to disease and suggests a role for TGFB2 in glaucoma and myopia.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2024.08.019},
pmid = {39293448},
issn = {1537-6605},
abstract = {Congenital microcoria (MCOR) is a rare hereditary developmental defect of the iris dilator muscle frequently associated with high axial myopia and high intraocular pressure (IOP) glaucoma. The condition is caused by submicroscopic rearrangements of chromosome 13q32.1. However, the mechanisms underlying the failure of iris development and the origin of associated features remain elusive. Here, we present a 3D architecture model of the 13q32.1 region, demonstrating that MCOR-related deletions consistently disrupt the boundary between two topologically associating domains (TADs). Deleting the critical MCOR-causing region in mice reveals ectopic Sox21 expression precisely aligning with Dct, each located in one of the two neighbor TADs. This observation is consistent with the TADs' boundary alteration and adoption of Dct regulatory elements by the Sox21 promoter. Additionally, we identify Tgfb2 as a target gene of SOX21 and show TGFΒ2 accumulation in the aqueous humor of an MCOR-affected subject. Accumulation of TGFB2 is recognized for its role in glaucoma and potential impact on axial myopia. Our results highlight the importance of SOX21-TGFB2 signaling in iris development and control of eye growth and IOP. Insights from MCOR studies may provide therapeutic avenues for this condition but also for glaucoma and high myopia conditions, affecting millions of people.},
}

@article {pmid39283464,
year = {2025},
author = {Wall, BPG and Nguyen, M and Harrell, JC and Dozmorov, MG},
title = {Machine and Deep Learning Methods for Predicting 3D Genome Organization.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2856},
number = {},
pages = {357-400},
pmid = {39283464},
issn = {1940-6029},
mesh = {*Chromatin/genetics/metabolism ; *Deep Learning ; Humans ; Computational Biology/methods ; Machine Learning ; Genomics/methods ; Enhancer Elements, Genetic ; Promoter Regions, Genetic ; Binding Sites ; Genome ; Software ; },
abstract = {Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers and transcription factor binding site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, and TAD boundaries) and analyze their pros and cons. We also point out obstacles to the computational prediction of 3D interactions and suggest future research directions.},
}

*Chromatin/genetics/metabolism
*Deep Learning
Humans
Computational Biology/methods
Machine Learning
Genomics/methods
Enhancer Elements, Genetic
Promoter Regions, Genetic
Binding Sites
Genome
Software

@article {pmid39283452,
year = {2025},
author = {Nakato, R},
title = {Exploring Contact Distance Distributions with Google Colaboratory.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2856},
number = {},
pages = {179-196},
pmid = {39283452},
issn = {1940-6029},
mesh = {*Software ; *High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Web Browser ; Workflow ; Humans ; Chromatin/genetics ; Genomics/methods ; },
abstract = {Hi-C and Micro-C are the three-dimensional (3D) genome assays that use high-throughput sequencing. In the analysis, the sequenced paired-end reads are mapped to a reference genome to generate a two-dimensional contact matrix for identifying topologically associating domains (TADs), chromatin loops, and chromosomal compartments. On the other hand, the distance distribution of the paired-end mapped reads also provides insight into the 3D genome structure by highlighting global contact frequency patterns at distances indicative of loops, TADs, and compartments. This chapter presents a basic workflow for visualizing and analyzing contact distance distributions from Hi-C data. The workflow can be run on Google Colaboratory, which provides a ready-to-use Python environment accessible through a web browser. The notebook that demonstrates the workflow is available in the GitHub repository at https://github.com/rnakato/Springer_contact_distance_plot.},
}

*Software
*High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
Web Browser
Workflow
Humans
Chromatin/genetics
Genomics/methods

@article {pmid39283443,
year = {2025},
author = {Okabe, A},
title = {Methods for Genome-Wide Chromatin Interaction Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2856},
number = {},
pages = {3-9},
pmid = {39283443},
issn = {1940-6029},
mesh = {*Chromatin/genetics/metabolism/chemistry ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Genome-Wide Association Study/methods ; Animals ; },
abstract = {Recent analyses revealed the essential function of chromatin structure in maintaining and regulating genomic information. Advancements in microscopy, nuclear structure observation techniques, and the development of methods utilizing next-generation sequencers (NGSs) have significantly progressed these discoveries. Methods utilizing NGS enable genome-wide analysis, which is challenging with microscopy, and have elucidated concepts of important chromatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.},
}

*Chromatin/genetics/metabolism/chemistry
Humans
*High-Throughput Nucleotide Sequencing/methods
Genomics/methods
Genome-Wide Association Study/methods
Animals

@article {pmid39273012,
year = {2024},
author = {Viushkov, VS and Lomov, NA and Rubtsov, MA},
title = {A Comparison of Two Versions of the CRISPR-Sirius System for the Live-Cell Visualization of the Borders of Topologically Associating Domains.},
journal = {Cells},
volume = {13},
number = {17},
pages = {},
doi = {10.3390/cells13171440},
pmid = {39273012},
issn = {2073-4409},
support = {22-24-00251//Russian Science Foundation/ ; },
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; Chromatin/metabolism/genetics ; HEK293 Cells ; RNA, Guide, CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; },
abstract = {In recent years, various technologies have emerged for the imaging of chromatin loci in living cells via catalytically inactive Cas9 (dCas9). These technologies facilitate a deeper understanding of the mechanisms behind the chromatin dynamics and provide valuable kinetic data that could not have previously been obtained via FISH applied to fixed cells. However, such technologies are relatively complicated, as they involve the expression of several chimeric proteins as well as sgRNAs targeting the visualized loci, a process that entails many technical subtleties. Therefore, the effectiveness in visualizing a specific target locus may be quite low. In this study, we directly compared two versions of a previously published CRISPR-Sirius method based on the use of sgRNAs containing eight MS2 or PP7 stem loops and the expression of MCP or PCP fused to fluorescent proteins. We assessed the visualization efficiency for several unique genomic loci by comparing the two approaches in delivering sgRNA genes (transient transfection and lentiviral transduction), as well as two CRISPR-Sirius versions (with PCP and with MCP). The efficiency of visualization varied among the loci, and not all loci could be visualized. However, the MCP-sfGFP version provided more efficient visualization in terms of the number of cells with signals than PCP-sfGFP for all tested loci. We also showed that lentiviral transduction was more efficient in locus imaging than transient transfection for both CRISPR-Sirius systems. Most of the target loci in our study were located at the borders of topologically associating domains, and we defined a set of TAD borders that could be effectively visualized using the MCP-sfGFP version of the CRISPR-Sirius system. Altogether, our study validates the use of the CRISPR-Sirius technology for live-cell visualization and highlights various technical details that should be considered when using this method.},
}

