@article {pmid37726281,
year = {2023},
author = {Nakato, R and Sakata, T and Wang, J and Nagai, LAE and Nagaoka, Y and Oba, GM and Bando, M and Shirahige, K},
title = {Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5647},
pmid = {37726281},
issn = {2041-1723},
support = {JP23gm6310012h0004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJCR18S5//MEXT | Japan Science and Technology Agency (JST)/ ; },
abstract = {Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.},
}

@article {pmid37725346,
year = {2023},
author = {He, X and Huang, X and Long, Y and Liu, Z and Chang, X and Zhang, X and Wang, M},
title = {Tcbf: A novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad576},
pmid = {37725346},
issn = {1367-4811},
abstract = {SUMMARY: TAD boundaries are essential for organizing the chromatin spatial structure and regulating gene expression in eukaryotes. However, for large-scale pan-3D genome research, identifying conserved and specific TAD boundaries across different species or individuals is computationally challenging. Here, we present Tcbf, a rapid and powerful Python/R tool that integrates gene synteny blocks and homologous sequences to automatically detect conserved and specific TAD boundaries among multiple species, which can efficiently analyze huge genome datasets, greatly reduce the computational burden and enable pan-3D genome research.

Tcbf is implemented by Python/R and is available at https://github.com/TcbfGroup/Tcbf under the MIT license.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid37705115,
year = {2023},
author = {Oprescu, SN and Baumann, N and Chen, X and Sun, Q and Zhao, Y and Yue, F and Wang, H and Kuang, S},
title = {Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle.},
journal = {Skeletal muscle},
volume = {13},
number = {1},
pages = {15},
pmid = {37705115},
issn = {2044-5040},
support = {F31AR077424/NH/NIH HHS/United States ; R01AR078695/NH/NIH HHS/United States ; },
abstract = {Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associating domains. Unexpectedly, Myod1[Cre]-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7[CreER]- or Rosa26[CreER]- driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remains to be elucidated.},
}

@article {pmid37699887,
year = {2023},
author = {Chang, LH and Ghosh, S and Papale, A and Luppino, JM and Miranda, M and Piras, V and Degrouard, J and Edouard, J and Poncelet, M and Lecouvreur, N and Bloyer, S and Leforestier, A and Joyce, EF and Holcman, D and Noordermeer, D},
title = {Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5615},
pmid = {37699887},
issn = {2041-1723},
support = {SPF201909009328//Fondation pour la Recherche Médicale (Foundation for Medical Research in France)/ ; SPF201909009284//Fondation pour la Recherche Médicale (Foundation for Medical Research in France)/ ; },
abstract = {Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.},
}

@article {pmid37608075,
year = {2023},
author = {Chen, Y and Zhou, T and Liao, Z and Gao, W and Wu, J and Zhang, S and Li, Y and Liu, H and Zhou, H and Xu, C and Su, P},
title = {Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {37608075},
issn = {1476-5403},
support = {92068105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172376//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82102518//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072385//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021M693630//China Postdoctoral Science Foundation/ ; },
abstract = {Proper development of the limb bud relies on the concordance of various signals, but its molecular mechanisms have not yet been fully illustrated. Here we report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. Its ablation in the limb bud results in limbless forelimbs and severe deformities of the hindlimbs. In terms of mechanism, hnRNPK functions as a transcription activator for the vital genes involved in the three regulatory axes of limb bud development. Simultaneously, for the first time we elucidate that hnRNPK binds to and coordinates with the insulator protein CCCTC binding factor (CTCF) to maintain a three-dimensional chromatin architecture. Ablation of hnRNPK weakens the binding strength of CTCF to topologically associating domain (TAD) boundaries, then leading to the loose TADs, and decreased interactions between promoters and enhancers, and further decreased transcription of developmental genes. Our study establishes a fundamental and novel role of hnRNPK in regulating limb bud development.},
}

@article {pmid37603403,
year = {2023},
author = {Agarwal, A and Korsak, S and Choudhury, A and Plewczynski, D},
title = {The dynamic role of cohesin in maintaining human genome architecture.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2200240},
doi = {10.1002/bies.202200240},
pmid = {37603403},
issn = {1521-1878},
abstract = {Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.},
}

@article {pmid37592325,
year = {2023},
author = {Yan, T and Wang, K and Feng, K and Gao, X and Jin, Y and Wu, H and Zhang, W and Wei, L},
title = {Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {16},
number = {1},
pages = {129},
pmid = {37592325},
issn = {2731-3654},
abstract = {BACKGROUND: Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.

RESULTS: Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the 'fatty acid metabolism', 'response to stress', 'carbon fixation' and 'photosynthesis' functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.

CONCLUSIONS: Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.},
}

@article {pmid37576549,
year = {2023},
author = {Tav, C and Fournier, É and Fournier, M and Khadangi, F and Baguette, A and Côté, MC and Silveira, MAD and Bérubé-Simard, FA and Bourque, G and Droit, A and Bilodeau, S},
title = {Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1237092},
pmid = {37576549},
issn = {1664-8021},
abstract = {Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.},
}

@article {pmid37498561,
year = {2023},
author = {Wang, Y and Guo, Z and Cheng, J},
title = {Single-cell Hi-C data enhancement with deep residual and generative adversarial networks.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {8},
pages = {},
pmid = {37498561},
issn = {1367-4811},
mesh = {Humans ; Reproducibility of Results ; *Chromosomes ; *Genome ; Chromosome Structures ; Software ; Chromatin ; },
abstract = {MOTIVATION: The spatial genome organization of a eukaryotic cell is important for its function. The development of single-cell technologies for probing the 3D genome conformation, especially single-cell chromosome conformation capture techniques, has enabled us to understand genome function better than before. However, due to extreme sparsity and high noise associated with single-cell Hi-C data, it is still difficult to study genome structure and function using the HiC-data of one single cell.