Humans
*CRISPR-Cas Systems/genetics
Chromatin/metabolism/genetics
HEK293 Cells
RNA, Guide, CRISPR-Cas Systems/genetics
Clustered Regularly Interspaced Short Palindromic Repeats/genetics

@article {pmid39272130,
year = {2024},
author = {Daly, AF and Dunnington, LA and Rodriguez-Buritica, DF and Spiegel, E and Brancati, F and Mantovani, G and Rawal, VM and Faucz, FR and Hijazi, H and Caberg, JH and Nardone, AM and Bengala, M and Fortugno, P and Del Sindaco, G and Ragonese, M and Gould, H and Cannavò, S and Pétrossians, P and Lania, A and Lupski, JR and Beckers, A and Stratakis, CA and Levy, B and Trivellin, G and Franke, M},
title = {Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {112},
pmid = {39272130},
issn = {1756-994X},
support = {GGP20130//Fondazione Telethon/ ; 2018/20//Centre Hospitalier Universitaire de Liège/ ; Z1A HD008920//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R35NS105078//National Institute of Health (NINDS)/ ; Ricerca Corrente"//Ministero della Salute/ ; T3-AN-14 "LifeMap"//Ministero della Salute/ ; PRIN PNRR 2022//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; PRIN 2022//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; 100010434//'la Caixa' Foundation/ ; fellowship code LCF/BQ/PR22/11920006//'la Caixa' Foundation/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/genetics ; *Chromatin/genetics/metabolism ; Female ; Male ; Gene Duplication ; Chromosome Duplication ; Chromosomes, Human, X/genetics ; Pedigree ; },
abstract = {BACKGROUND: X-linked acrogigantism (X-LAG; MIM: 300942) is a severe form of pituitary gigantism caused by chromosome Xq26.3 duplications involving GPR101. X-LAG-associated duplications disrupt the integrity of the topologically associating domain (TAD) containing GPR101 and lead to the formation of a neo-TAD that drives pituitary GPR101 misexpression and gigantism. As X-LAG is fully penetrant and heritable, duplications involving GPR101 identified on prenatal screening studies, like amniocentesis, can pose an interpretation challenge for medical geneticists and raise important concerns for patients and families. Therefore, providing robust information on the functional genomic impact of such duplications has important research and clinical value with respect to gene regulation and triplosensitivity traits.

METHODS: We employed 4C/HiC-seq as a clinical tool to determine the functional impact of incidentally discovered GPR101 duplications on TAD integrity in three families. After defining duplications and breakpoints around GPR101 by clinical-grade and high-density aCGH, we constructed 4C/HiC chromatin contact maps for our study population and compared them with normal and active (X-LAG) controls.

RESULTS: We showed that duplications involving GPR101 that preserved the centromeric invariant TAD boundary did not generate a pathogenic neo-TAD and that ectopic enhancers were not adopted. This allowed us to discount presumptive/suspected X-LAG diagnoses and GPR101 misexpression, obviating the need for intensive clinical follow-up.

CONCLUSIONS: This study highlights the importance of TAD boundaries and chromatin interactions in determining the functional impact of copy number variants and provides proof-of-concept for using 4C/HiC-seq as a clinical tool to acquire crucial information for genetic counseling and to support clinical decision-making in cases of suspected TADopathies.},
}

Humans
*Receptors, G-Protein-Coupled/genetics
*Chromatin/genetics/metabolism
Female
Male
Gene Duplication
Chromosome Duplication
Chromosomes, Human, X/genetics
Pedigree

@article {pmid39257002,
year = {2024},
author = {Maroofian, R and Pagnamenta, AT and Navabazam, A and Schwessinger, R and Roberts, HE and Lopopolo, M and Dehghani, M and Vahidi Mehrjardi, MY and Haerian, A and Soltanianzadeh, M and Noori Kooshki, MH and Knight, SJ and Miller, KA and McGowan, SJ and Chatron, N and Timberlake, AT and Melo, US and Mundlos, S and Buck, D and Twigg, SR and Taylor, JC and Wilkie, AO and Calpena, E},
title = {Familial severe skeletal Class II malocclusion with gingival hyperplasia caused by a complex structural rearrangement at the KCNJ2-KCNJ16 locus.},
journal = {HGG advances},
volume = {},
number = {},
pages = {100352},
doi = {10.1016/j.xhgg.2024.100352},
pmid = {39257002},
issn = {2666-2477},
abstract = {The aim of this work was to identify the underlying genetic cause in a four-generation family segregating an unusual phenotype comprising a severe form of skeletal Class II malocclusion with gingival hyperplasia. SNP-array identified a copy number gain on chr1, however this chromosomal region did not segregate correctly in the extended family. Exome sequencing also failed to identify a candidate causative variant, but highlighted co-segregating genetic markers on chr17 and chr19. Short- and long-read genome sequencing allowed us to pinpoint and characterize at nucleotide-level resolution a chromothripsis-like complex rearrangement (CR) inserted into the chr17 co-segregating region at the KCNJ2-SOX9 locus. The CR involved the gain of five different regions from chr1 that are shuffled, chained and inserted as a single block (∼828 kb) at chr17q24.3. The inserted sequences contain craniofacial enhancers that are predicted to interact with KCNJ2/KCNJ16 through neo-topologically associating domain (TAD) formation to induce ectopic activation. Our findings suggest that the CR inserted at chr17q24.3 is the cause of the severe skeletal Class II malocclusion with gingival hyperplasia in this family and expands the panoply of phenotypes linked to variation at the KCNJ2-SOX9 locus. In addition, we highlight a previously overlooked potential role for misregulation of the KCNJ2/KCNJ16 genes in the pathomechanism of gingival hyperplasia associated with deletions and other rearrangements of the 17q24.2-q24.3 region (MIM 135400).},
}