RESULTS: In this work, we developed a deep learning method ScHiCEDRN based on deep residual networks and generative adversarial networks for the imputation and enhancement of Hi-C data of a single cell. In terms of both image evaluation and Hi-C reproducibility metrics, ScHiCEDRN outperforms the four deep learning methods (DeepHiC, HiCPlus, HiCSR, and Loopenhance) on enhancing the raw single-cell Hi-C data of human and Drosophila. The experiments also show that it can generate single-cell Hi-C data more suitable for identifying topologically associating domain boundaries and reconstructing 3D chromosome structures than the existing methods. Moreover, ScHiCEDRN's performance generalizes well across different single cells and cell types, and it can be applied to improving population Hi-C data.

The source code of ScHiCEDRN is available at the GitHub repository: https://github.com/BioinfoMachineLearning/ScHiCEDRN.},
}

Humans
Reproducibility of Results
*Chromosomes
*Genome
Chromosome Structures
Software
Chromatin

@article {pmid37292994,
year = {2023},
author = {Xiong, K and Zhang, R and Ma, J},
title = {scGHOST: Identifying single-cell 3D genome subcompartments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37292994},
abstract = {New single-cell Hi-C (scHi-C) technologies enable probing of the genome-wide cell-to-cell variability in 3D genome organization from individual cells. Several computational methods have been developed to reveal single-cell 3D genome features based on scHi-C data, including A/B compartments, topologically-associating domains, and chromatin loops. However, no scHi-C analysis method currently exists for annotating single-cell subcompartments, which are crucial for providing a more refined view of large-scale chromosome spatial localization in single cells. Here, we present SCGHOST, a single-cell subcompartment annotation method based on graph embedding with constrained random walk sampling. Applications of SCGHOST to scHi-C data and single-cell 3D genome imaging data demonstrate the reliable identification of single-cell subcompartments and offer new insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from the human prefrontal cortex, SCGHOST identifies cell type-specific subcompartments that are strongly connected to cell type-specific gene expression, suggesting the functional implications of single-cell subcompartments. Overall, SCGHOST is an effective new method for single-cell 3D genome subcompartment annotation based on scHi-C data for a broad range of biological contexts.},
}

@article {pmid37085539,
year = {2023},
author = {Okonechnikov, K and Camgöz, A and Chapman, O and Wani, S and Park, DE and Hübner, JM and Chakraborty, A and Pagadala, M and Bump, R and Chandran, S and Kraft, K and Acuna-Hidalgo, R and Reid, D and Sikkink, K and Mauermann, M and Juarez, EF and Jenseit, A and Robinson, JT and Pajtler, KW and Milde, T and Jäger, N and Fiesel, P and Morgan, L and Sridhar, S and Coufal, NG and Levy, M and Malicki, D and Hobbs, C and Kingsmore, S and Nahas, S and Snuderl, M and Crawford, J and Wechsler-Reya, RJ and Davidson, TB and Cotter, J and Michaiel, G and Fleischhack, G and Mundlos, S and Schmitt, A and Carter, H and Michealraj, KA and Kumar, SA and Taylor, MD and Rich, J and Buchholz, F and Mesirov, JP and Pfister, SM and Ay, F and Dixon, JR and Kool, M and Chavez, L},
title = {3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2300},
pmid = {37085539},
issn = {2041-1723},
support = {R21 NS120075/NS/NINDS NIH HHS/United States ; R01 GM074024/GM/NIGMS NIH HHS/United States ; DP5 OD023071/OD/NIH HHS/United States ; R21 NS130137/NS/NINDS NIH HHS/United States ; U24 CA210004/CA/NCI NIH HHS/United States ; U01 CA184898/CA/NCI NIH HHS/United States ; U01 CA217885/CA/NCI NIH HHS/United States ; U24 CA258406/CA/NCI NIH HHS/United States ; R21 NS116455/NS/NINDS NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; },
mesh = {Child ; Humans ; Child, Preschool ; *Neoplasm Recurrence, Local/genetics ; Chromosomes ; Chromosome Mapping ; *Ependymoma/genetics/pathology ; Genome ; Chromatin/genetics ; },
abstract = {Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.},
}

Child
Humans
Child, Preschool
*Neoplasm Recurrence, Local/genetics
Chromosomes
Chromosome Mapping
*Ependymoma/genetics/pathology
Genome
Chromatin/genetics

@article {pmid36840746,
year = {2023},
author = {Sabaté, T and Lelandais, B and Bertrand, E and Zimmer, C},
title = {Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.},
journal = {Nucleic acids research},
volume = {51},
number = {6},
pages = {2614-2632},
pmid = {36840746},
issn = {1362-4962},
mesh = {*Chromosomal Proteins, Non-Histone/genetics ; *Polymers ; Chromatin ; Chromosomes ; DNA ; Cell Cycle Proteins/genetics ; },
abstract = {Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of loop formation can be quantified from fixed cell images alone, while the lifetime of loops and the speed of extrusion can be estimated from dynamic live-cell data. Our delineation of appropriate imaging conditions and the proposed analytical methods lay the groundwork for a systematic quantitative characterization of loop extrusion in fixed or living cells.},
}