@article {pmid39222712,
year = {2024},
author = {Liu, H and Ma, W},
title = {DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.},
journal = {Genomics, proteomics & bioinformatics},
volume = {22},
number = {2},
pages = {},
doi = {10.1093/gpbjnl/qzae028},
pmid = {39222712},
issn = {2210-3244},
mesh = {Humans ; Mice ; Animals ; *Chromatin/genetics/metabolism ; *Software ; Genomics/methods ; Chromosome Mapping/methods ; },
abstract = {Recent advances in high-throughput chromosome conformation capture (Hi-C) techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures, thereby shedding light on the principles of genome architecture and functions. However, statistical methods for detecting changes in large-scale chromatin organization such as topologically associating domains (TADs) are still lacking. Here, we proposed a new statistical method, DiffGR, for detecting differentially interacting genomic regions at the TAD level between Hi-C contact maps. We utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD regions. We then developed a nonparametric approach to identify statistically significant changes of genomic interacting regions. Through simulation studies, we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various conditions. Furthermore, we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets, and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection methods. The DiffGR R package is published under the GNU General Public License (GPL) ≥ 2 license and is publicly available at https://github.com/wmalab/DiffGR.},
}

Humans
Mice
Animals
*Chromatin/genetics/metabolism
*Software
Genomics/methods
Chromosome Mapping/methods

@article {pmid39198689,
year = {2024},
author = {Lu, B and Qiu, R and Wei, J and Wang, L and Zhang, Q and Li, M and Zhan, X and Chen, J and Hsieh, IY and Yang, C and Zhang, J and Sun, Z and Zhu, Y and Jiang, T and Zhu, H and Li, J and Zhao, W},
title = {Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {39198689},
issn = {2662-1347},
support = {81972651//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172698//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82372857//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {How dysregulated liquid-liquid phase separation (LLPS) contributes to the oncogenesis of female triple-negative breast cancer (TNBC) remains unknown. Here we demonstrate that phosphorylated histone deacetylase 6 (phospho-HDAC6) forms LLPS condensates in the nuclei of TNBC cells that are essential for establishing aberrant chromatin architecture. The disordered N-terminal domain and phosphorylated residue of HDAC6 facilitate effective LLPS, whereas nuclear export regions exert a negative dominant effect. Through phase-separation-based screening, we identified Nexturastat A as a specific disruptor of phospho-HDAC6 condensates, which effectively suppresses tumor growth. Mechanistically, importin-β interacts with phospho-HDAC6, promoting its translocation to the nucleus, where 14-3-3θ mediates the condensate formation. Disruption of phospho-HDAC6 LLPS re-established chromatin compartments and topologically associating domain boundaries, leading to disturbed chromatin loops. The phospho-HDAC6-induced aberrant chromatin architecture affects chromatin accessibility, histone acetylation, RNA polymerase II elongation and transcriptional profiles in TNBC. This study demonstrates phospho-HDAC6 LLPS as an emerging mechanism underlying the dysregulation of chromatin architecture in TNBC.},
}

@article {pmid39190242,
year = {2024},
author = {Carballo-Pacoret, P and Carracedo, A and Rodriguez-Fontenla, C},
title = {Unraveling the three-dimensional (3D) genome architecture in Neurodevelopmental Disorders (NDDs).},
journal = {Neurogenetics},
volume = {},
number = {},
pages = {},
pmid = {39190242},
issn = {1364-6753},
support = {PI22/00208//Instituto de Salud Carlos III/ ; PI22/00208//Instituto de Salud Carlos III/ ; PI22/00208//Instituto de Salud Carlos III/ ; },
abstract = {The human genome, comprising millions of pairs of bases, serves as the blueprint of life, encoding instructions for cellular processes. However, genomes are not merely linear sequences; rather, the complex of DNA and histones, known as chromatin, exhibits complex organization across various levels, which profoundly influence gene expression and cellular function. Central to understanding genome organization is the emerging field of three-dimensional (3D) genome studies. Utilizing advanced techniques such as Hi-C, researchers have unveiled non-random dispositions of genomic elements, highlighting their importance in transcriptional regulation and disease mechanisms. Topologically Associating Domains (TADs), that demarcate regions of chromatin with preferential internal interactions, play crucial roles in gene regulation and are increasingly implicated in various diseases such as cancer and schizophrenia. However, their role in Neurodevelopmental Disorders (NDDs) remains poorly understood. Here, we focus on TADs and 3D conservation across the evolution and between cell types in NDDs. The investigation into genome organization and its impact on disease has led to significant breakthroughs in understanding NDDs etiology such ASD (Autism Spectrum Disorder). By elucidating the wide spectrum of ASD manifestations, researchers aim to uncover the underlying genetic and epigenetic factors contributing to its heterogeneity. Moreover, studies linking TAD disruption to NDDs underscore the importance of spatial genome organization in maintaining proper brain development and function. In summary, this review highlights the intricate interplay between genome organization, transcriptional control, and disease pathology, shedding light on fundamental biological processes and offering insights into the mechanisms underlying NDDs like ASD.},
}

@article {pmid39179577,
year = {2024},
author = {Ealo, T and Sanchez-Gaya, V and Respuela, P and Muñoz-San Martín, M and Martin-Batista, E and Haro, E and Rada-Iglesias, A},
title = {Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7258},
pmid = {39179577},
issn = {2041-1723},
support = {862022//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; H2020-MSCA-ITN-2019-860002//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; MSCA-2021-DN-01-101073334//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; PID2021-123030NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RED2022-134100-T//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
mesh = {Animals ; *CCCTC-Binding Factor/metabolism/genetics ; Mice ; *Promoter Regions, Genetic/genetics ; *Enhancer Elements, Genetic/genetics ; *Mouse Embryonic Stem Cells/metabolism ; Gene Expression Regulation, Developmental ; Insulator Elements/genetics ; },
abstract = {The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across regulatory domains, which is at odds with the specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites cooperatively foster the robust insulation of regulatory domains. By genetically dissecting a couple of representative loci in mouse embryonic stem cells, we show that CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), while developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the insulation of regulatory domains, which in turn might help interpreting the pathological consequences of certain structural variants.},
}