*Chromosomal Proteins, Non-Histone/genetics
*Polymers
Chromatin
Chromosomes
DNA
Cell Cycle Proteins/genetics

@article {pmid37559123,
year = {2023},
author = {Lyu, J and Chen, C},
title = {LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {184},
pmid = {37559123},
issn = {1474-760X},
abstract = {Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.},
}

@article {pmid37550699,
year = {2023},
author = {Deng, L and Zhou, Q and Zhou, J and Zhang, Q and Jia, Z and Zhu, G and Cheng, S and Cheng, L and Yin, C and Yang, C and Shen, J and Nie, J and Zhu, JK and Li, G and Zhao, L},
title = {3D organization of regulatory elements for transcriptional regulation in Arabidopsis.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {181},
pmid = {37550699},
issn = {1474-760X},
support = {32222063//National Natural Science Foundation of China/ ; 32188102//National Natural Science Foundation of China/ ; 31930032//National Natural Science Foundation of China/ ; 2662021PY005//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.

RESULTS: Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression.

CONCLUSION: The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.},
}

@article {pmid37537310,
year = {2023},
author = {Tettey, TT and Rinaldi, L and Hager, GL},
title = {Long-range gene regulation in hormone-dependent cancer.},
journal = {Nature reviews. Cancer},
volume = {},
number = {},
pages = {},
pmid = {37537310},
issn = {1474-1768},
abstract = {The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.},
}

@article {pmid37536338,
year = {2023},
author = {Mohana, G and Dorier, J and Li, X and Mouginot, M and Smith, RC and Malek, H and Leleu, M and Rodriguez, D and Khadka, J and Rosa, P and Cousin, P and Iseli, C and Restrepo, S and Guex, N and McCabe, BD and Jankowski, A and Levine, MS and Gambetta, MC},
title = {Chromosome-level organization of the regulatory genome in the Drosophila nervous system.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2023.07.008},
pmid = {37536338},
issn = {1097-4172},
abstract = {Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.},
}

@article {pmid37516964,
year = {2023},
author = {Oka, M and Otani, M and Miyamoto, Y and Oshima, R and Adachi, J and Tomonaga, T and Asally, M and Nagaoka, Y and Tanaka, K and Toyoda, A and Ichikawa, K and Morishita, S and Isono, K and Koseki, H and Nakato, R and Ohkawa, Y and Yoneda, Y},
title = {Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure.},
journal = {Cell reports},
volume = {42},
number = {8},
pages = {112884},
doi = {10.1016/j.celrep.2023.112884},
pmid = {37516964},
issn = {2211-1247},
abstract = {NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure.},
}

@article {pmid37478379,
year = {2023},
author = {Liu, T and Wang, Z},
title = {HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbad263},
pmid = {37478379},
issn = {1477-4054},
support = {/GM/NIGMS NIH HHS/United States ; R35GM137974/NH/NIH HHS/United States ; },
abstract = {The Hi-C experiments have been extensively used for the studies of genomic structures. In the last few years, spatiotemporal Hi-C has largely contributed to the investigation of genome dynamic reorganization. However, computationally modeling and forecasting spatiotemporal Hi-C data still have not been seen in the literature. We present HiC4D for dealing with the problem of forecasting spatiotemporal Hi-C data. We designed and benchmarked a novel network and named it residual ConvLSTM (ResConvLSTM), which is a combination of residual network and convolutional long short-term memory (ConvLSTM). We evaluated our new ResConvLSTM networks and compared them with the other five methods, including a naïve network (NaiveNet) that we designed as a baseline method and four outstanding video-prediction methods from the literature: ConvLSTM, spatiotemporal LSTM (ST-LSTM), self-attention LSTM (SA-LSTM) and simple video prediction (SimVP). We used eight different spatiotemporal Hi-C datasets for the blind test, including two from mouse embryogenesis, one from somatic cell nuclear transfer (SCNT) embryos, three embryogenesis datasets from different species and two non-embryogenesis datasets. Our evaluation results indicate that our ResConvLSTM networks almost always outperform the other methods on the eight blind-test datasets in terms of accurately predicting the Hi-C contact matrices at future time-steps. Our benchmarks also indicate that all of the methods that we benchmarked can successfully recover the boundaries of topologically associating domains called on the experimental Hi-C contact matrices. Taken together, our benchmarks suggest that HiC4D is an effective tool for predicting spatiotemporal Hi-C data. HiC4D is publicly available at both http://dna.cs.miami.edu/HiC4D/ and https://github.com/zwang-bioinformatics/HiC4D/.},
}

@article {pmid37467757,
year = {2023},
author = {Senapati, S and Irshad, IU and Sharma, AK and Kumar, H},
title = {Fundamental insights into the correlation between chromosome configuration and transcription.},
journal = {Physical biology},
volume = {},
number = {},
pages = {},
doi = {10.1088/1478-3975/ace8e5},
pmid = {37467757},
issn = {1478-3975},
abstract = {Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain (TAD), and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research. .},
}