Animals
*CCCTC-Binding Factor/metabolism/genetics
Mice
*Promoter Regions, Genetic/genetics
*Enhancer Elements, Genetic/genetics
*Mouse Embryonic Stem Cells/metabolism
Gene Expression Regulation, Developmental
Insulator Elements/genetics

@article {pmid39169755,
year = {2024},
author = {Huang, H and Wu, Q},
title = {Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2400121},
doi = {10.1002/bies.202400121},
pmid = {39169755},
issn = {1521-1878},
support = {32330016//National Natural Science Foundation of China/ ; 2022YFC3400200//National Key R&D Program of China/ ; },
abstract = {Topologically associating domain (TAD) boundaries are the flanking edges of TADs, also known as insulated neighborhoods, within the 3D structure of genomes. A prominent feature of TAD boundaries in mammalian genomes is the enrichment of clustered CTCF sites often with mixed orientations, which can either block or facilitate enhancer-promoter (E-P) interactions within or across distinct TADs, respectively. We will discuss recent progress in the understanding of fundamental organizing principles of the clustered CTCF insulator codes at TAD boundaries. Specifically, both inward- and outward-oriented CTCF sites function as topological chromatin insulators by asymmetrically blocking improper TAD-boundary-crossing cohesin loop extrusion. In addition, boundary stacking and enhancer clustering facilitate long-distance E-P interactions across multiple TADs. Finally, we provide a unified mechanism for RNA-mediated TAD boundary function via R-loop formation for both insulation and facilitation. This mechanism of TAD boundary formation and insulation has interesting implications not only on how the 3D genome folds in the Euclidean nuclear space but also on how the specificity of E-P interactions is developmentally regulated.},
}

@article {pmid39152239,
year = {2024},
author = {Denaud, S and Bardou, M and Papadopoulos, GL and Grob, S and Di Stefano, M and Sabarís, G and Nollmann, M and Schuettengruber, B and Cavalli, G},
title = {A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
pmid = {39152239},
issn = {1545-9985},
abstract = {Three-dimensional (3D) genome folding has a fundamental role in the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CRE involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TAD) called a Polycomb domain. PREs can establish looping contacts that stabilize the gene repression of key developmental genes during development. However, the mechanism by which PRE loops fine-tune gene expression is unknown. Using clustered regularly interspaced short palindromic repeats and Cas9 genome engineering, we specifically perturbed PRE contacts or enhancer function and used complementary approaches including 4C-seq, Hi-C and Hi-M to analyze how chromatin architecture perturbation affects gene expression. Our results suggest that the PRE loop at the dac gene locus acts as a constitutive 3D chromatin scaffold during Drosophila development that forms independently of gene expression states and has a versatile function; it restricts enhancer-promoter communication and contributes to enhancer specificity.},
}

@article {pmid39152238,
year = {2024},
author = {Yao, Q and Zhu, L and Shi, Z and Banerjee, S and Chen, C},
title = {Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
pmid = {39152238},
issn = {1545-9985},
abstract = {DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.},
}

@article {pmid39149372,
year = {2024},
author = {Kearly, A and Saelee, P and Bard, J and Sinha, S and Satterthwaite, A and Garrett-Sinha, LA},
title = {Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.02.606433},
pmid = {39149372},
issn = {2692-8205},
abstract = {The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1 .},
}

@article {pmid39094522,
year = {2024},
author = {Na, J and Tai, C and Wang, Z and Yang, Z and Chen, X and Zhang, J and Zheng, L and Fan, Y},
title = {Stiff extracellular matrix drives the differentiation of mesenchymal stem cells toward osteogenesis by the multiscale 3D genome reorganization.},
journal = {Biomaterials},
volume = {312},
number = {},
pages = {122715},
doi = {10.1016/j.biomaterials.2024.122715},
pmid = {39094522},
issn = {1878-5905},
abstract = {Extracellular matrix (ECM) stiffness is a major driver of stem cell fate. However, the involvement of the three-dimensional (3D) genomic reorganization in response to ECM stiffness remains unclear. Here, we generated comprehensive 3D chromatin landscapes of mesenchymal stem cells (MSCs) exposed to various ECM stiffness. We found that there were more long-range chromatin interactions, but less compartment A in MSCs cultured on stiff ECM than those cultured on soft ECM. However, the switch from compartment B in MSCs cultured on soft ECM to compartment A in MSCs cultured on stiff ECM included genes encoding proteins primarily enriched in cytoskeleton organization. At the topologically associating domains (TADs) level, stiff ECM tends to have merged TADs on soft ECM. These merged TADs on stiff ECM include upregulated genes encoding proteins enriched in osteogenesis, such as SP1, ETS1, and DCHS1, which were validated by quantitative real-time polymerase chain reaction and found to be consistent with the increase of alkaline phosphatase staining. Knockdown of SP1 or ETS1 led to the downregulation of osteogenic marker genes, including COL1A1, RUNX2, ALP, and OCN in MSCs cultured on stiff ECM. Our study provides an important insight into the stiff ECM-mediated promotion of MSC differentiation towards osteogenesis, emphasizing the influence of mechanical cues on the reorganization of 3D genome architecture and stem cell fate.},
}

@article {pmid39093600,
year = {2024},
author = {Chang, LH and Noordermeer, D},
title = {Permeable TAD boundaries and their impact on genome-associated functions.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2400137},
doi = {10.1002/bies.202400137},
pmid = {39093600},
issn = {1521-1878},
support = {ANR-21-CE12-0034//Agence Nationale de la Recherche/ ; ANR-21-CE12-0034//Agence Nationale de la Recherche/ ; ANR-22-CE12-0016//Agence Nationale de la Recherche/ ; ANR-22-CE14-0021//Agence Nationale de la Recherche/ ; //Blood and Transplant Research Unit in Precision Cellular Therapeutics/ ; },
abstract = {TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.},
}

@article {pmid39083950,
year = {2024},
author = {Oji, A and Choubani, L and Miura, H and Hiratani, I},
title = {Structure and dynamics of nuclear A/B compartments and subcompartments.},
journal = {Current opinion in cell biology},
volume = {90},
number = {},
pages = {102406},
doi = {10.1016/j.ceb.2024.102406},
pmid = {39083950},
issn = {1879-0410},
abstract = {Mammalian chromosomes form a hierarchical structure within the cell nucleus, from chromatin loops, megabase (Mb)-sized topologically associating domains (TADs) to larger-scale A/B compartments. The molecular basis of the structures of loops and TADs has been actively studied. However, the A and B compartments, which correspond to early-replicating euchromatin and late-replicating heterochromatin, respectively, are still relatively unexplored. In this review, we focus on the A/B compartments, discuss their close relationship to DNA replication timing (RT), and introduce recent findings on the features of subcompartments revealed by detailed classification of the A/B compartments. In doing so, we speculate on the structure, potential function, and developmental dynamics of A/B compartments and subcompartments in mammalian cells.},
}

@article {pmid39078102,
year = {2024},
author = {Dimartino, P and Zadorozhna, M and Yumiceba, V and Basile, A and Cani, I and Melo, US and Henck, J and Breur, M and Tonon, C and Lodi, R and Brusco, A and Pippucci, T and Koufi, FD and Boschetti, E and Ramazzotti, G and Manzoli, L and Ratti, S and Pinto E Vairo, F and Delatycki, MB and Vaula, G and Cortelli, P and Bugiani, M and Spielmann, M and Giorgio, E},
title = {Structural Variants at the LMNB1 Locus: Deciphering Pathomechanisms in Autosomal Dominant Adult-Onset Demyelinating Leukodystrophy.},
journal = {Annals of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ana.27038},
pmid = {39078102},
issn = {1531-8249},
support = {GR-2021-12373348//Ministero della Salute, Ricerca Finalizzata/ ; MNESYS (PE0000006)//Ministero dell'Università e della Ricerca, National Recovery and Resilience Plan (NRRP)/ ; },
abstract = {OBJECTIVES: We aimed to elucidate the pathogenic mechanisms underlying autosomal dominant adult-onset demyelinating leukodystrophy (ADLD), and to understand the genotype/phenotype correlation of structural variants (SVs) in the LMNB1 locus.

BACKGROUND: Since the discovery of 3D genome architectures and topologically associating domains (TADs), new pathomechanisms have been postulated for SVs, regardless of gene dosage changes. ADLD is a rare genetic disease associated with duplications (classical ADLD) or noncoding deletions (atypical ADLD) in the LMNB1 locus.

METHODS: High-throughput chromosome conformation capture, RNA sequencing, histopathological analyses of postmortem brain tissues, and clinical and neuroradiological investigations were performed.

RESULTS: We collected data from >20 families worldwide carrying SVs in the LMNB1 locus and reported strong clinical variability, even among patients carrying duplications of the entire LMNB1 gene, ranging from classical and atypical ADLD to asymptomatic carriers. We showed that patients with classic ADLD always carried intra-TAD duplications, resulting in a simple gene dose gain. Atypical ADLD was caused by LMNB1 forebrain-specific misexpression due to inter-TAD deletions or duplications. The inter-TAD duplication, which extends centromerically and crosses the 2 TAD boundaries, did not cause ADLD. Our results provide evidence that astrocytes are key players in ADLD pathology.

INTERPRETATION: Our study sheds light on the 3D genome and TAD structural changes associated with SVs in the LMNB1 locus, and shows that a duplication encompassing LMNB1 is not sufficient per se to diagnose ADLD, thereby strongly affecting genetic counseling. Our study supports breaking TADs as an emerging pathogenic mechanism that should be considered when studying brain diseases. ANN NEUROL 2024.},
}

@article {pmid39061232,
year = {2024},
author = {Zhou, T and Nguyen, S and Wu, J and He, B and Feng, Q},
title = {LncRNA LOC730101 Promotes Darolutamide Resistance in Prostate Cancer by Suppressing miR-1-3p.},
journal = {Cancers},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/cancers16142594},
pmid = {39061232},
issn = {2072-6694},
support = {1R33AI133697-03A1/NH/NIH HHS/United States ; 1R01CA211861-05A1/NH/NIH HHS/United States ; },
abstract = {Antiandrogen is part of the standard-of-care treatment option for metastatic prostate cancer. However, prostate cancers frequently relapse, and the underlying resistance mechanism remains incompletely understood. This study seeks to investigate whether long non-coding RNAs (lncRNAs) contribute to the resistance against the latest antiandrogen drug, darolutamide. Our RNA sequencing analysis revealed significant overexpression of LOC730101 in darolutamide-resistant cancer cells compared to the parental cells. Elevated LOC730101 levels were also observed in clinical samples of metastatic castration-resistant prostate cancer (CRPC) compared to primary prostate cancer samples. Silencing LOC730101 with siRNA significantly impaired the growth of darolutamide-resistant cells. Additional RNA sequencing analysis identified a set of genes regulated by LOC730101, including key players in the cell cycle regulatory pathway. We further demonstrated that LOC730101 promotes darolutamide resistance by competitively inhibiting microRNA miR-1-3p. Moreover, by Hi-C sequencing, we found that LOC730101 is located in a topologically associating domain (TAD) that undergoes specific gene induction in darolutamide-resistant cells. Collectively, our study demonstrates the crucial role of the lncRNA LOC730101 in darolutamide resistance and its potential as a target for overcoming antiandrogen resistance in CRPC.},
}

@article {pmid39047029,
year = {2024},
author = {Ling, Z and Zhang, YW and Li, SC},
title = {SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0490},
pmid = {39047029},
issn = {1557-8666},
abstract = {High-throughput chromosome conformation capture (Hi-C) technology captures spatial interactions of DNA sequences into matrices, and software tools are developed to identify topologically associating domains (TADs) from the Hi-C matrices. With structural information theory, SuperTAD adopted a dynamic programming approach to find the TAD hierarchy with minimal structural entropy. However, the algorithm suffers from high time complexity. To accelerate this algorithm, we design and implement an approximation algorithm with a theoretical performance guarantee. We implemented a package, SuperTAD-Fast. Using Hi-C matrices and simulated data, we demonstrated that SuperTAD-Fast achieved great runtime improvement compared with SuperTAD. SuperTAD-Fast shows high consistency and significant enrichment of structural proteins from Hi-C data of human cell lines in comparison with the existing six hierarchical TADs detecting methods.},
}