@article {pmid37461500,
year = {2023},
author = {Goudarzi, S and Pagadala, M and Klie, A and Talwar, JV and Carter, H},
title = {Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.07.04.547722},
pmid = {37461500},
abstract = {Cancer is a highly heterogeneous disease caused by genetic and epigenetic alterations in normal cells. A recent study uncovered methylation quantitative trait loci (meQTLs) associated with different levels of local DNA methylation in cancers. Here, we investigated whether the distribution of cancer meQTLs reflected functional organization of the genome in the form of chromatin topologically associated domains (TADs), and evaluated whether cancer meQTLs near known driver genes have the potential to influence cancer risk or progression. At TAD boundaries, we observed differences in the distribution of meQTLs when one or both of the adjacent TADs was transcriptionally active, with higher densities near inactive TADs. Furthermore, we found differences in cancer meQTL distributions in active versus inactive TADs and observed an enrichment of meQTLs in active TADs near tumor suppressors, whereas there was a depletion of such meQTLs near oncogenes. Several meQTLs were associated with cancer risk in the UKBioBank, and we were able to reproduce breast cancer risk associations in the DRIVE cohort. Survival analysis in TCGA implicated a number of meQTLs in 13 tumor types. In 10 of these, polygenic meQTL scores were associated with increased hazard in a CoxPH analysis. Risk and survival-associated meQTLs tended to affect cancer genes involved in DNA damage repair and cellular adhesion and reproduced cancer-specific associations reported in prior literature. In summary, this study provides evidence that genetic variants that influence local DNA methylation are affected by chromatin structure and can impact tumor evolution.},
}

@article {pmid37453058,
year = {2023},
author = {Kim, K and Kim, M and Lee, AJ and Song, SH and Kang, JK and Eom, J and Kang, GH and Bae, JM and Min, S and Kim, Y and Lim, Y and Kim, HS and Kim, YJ and Kim, TY and Jung, I},
title = {Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer.},
journal = {Cell reports},
volume = {42},
number = {7},
pages = {112778},
doi = {10.1016/j.celrep.2023.112778},
pmid = {37453058},
issn = {2211-1247},
abstract = {The regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation remains unclear. This study investigated SV-mediated gene dysregulation by profiling 3D cancer genome maps from 40 patients with colorectal cancer (CRC). We developed a machine learning-based method for spatial characterization of the altered 3D cancer genome. This revealed a frequent establishment of "de novo chromatin contacts" that can span multiple topologically associating domains (TADs) in addition to the canonical TAD fusion/shuffle model. Using this information, we precisely identified super-enhancer (SE)-hijacking and its clonal characteristics. Clonal SE-hijacking genes, such as TOP2B, are recurrently associated with cell-cycle/DNA-processing functions, which can potentially be used as CRC prognostic markers. Oncogene activation and increased drug resistance due to SE-hijacking were validated by reconstructing the patient's SV using CRISPR-Cas9. Collectively, the spatial and clonality-resolved analysis of the 3D cancer genome reveals regulatory principles of large-scale SVs in oncogene activation and their clinical implications.},
}

@article {pmid37445616,
year = {2023},
author = {Lee, EG and Leong, L and Chen, S and Tulloch, J and Yu, CE},
title = {APOE Locus-Associated Mitochondrial Function and Its Implication in Alzheimer's Disease and Aging.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
doi = {10.3390/ijms241310440},
pmid = {37445616},
issn = {1422-0067},
support = {BX000933 and BX004823//U.S. Department of Veterans Affairs Office of Research and Development Biomedical Laboratory Research Program/ ; },
abstract = {The Apolipoprotein E (APOE) locus has garnered significant clinical interest because of its association with Alzheimer's disease (AD) and longevity. This genetic association appears across multiple genes in the APOE locus. Despite the apparent differences between AD and longevity, both conditions share a commonality of aging-related changes in mitochondrial function. This commonality is likely due to accumulative biological effects partly exerted by the APOE locus. In this study, we investigated changes in mitochondrial structure/function-related markers using oxidative stress-induced human cellular models and postmortem brains (PMBs) from individuals with AD and normal controls. Our results reveal a range of expressional alterations, either upregulated or downregulated, in these genes in response to oxidative stress. In contrast, we consistently observed an upregulation of multiple APOE locus genes in all cellular models and AD PMBs. Additionally, the effects of AD status on mitochondrial DNA copy number (mtDNA CN) varied depending on APOE genotype. Our findings imply a potential coregulation of APOE locus genes possibly occurring within the same topologically associating domain (TAD) of the 3D chromosome conformation. The coordinated expression of APOE locus genes could impact mitochondrial function, contributing to the development of AD or longevity. Our study underscores the significant role of the APOE locus in modulating mitochondrial function and provides valuable insights into the underlying mechanisms of AD and aging, emphasizing the importance of this locus in clinical research.},
}

@article {pmid37438531,
year = {2023},
author = {Park, DS and Nguyen, SC and Isenhart, R and Shah, PP and Kim, W and Barnett, RJ and Chandra, A and Luppino, JM and Harke, J and Wai, M and Walsh, PJ and Abdill, RJ and Yang, R and Lan, Y and Yoon, S and Yunker, R and Kanemaki, MT and Vahedi, G and Phillips-Cremins, JE and Jain, R and Joyce, EF},
title = {High-throughput Oligopaint screen identifies druggable 3D genome regulators.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37438531},
issn = {1476-4687},
abstract = {The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions[1-3]. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.},
}

@article {pmid37433821,
year = {2023},
author = {Kadam, S and Kumari, K and Manivannan, V and Dutta, S and Mitra, MK and Padinhateeri, R},
title = {Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4108},
pmid = {37433821},
issn = {2041-1723},
support = {BT/HRD/NBA/39/12/2018-19//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; },
abstract = {Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.},
}

@article {pmid37426677,
year = {2023},
author = {Liu, H and Tsai, H and Yang, M and Li, G and Bian, Q and Ding, G and Wu, D and Dai, J},
title = {Three-dimensional genome structure and function.},
journal = {MedComm},
volume = {4},
number = {4},
pages = {e326},
pmid = {37426677},
issn = {2688-2663},
abstract = {Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.},
}

@article {pmid37418545,
year = {2023},
author = {Onrust-van Schoonhoven, A and de Bruijn, MJW and Stikker, B and Brouwer, RWW and Braunstahl, GJ and van IJcken, WFJ and Graf, T and Huylebroeck, D and Hendriks, RW and Stik, G and Stadhouders, R},
title = {3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction.},
journal = {Science immunology},
volume = {8},
number = {85},
pages = {eadg3917},
doi = {10.1126/sciimmunol.adg3917},
pmid = {37418545},
issn = {2470-9468},
abstract = {Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4[+] memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.},
}

@article {pmid37398486,
year = {2023},
author = {Syed, SA and Shqillo, K and Nand, A and Zhan, Y and Dekker, J and Imbalzano, AN},
title = {Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.06.13.544859},
pmid = {37398486},
abstract = {Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.},
}

@article {pmid37387127,
year = {2023},
author = {Zhang, Y and Blanchette, M},
title = {Reference panel-guided super-resolution inference of Hi-C data.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {Supplement_1},
pages = {i386-i393},
doi = {10.1093/bioinformatics/btad266},
pmid = {37387127},
issn = {1367-4811},
support = {//Genome Quebec/ ; //Canada and Genome Quebec/ ; },
abstract = {MOTIVATION: Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types.

RESULTS: Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains.

https://github.com/BlanchetteLab/RefHiC.},
}

@article {pmid37386239,
year = {2023},
author = {Pandupuspitasari, NS and Khan, FA and Huang, C and Ali, A and Yousaf, MR and Shakeel, F and Putri, EM and Negara, W and Muktiani, A and Prasetiyono, BWHE and Kustiawan, L and Wahyuni, DS},
title = {Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease.},
journal = {Functional & integrative genomics},
volume = {23},
number = {3},
pages = {214},
pmid = {37386239},
issn = {1438-7948},
abstract = {In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.},
}

@article {pmid37381832,
year = {2023},
author = {Zhang, Y and Cao, X and Gao, Z and Ma, X and Wang, Q and Xu, X and Cai, X and Zhang, Y and Zhang, Z and Wei, G and Wen, B},
title = {MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {e57550},
doi = {10.15252/embr.202357550},
pmid = {37381832},
issn = {1469-3178},
support = {2021YFA1100203//MOST | National Key Research and Development Program of China (NKPs)/ ; 32130019//MOST | National Natural Science Foundation of China (NSFC)/ ; },
abstract = {Long interspersed nuclear elements (LINEs) play essential roles in shaping chromatin states, while the factors that cooperate with LINEs and their roles in higher-order chromatin organization remain poorly understood. Here, we show that MATR3, a nuclear matrix protein, interplays with antisense LINE1 (AS L1) RNAs to form a meshwork via phase separation, providing a dynamic platform for chromatin spatial organization. MATR3 and AS L1 RNAs affect the nuclear localization of each other. After MATR3 depletion, the chromatin, particularly H3K27me3-modified chromatin, redistributes in the cell nuclei. Topologically associating domains (TADs) that highly transcribe MATR3-associated AS L1 RNAs show decreased intra-TAD interactions in both AML12 and ES cells. MATR3 depletion increases the accessibility of H3K27me3 domains adjacent to MATR3-associated AS L1, without affecting H3K27me3 modifications. Furthermore, amyotrophic lateral sclerosis (ALS)-associated MATR3 mutants alter biophysical features of the MATR3-AS L1 RNA meshwork and cause an abnormal H3K27me3 staining. Collectively, we reveal a role of the meshwork formed by MATR3 and AS L1 RNAs in gathering chromatin in the nucleus.},
}

@article {pmid37381036,
year = {2023},
author = {Sun, Y and Xu, X and Zhao, W and Zhang, Y and Chen, K and Li, Y and Wang, X and Zhang, M and Xue, B and Yu, W and Hou, Y and Wang, C and Xie, W and Li, C and Kong, D and Wang, S and Sun, Y},
title = {RAD21 is the core subunit of the cohesin complex involved in directing genome organization.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {155},
pmid = {37381036},
issn = {1474-760X},
support = {21825401//National Natural Science Foundation of China/ ; No. 2022YFA1303103//National Key Research and Development Program of China Stem Cell and Translational Research/ ; },
abstract = {BACKGROUND: The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we use super-resolution imaging to reveal the unique role of cohesin subunit RAD21 in cohesin loading and chromatin structure regulation.