@article {pmid39039278,
year = {2024},
author = {Das, M and Semple, JI and Haemmerli, A and Volodkina, V and Scotton, J and Gitchev, T and Annan, A and Campos, J and Statzer, C and Dakhovnik, A and Ewald, CY and Mozziconacci, J and Meister, P},
title = {Condensin I folds the Caenorhabditis elegans genome.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {39039278},
issn = {1546-1718},
support = {31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_176226/PP00P3_159320//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {The structural maintenance of chromosome (SMC) complexes-cohesin and condensins-are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans, a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin I[DC], leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/I[DC] inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin I[DC]. C. elegans condensin I/I[DC] thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression.},
}

@article {pmid39008525,
year = {2024},
author = {Maisuradze, L and King, MC and Surovtsev, IV and Mochrie, SGJ and Shattuck, MD and O'Hern, CS},
title = {Identifying topologically associating domains using differential kernels.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012221},
doi = {10.1371/journal.pcbi.1012221},
pmid = {39008525},
issn = {1553-7358},
mesh = {*Algorithms ; *Chromatin/chemistry/genetics/metabolism ; *Computational Biology/methods ; Humans ; Image Processing, Computer-Assisted/methods ; Animals ; },
abstract = {Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix [Formula: see text], where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in [Formula: see text] within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states.},
}

*Algorithms
*Chromatin/chemistry/genetics/metabolism
*Computational Biology/methods
Humans
Image Processing, Computer-Assisted/methods
Animals

@article {pmid38968127,
year = {2024},
author = {An, J and Brik Chaouche, R and Pereyra-Bistraín, LI and Zalzalé, H and Wang, Q and Huang, Y and He, X and Dias Lopes, C and Antunez-Sanchez, J and Bergounioux, C and Boulogne, C and Dupas, C and Gillet, C and Pérez-Pérez, JM and Mathieu, O and Bouché, N and Fragkostefanakis, S and Zhang, Y and Zheng, S and Crespi, M and Mahfouz, MM and Ariel, F and Gutierrez-Marcos, J and Raynaud, C and Latrasse, D and Benhamed, M},
title = {An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {28},
pages = {e2400737121},
doi = {10.1073/pnas.2400737121},
pmid = {38968127},
issn = {1091-6490},
support = {Project 101044399-3Dwheat//EC | European Research Council (ERC)/ ; ANR-21-CE20-0036-4D Heat Tomato//Agence Nationale de la Recherche (ANR)/ ; ANR-17-EUR-0007//Agence Nationale de la Recherche (ANR)/ ; 202108320109//China Scholarship Council (CSC)/ ; 202308620118//China Scholarship Council (CSC)/ ; },
mesh = {*Solanum lycopersicum/genetics/metabolism ; *Histones/metabolism/genetics ; *Epigenome ; Epigenesis, Genetic ; Genome, Plant ; Chromatin/metabolism/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Heterochromatin/metabolism/genetics ; Histone Code/genetics ; },
abstract = {In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.},
}

*Solanum lycopersicum/genetics/metabolism
*Histones/metabolism/genetics
*Epigenome
Epigenesis, Genetic
Genome, Plant
Chromatin/metabolism/genetics
Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Heterochromatin/metabolism/genetics
Histone Code/genetics

@article {pmid38967009,
year = {2024},
author = {Mulero-Hernández, J and Mironov, V and Miñarro-Giménez, JA and Kuiper, M and Fernández-Breis, JT},
title = {Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae566},
pmid = {38967009},
issn = {1362-4962},
support = {FPU18/03264//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop new strategies to enable advanced data querying. Many databases have been developed to provide information about enhancers, but a schema that allows the standardized representation of data, securing interoperability between resources, has been lacking. In this work, we use knowledge graphs for the standardized representation of enhancers and topologically associating domains, together with data about their target genes, transcription factors, location on the human genome, and functional data about diseases and gene ontology annotations. We used this schema to integrate twenty-five enhancer datasets and two domain datasets, creating the most powerful integrative resource in this field to date. The knowledge graphs have been implemented using the Resource Description Framework and integrated within the open-access BioGateway knowledge network, generating a resource that contains an interoperable set of knowledge graphs (enhancers, TADs, genes, proteins, diseases, GO terms, and interactions between domains). We show how advanced queries, which combine functional and location restrictions, can be used to develop new hypotheses about functional aspects of gene expression regulation.},
}

@article {pmid38940151,
year = {2024},
author = {Murtaza, G and Butaney, B and Wagner, J and Singh, R},
title = {scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_1},
pages = {i490-i500},
doi = {10.1093/bioinformatics/btae223},
pmid = {38940151},
issn = {1367-4811},
support = {1R35HG011939-01/GF/NIH HHS/United States ; },
mesh = {*Deep Learning ; *Single-Cell Analysis/methods ; *Chromatin/metabolism/chemistry ; Humans ; },
abstract = {SUMMARY: Single-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progression. Despite providing crucial insights, scHi-C data is often underutilized due to the high cost and the complexity of the experimental protocol. We present a deep learning framework, scGrapHiC, that predicts pseudo-bulk scHi-C contact maps using pseudo-bulk scRNA-seq data. Specifically, scGrapHiC performs graph deconvolution to extract genome-wide single-cell interactions from a bulk Hi-C contact map using scRNA-seq as a guiding signal. Our evaluations show that scGrapHiC, trained on seven cell-type co-assay datasets, outperforms typical sequence encoder approaches. For example, scGrapHiC achieves a substantial improvement of 23.2% in recovering cell-type-specific Topologically Associating Domains over the baselines. It also generalizes to unseen embryo and brain tissue samples. scGrapHiC is a novel method to generate cell-type-specific scHi-C contact maps using widely available genomic signals that enables the study of cell-type-specific chromatin interactions.