RESULTS: We directly visualize that up-regulation of RAD21 leads to excessive chromatin loop extrusion into a vermicelli-like morphology with RAD21 clustered into foci and excessively loaded cohesin bow-tying a TAD to form a beads-on-a-string-type pattern. In contrast, up-regulation of the other four cohesin subunits results in even distributions. Mechanistically, we identify that the essential role of RAD21 is attributed to the RAD21-loader interaction, which facilitates the cohesin loading process rather than increasing the abundance of cohesin complex upon up-regulation of RAD21. Furthermore, Hi-C and genomic analysis reveal how RAD21 up-regulation affects genome-wide higher-order chromatin structure. Accumulated contacts are shown at TAD corners while inter-TAD interactions increase after vermicelli formation. Importantly, we find that in breast cancer cells, the expression of RAD21 is aberrantly high with poor patient survival and RAD21 forms beads in the nucleus. Up-regulated RAD21 in HeLa cells leads to compartment switching and up-regulation of cancer-related genes.

CONCLUSIONS: Our results provide key insights into the molecular mechanism by which RAD21 facilitates the cohesin loading process and provide an explanation to how cohesin and loader work cooperatively to promote chromatin extrusion, which has important implications in construction of three-dimensional genome organization.},
}

@article {pmid37325549,
year = {2023},
author = {Wang, M and Sreenivas, P and Sunkel, BD and Wang, L and Ignatius, M and Stanton, BZ},
title = {The 3D chromatin landscape of rhabdomyosarcoma.},
journal = {NAR cancer},
volume = {5},
number = {3},
pages = {zcad028},
pmid = {37325549},
issn = {2632-8674},
abstract = {Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with a lack of precision therapy options for patients. We hypothesized that with a general paucity of known mutations in RMS, chromatin structural driving mechanisms are essential for tumor proliferation. Thus, we carried out high-depth in situ Hi-C in representative cell lines and patient-derived xenografts (PDXs) to define chromatin architecture in each major RMS subtype. We report a comprehensive 3D chromatin structural analysis and characterization of fusion-positive (FP-RMS) and fusion-negative RMS (FN-RMS). We have generated spike-in in situ Hi-C chromatin interaction maps for the most common FP-RMS and FN-RMS cell lines and compared our data with PDX models. In our studies, we uncover common and distinct structural elements in large Mb-scale chromatin compartments, tumor-essential genes within variable topologically associating domains and unique patterns of structural variation. Our high-depth chromatin interactivity maps and comprehensive analyses provide context for gene regulatory events and reveal functional chromatin domains in RMS.},
}

@article {pmid37322110,
year = {2023},
author = {Rekaik, H and Lopez-Delisle, L and Hintermann, A and Mascrez, B and Bochaton, C and Mayran, A and Duboule, D},
title = {Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {37322110},
issn = {1546-1718},
abstract = {During development, Hox genes are temporally activated according to their relative positions on their clusters, contributing to the proper identities of structures along the rostrocaudal axis. To understand the mechanism underlying this Hox timer, we used mouse embryonic stem cell-derived stembryos. Following Wnt signaling, the process involves transcriptional initiation at the anterior part of the cluster and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, that is, with an asymmetric distribution favoring the anterior part of the cluster. Chromatin extrusion then occurs with successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time delay in the activation of more posterior-located genes due to long-range contacts with a flanking topologically associating domain. Mutant stembryos support this model and reveal that the presence of evolutionary conserved and regularly spaced intergenic CTCF sites controls the precision and the pace of this temporal mechanism.},
}

@article {pmid37302180,
year = {2023},
author = {da Costa-Nunes, JA and Noordermeer, D},
title = {TADs: Dynamic structures to create stable regulatory functions.},
journal = {Current opinion in structural biology},
volume = {81},
number = {},
pages = {102622},
doi = {10.1016/j.sbi.2023.102622},
pmid = {37302180},
issn = {1879-033X},
abstract = {Mammalian chromosomes are organized at different length scales within the cell nucleus. Topologically Associating Domains (TADs) are structural units of 3D genome organization with functions in gene regulation, DNA replication, recombination and repair. Whereas TADs were initially interpreted as insulated domains, recent studies are revealing that these domains should be interpreted as dynamic collections of actively extruding loops. This process of loop extrusion is subsequently blocked at dedicated TAD boundaries, thereby promoting intra-domain interactions over their surroundings. In this review, we discuss how mammalian TAD structure can emerge from this dynamic process and we discuss recent evidence that TAD boundaries can have regulatory functions.},
}

@article {pmid37279476,
year = {2023},
author = {Peng, X and Li, Y and Zou, M and Kong, X and Sheng, Y},
title = {CATAD: exploring topologically associating domains from an insight of core-attachment structure.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbad204},
pmid = {37279476},
issn = {1477-4054},
abstract = {Identifying topologically associating domains (TADs), which are considered as the basic units of chromosome structure and function, can facilitate the exploration of the 3D-structure of chromosomes. Methods have been proposed to identify TADs by detecting the boundaries of TADs or identifying the closely interacted regions as TADs, while the possible inner structure of TADs is seldom investigated. In this study, we assume that a TAD is composed of a core and its surrounding attachments, and propose a method, named CATAD, to identify TADs based on the core-attachment structure model. In CATAD, the cores of TADs are identified based on the local density and cosine similarity, and the surrounding attachments are determined based on boundary insulation. CATAD was applied to the Hi-C data of two human cell lines and two mouse cell lines, and the results show that the boundaries of TADs identified by CATAD are significantly enriched by structural proteins, histone modifications, transcription start sites and enzymes. Furthermore, CATAD outperforms other methods in many cases, in terms of the average peak, boundary tagged ratio and fold change. In addition, CATAD is robust and rarely affected by the different resolutions of Hi-C matrices. Conclusively, identifying TADs based on the core-attachment structure is useful, which may inspire researchers to explore TADs from the angles of possible spatial structures and formation process.},
}

@article {pmid37277355,
year = {2023},
author = {Kessler, S and Minoux, M and Joshi, O and Ben Zouari, Y and Ducret, S and Ross, F and Vilain, N and Salvi, A and Wolff, J and Kohler, H and Stadler, MB and Rijli, FM},
title = {A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3242},
pmid = {37277355},
issn = {2041-1723},
abstract = {Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.},
}

@article {pmid37259205,
year = {2023},
author = {Gu, J and Li, S and Zhu, B and Liang, Q and Chen, B and Tang, X and Chen, C and Wu, DD and Li, Y},
title = {Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13818},
pmid = {37259205},
issn = {1755-0998},
abstract = {Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.},
}

@article {pmid37254808,
year = {2023},
author = {Li, D and Zhao, XY and Zhou, S and Hu, Q and Wu, F and Lee, HY},
title = {Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad468},
pmid = {37254808},
issn = {1362-4962},
abstract = {Mammalian erythroid development can be divided into three stages: hematopoietic stem and progenitor cell (HSPC), erythroid progenitor (Ery-Pro), and erythroid precursor (Ery-Pre). However, the mechanisms by which the 3D genome changes to establish the stage-specific transcription programs that are critical for erythropoiesis remain unclear. Here, we analyze the chromatin landscape at multiple levels in defined populations from primary human erythroid culture. While compartments and topologically associating domains remain largely unchanged, ∼50% of H3K27Ac-marked enhancers are dynamic in HSPC versus Ery-Pre. The enhancer anchors of enhancer-promoter loops are enriched for occupancy of respective stage-specific transcription factors (TFs), indicating these TFs orchestrate the enhancer connectome rewiring. The master TF of erythropoiesis, GATA1, is found to occupy most erythroid gene promoters at the Ery-Pro stage, and mediate conspicuous local rewiring through acquiring binding at the distal regions in Ery-Pre, promoting productive erythroid transcription output. Knocking out GATA1 binding sites precisely abrogates local rewiring and corresponding gene expression. Interestingly, knocking down GATA1 can transiently revert the cell state to an earlier stage and prolong the window of progenitor state. This study reveals mechanistic insights underlying chromatin rearrangements during development by integrating multidimensional chromatin landscape analyses to associate with transcription output and cellular states.},
}

@article {pmid37254161,
year = {2023},
author = {Tolokh, IS and Kinney, NA and Sharakhov, IV and Onufriev, AV},
title = {Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.},
journal = {Epigenetics & chromatin},
volume = {16},
number = {1},
pages = {21},
pmid = {37254161},
issn = {1756-8935},
support = {R01 GM144596/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult.

RESULTS: We have developed a coarse-grained dynamical model of D. melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. The simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same strong effect on the predicted positioning of individual TADs -- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region.

CONCLUSIONS: A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.},
}

@article {pmid37250307,
year = {2023},
author = {Hamba, Y and Kamatani, T and Miya, F and Boroevich, KA and Tsunoda, T},
title = {Topologically associating domain underlies tissue specific expression of long intergenic non-coding RNAs.},
journal = {iScience},
volume = {26},
number = {5},
pages = {106640},
pmid = {37250307},
issn = {2589-0042},
abstract = {Accumulating evidence indicates that long intergenic non-coding RNAs (lincRNAs) show more tissue-specific expression patterns than protein-coding genes (PCGs). However, although lincRNAs are subject to canonical transcriptional regulation like PCGs, the molecular basis for the specificity of their expression patterns remains unclear. Here, using expression data and coordinates of topologically associating domains (TADs) in human tissues, we show that lincRNA loci are significantly enriched in the more internal region of TADs compared to PCGs and that lincRNAs within TADs have higher tissue specificity than those outside TADs. Based on these, we propose an analytical framework to interpret transcriptional status using lincRNA as an indicator. We applied it to hypertrophic cardiomyopathy data and found disease-specific transcriptional regulation: ectopic expression of keratin at the TAD level and derepression of myocyte differentiation-related genes by E2F1 with down-regulation of LINC00881. Our results provide understanding of the function and regulation of lincRNAs according to genomic structure.},
}

@article {pmid37193952,
year = {2023},
author = {Zhang, X and Yu, G and Dai, Y and Zhang, H and Wang, K and Han, J},
title = {High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {260},
pmid = {37193952},
issn = {1471-2229},
abstract = {BACKGROUND: The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear.

RESULTS: In this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated ~ 1.5 kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response.

CONCLUSIONS: Our study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.},
}

@article {pmid37162822,
year = {2023},
author = {Parodi, L and Comeau, ME and Georgakis, MK and Mayerhofer, E and Chung, J and Falcone, GJ and Malik, R and Demel, SL and Worrall, BB and Koch, S and Testai, FD and Kittner, SJ and McCauley, JL and Hall, CE and Mayson, DJ and Elkind, MS and James, ML and Woo, D and Rosand, J and Langefeld, CD and Anderson, CD},
title = {Deep resequencing of the 1q22 locus in non-lobar intracerebral hemorrhage.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.18.23288754},
pmid = {37162822},
abstract = {OBJECTIVE: Genome-wide association studies have identified 1q22 as a susceptibility locus for cerebral small vessel diseases (CSVDs), including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study we performed targeted high-depth sequencing of 1q22 in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown.