The GitHub link: https://github.com/rsinghlab/scGrapHiC contains the source code of scGrapHiC and associated scripts to preprocess publicly available datasets to produce the results and visualizations we have discuss in this manuscript.},
}

*Deep Learning
*Single-Cell Analysis/methods
*Chromatin/metabolism/chemistry
Humans

@article {pmid38935071,
year = {2024},
author = {Chen, B and Ren, C and Ouyang, Z and Xu, J and Xu, K and Li, Y and Guo, H and Bai, X and Tian, M and Xu, X and Wang, Y and Li, H and Bo, X and Chen, H},
title = {Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
doi = {10.1093/bib/bbae306},
pmid = {38935071},
issn = {1477-4054},
support = {62173338//National Natural Science Foundation of China/ ; 20220484198//Beijing Nova Program of Science and Technology/ ; },
mesh = {*DNA Repair ; Humans ; *DNA Breaks, Double-Stranded ; *Chromatin/metabolism/genetics ; *Gene Expression Regulation ; Transcription Factors/metabolism/genetics ; Animals ; Genomics/methods ; Genomic Instability ; Chromatin Assembly and Disassembly ; },
abstract = {Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.},
}

*DNA Repair
Humans
*DNA Breaks, Double-Stranded
*Chromatin/metabolism/genetics
*Gene Expression Regulation
Transcription Factors/metabolism/genetics
Animals
Genomics/methods
Genomic Instability
Chromatin Assembly and Disassembly

@article {pmid38927609,
year = {2024},
author = {Zhu, H and Liu, T and Wang, Z},
title = {C2c: Predicting Micro-C from Hi-C.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060673},
pmid = {38927609},
issn = {2073-4425},
support = {1R35GM137974/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chromatin/genetics ; Humans ; Computational Biology/methods ; Neural Networks, Computer ; Micrococcal Nuclease/metabolism/genetics ; Nucleosomes/genetics ; Software ; },
abstract = {MOTIVATION: High-resolution Hi-C data, capable of detecting chromatin features below the level of Topologically Associating Domains (TADs), significantly enhance our understanding of gene regulation. Micro-C, a variant of Hi-C incorporating a micrococcal nuclease (MNase) digestion step to examine interactions between nucleosome pairs, has been developed to overcome the resolution limitations of Hi-C. However, Micro-C experiments pose greater technical challenges compared to Hi-C, owing to the need for precise MNase digestion control and higher-resolution sequencing. Therefore, developing computational methods to derive Micro-C data from existing Hi-C datasets could lead to better usage of a large amount of existing Hi-C data in the scientific community and cost savings.

RESULTS: We developed C2c ("high" or upper case C to "micro" or lower case c), a computational tool based on a residual neural network to learn the mapping between Hi-C and Micro-C contact matrices and then predict Micro-C contact matrices based on Hi-C contact matrices. Our evaluation results show that the predicted Micro-C contact matrices reveal more chromatin loops than the input Hi-C contact matrices, and more of the loops detected from predicted Micro-C match the promoter-enhancer interactions. Furthermore, we found that the mutual loops from real and predicted Micro-C better match the ChIA-PET data compared to Hi-C and real Micro-C loops, and the predicted Micro-C leads to more TAD-boundaries detected compared to the Hi-C data. The website URL of C2c can be found in the Data Availability Statement.},
}

*Chromatin/genetics
Humans
Computational Biology/methods
Neural Networks, Computer
Micrococcal Nuclease/metabolism/genetics
Nucleosomes/genetics
Software

@article {pmid38895201,
year = {2024},
author = {Wong, EWP and Sahin, M and Yang, R and Lee, U and Zhan, YA and Misra, R and Tomas, F and Alomran, N and Polyzos, A and Lee, CJ and Trieu, T and Fundichely, AM and Wiesner, T and Rosowicz, A and Cheng, S and Liu, C and Lallo, M and Merghoub, T and Hamard, PJ and Koche, R and Khurana, E and Apostolou, E and Zheng, D and Chen, Y and Leslie, CS and Chi, P},
title = {TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.31.596845},
pmid = {38895201},
abstract = {Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.},
}

@article {pmid38871723,
year = {2024},
author = {Sun, W and Xiong, D and Ouyang, J and Xiao, X and Jiang, Y and Wang, Y and Li, S and Xie, Z and Wang, J and Tang, Z and Zhang, Q},
title = {Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5048},
pmid = {38871723},
issn = {2041-1723},
support = {82171056//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Translocation, Genetic ; *Chromatin/metabolism/genetics ; *Iris/metabolism ; Male ; Female ; *Pedigree ; Chromosomes, Human, Pair 6/genetics ; Chromosomes, Human, Pair 18/genetics ; Induced Pluripotent Stem Cells/metabolism ; Adult ; Iris Diseases/genetics/metabolism/pathology ; Genetic Linkage ; },
abstract = {Despite the advent of genomic sequencing, molecular diagnosis remains unsolved in approximately half of patients with Mendelian disorders, largely due to unclarified functions of noncoding regions and the difficulty in identifying complex structural variations. In this study, we map a unique form of central iris hypoplasia in a large family to 6q15-q23.3 and 18p11.31-q12.1 using a genome-wide linkage scan. Long-read sequencing reveals a balanced translocation t(6;18)(q22.31;p11.22) with intergenic breakpoints. By performing Hi-C on induced pluripotent stem cells from a patient, we identify two chromatin topologically associating domains spanning across the breakpoints. These alterations lead the ectopic chromatin interactions between APCDD1 on chromosome 18 and enhancers on chromosome 6, resulting in upregulation of APCDD1. Notably, APCDD1 is specifically localized in the iris of human eyes. Our findings demonstrate that noncoding structural variations can lead to Mendelian diseases by disrupting the 3D genome structure and resulting in altered gene expression.},
}

Humans
*Translocation, Genetic
*Chromatin/metabolism/genetics
*Iris/metabolism
Male
Female
*Pedigree
Chromosomes, Human, Pair 6/genetics
Chromosomes, Human, Pair 18/genetics
Induced Pluripotent Stem Cells/metabolism
Adult
Iris Diseases/genetics/metabolism/pathology
Genetic Linkage

@article {pmid38826443,
year = {2024},
author = {Aharonoff, A and Kim, J and Washington, A and Ercan, S},
title = {SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.21.595224},
pmid = {38826443},
abstract = {UNLABELLED: Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans , for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegan s dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae , which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained.

SIGNIFICANCE STATEMENT: X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus . Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.},
}

@article {pmid38810546,
year = {2024},
author = {Bhattacharya, M and Lyda, SF and Lei, EP},
title = {Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization.},
journal = {Current opinion in genetics & development},
volume = {87},
number = {},
pages = {102208},
doi = {10.1016/j.gde.2024.102208},
pmid = {38810546},
issn = {1879-0380},
abstract = {Chromatin insulators are DNA-protein complexes that promote specificity of enhancer-promoter interactions and maintain distinct transcriptional states through control of 3D genome organization. In this review, we highlight recent work visualizing how mammalian CCCTC-binding factor acts as a boundary to dynamic DNA loop extrusion mediated by cohesin. We also discuss new studies in both mammals and Drosophila that elucidate biological redundancy of chromatin insulator function and interplay with transcription with respect to topologically associating domain formation. Finally, we present novel concepts in spatiotemporal regulation of chromatin insulator function during differentiation and development and possible consequences of disrupted insulator activity on cellular proliferation.},
}

@article {pmid38783373,
year = {2024},
author = {Zagirova, D and Kononkova, A and Vaulin, N and Khrameeva, E},
title = {From compartments to loops: understanding the unique chromatin organization in neuronal cells.},
journal = {Epigenetics & chromatin},
volume = {17},
number = {1},
pages = {18},
pmid = {38783373},
issn = {1756-8935},
support = {21-74-10102//Russian Science Foundation/ ; },
abstract = {The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.},
}

@article {pmid38782890,
year = {2024},
author = {Xu, J and Xu, X and Huang, D and Luo, Y and Lin, L and Bai, X and Zheng, Y and Yang, Q and Cheng, Y and Huang, A and Shi, J and Bo, X and Gu, J and Chen, H},
title = {A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4376},
pmid = {38782890},
issn = {2041-1723},
support = {62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62173338//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20220484198//Beijing Nova Program/ ; 20220484198//Beijing Nova Program/ ; 20220484198//Beijing Nova Program/ ; },
mesh = {*Benchmarking ; *Chromatin/chemistry ; Humans ; Computational Biology/methods ; Software ; Chromatin Assembly and Disassembly ; },
abstract = {Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.},
}

*Benchmarking
*Chromatin/chemistry
Humans
Computational Biology/methods
Software
Chromatin Assembly and Disassembly

@article {pmid38778427,
year = {2024},
author = {Sui, P and Wang, Z and Zhang, P and Pan, F},
title = {Three-dimensional chromatin landscapes in MLLr AML.},
journal = {Experimental hematology & oncology},
volume = {13},
number = {1},
pages = {56},
pmid = {38778427},
issn = {2162-3619},
abstract = {Rearrangements of the mixed lineage leukemia (MLLr) gene are frequently associated with aggressive acute myeloid leukemia (AML). However, the treatment options are limited due to the genomic complexity and dynamics of 3D structure, which regulate oncogene transcription and leukemia development. Here, we carried out an integrative analysis of 3D genome structure, chromatin accessibility, and gene expression in gene-edited MLL-AF9 AML samples. Our data revealed profound MLLr-specific alterations of chromatin accessibility, A/B compartments, topologically associating domains (TAD), and chromatin loops in AML. The local 3D configuration of the AML genome was rewired specifically at loci associated with AML-specific gene expression. Together, we demonstrate that MLL-AF9 fusion disrupts the 3D chromatin landscape, potentially contributing to the dramatic transcriptome remodeling in MLLr AML.},
}

@article {pmid38775198,
year = {2024},
author = {Moindrot, B and Imaizumi, Y and Feil, R},
title = {Differential 3D genome architecture and imprinted gene expression: cause or consequence?.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20230143},
pmid = {38775198},
issn = {1470-8752},
abstract = {Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.},
}

@article {pmid38766012,
year = {2024},
author = {Irastorza-Azcarate, I and Kukalev, A and Kempfer, R and Thieme, CJ and Mastrobuoni, G and Markowski, J and Loof, G and Sparks, TM and Brookes, E and Natarajan, KN and Sauer, S and Fisher, AG and Nicodemi, M and Ren, B and Schwarz, RF and Kempa, S and Pombo, A},
title = {Extensive folding variability between homologous chromosomes in mammalian cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.08.591087},
pmid = {38766012},
abstract = {Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.},
}

@article {pmid38764013,
year = {2024},
author = {Zhang, B and Long, Y and Pei, L and Huang, X and Li, B and Han, B and Zhang, M and Lindsey, K and Zhang, X and Wang, M and Yang, X},
title = {Drought response revealed by chromatin organization variation and transcriptional regulation in cotton.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {114},
pmid = {38764013},
issn = {1741-7007},
mesh = {*Gossypium/genetics/physiology ; *Droughts ; *Gene Expression Regulation, Plant ; *Chromatin/metabolism ; Stress, Physiological/genetics ; Genes, Plant ; },
abstract = {BACKGROUND: Cotton is a major world cash crop and an important source of natural fiber, oil, and protein. Drought stress is becoming a restrictive factor affecting cotton production. To facilitate the development of drought-tolerant cotton varieties, it is necessary to study the molecular mechanism of drought stress response by exploring key drought-resistant genes and related regulatory factors.

RESULTS: In this study, two cotton varieties, ZY007 (drought-sensitive) and ZY168 (drought-tolerant), showing obvious phenotypic differences under drought stress, were selected. A total of 25,898 drought-induced genes were identified, exhibiting significant enrichment in pathways related to plant stress responses. Under drought induction, At subgenome expression bias was observed at the whole-genome level, which may be due to stronger inhibition of Dt subgenome expression. A gene co-expression module that was significantly associated with drought resistance was identified. About 90% of topologically associating domain (TAD) boundaries were stable, and 6613 TAD variation events were identified between the two varieties under drought. We identified 92 genes in ZY007 and 98 in ZY168 related to chromatin 3D structural variation and induced by drought stress. These genes are closely linked to the cotton response to drought stress through canonical hormone-responsive pathways, modulation of kinase and phosphatase activities, facilitation of calcium ion transport, and other related molecular mechanisms.

CONCLUSIONS: These results lay a foundation for elucidating the molecular mechanism of the cotton drought response and provide important regulatory locus and gene resources for the future molecular breeding of drought-resistant cotton varieties.},
}

*Gossypium/genetics/physiology
*Droughts
*Gene Expression Regulation, Plant
*Chromatin/metabolism
Stress, Physiological/genetics
Genes, Plant