METHODS: 95,000 base pairs spanning 1q22 , including SEMA4A, SLC25A44 and PMF1 / PMF1-BGLAP were sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and RIFT analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, ChIP-Seq and ChIA-PET databases. Multivariable Mendelian randomization (MVMR) assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at 1q22 could be causally related to ICH risk.

RESULTS: Common and rare variant analyses prioritized variants in SEMA4A 5'-UTR and PMF1 intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that 1q22 is spatially organized in a single chromatin loop and that the genes therein belong to the same Topologically Associating Domain. ChIP-Seq and ChIA-PET data analysis highlighted the presence of long-range interactions between the SEMA4A -promoter and PMF1 -enhancer regions prioritized by association testing. MVMR analyses demonstrated that PMF1 overexpression could be causally related to non-lobar ICH risk.

INTERPRETATION: Altered promoter-enhancer interactions leading to PMF1 overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non-lobar ICH risk at 1q22 , offering a potential new target for prevention of ICH and CSVD.},
}

@article {pmid37162225,
year = {2023},
author = {Li, A and Zeng, G and Wang, H and Li, X and Zhang, Z},
title = {DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2300366},
doi = {10.1002/advs.202300366},
pmid = {37162225},
issn = {2198-3844},
abstract = {Topologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state-of-the-art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.},
}

@article {pmid37139561,
year = {2023},
author = {Liu, J and Li, P and Sun, J and Guo, J},
title = {LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbad165},
pmid = {37139561},
issn = {1477-4054},
abstract = {With the development of chromosome conformation capture technique, the study of spatial conformation of a genome based on Hi-C technique has made a quantum leap. Previous studies reveal that genomes are folded into hierarchy of three-dimensional (3D) structures associated with topologically associating domains (TADs), and detecting TAD boundaries is of great significance in the chromosome-level analysis of 3D genome architecture. In this paper, we propose a novel TAD identification method, LPAD, which first extracts node correlations from global interactions of chromosomes based on the random walk with restart and then builds an undirected graph from Hi-C contact matrix. Next, LPAD designs a label propagation-based approach to discover communities and generates TADs. Experimental results verify the effectiveness and quality of TAD detections compared with existing methods. Furthermore, experimental evaluation of chromatin immunoprecipitation sequencing data shows that LPAD performs high enrichment of histone modifications remarkably nearby the TAD boundaries, and these results demonstrate LPAD's advantages on TAD identification accuracy.},
}

@article {pmid37116707,
year = {2023},
author = {Liu, P and Li, D and Zhang, J and He, M and Gao, D and Wang, Y and Lin, Y and Pan, D and Li, P and Wang, T and Li, J and Kong, F and Zeng, B and Lu, L and Ma, J and Long, K and Li, G and Tang, Q and Jin, L and Li, M},
title = {Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {104757},
doi = {10.1016/j.jbc.2023.104757},
pmid = {37116707},
issn = {1083-351X},
abstract = {Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is essential for understanding human-specific metabolic regulation, but the functional importance and evolutionary dynamics of three-dimensional (3D) genome organizations of ATs are not well defined. Here, we compared the 3D genome architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation in ATs at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI), which have not been described previously. We found promoter-enhancer interaction (PEI) are much more evolutionarily dynamic with respect to compartmentalization and topologically associating domain (TAD). Compared to conserved PEIs, human-specific PEIs are enriched for human-specific sequence and the binding motifs of their potential mediators (transcription factors) are less conserved. Our data also demonstrated that genes involved in the evolutionarily dynamics of chromatin organization have weaker transcriptional conservation than those associated with conserved chromatin organization. Furthermore, the genes involved in energy metabolism and the maintenance of metabolic homeostasis are enriched in human-specific chromatin organization, while housekeeping genes, health-related genes and genetic variations are enriched in evolutionarily conserved compared to human-specific chromatin organization. Finally, we showed extensively divergent human-specific 3D genome organizations among one subcutaneous and three visceral ATs. Together, these findings provide a global overview of 3D genome architecture dynamics between ATs from human and mammalian models, and new insights into understanding the regulatory evolution of human ATs.},
}

@article {pmid37104607,
year = {2023},
author = {Keough, KC and Whalen, S and Inoue, F and Przytycki, PF and Fair, T and Deng, C and Steyert, M and Ryu, H and Lindblad-Toh, K and Karlsson, E and , and Nowakowski, T and Ahituv, N and Pollen, A and Pollard, KS and Andrews, G and Armstrong, JC and Bianchi, M and Birren, BW and Bredemeyer, KR and Breit, AM and Christmas, MJ and Clawson, H and Damas, J and Di Palma, F and Diekhans, M and Dong, MX and Eizirik, E and Fan, K and Fanter, C and Foley, NM and Forsberg-Nilsson, K and Garcia, CJ and Gatesy, J and Gazal, S and Genereux, DP and Goodman, L and Grimshaw, J and Halsey, MK and Harris, AJ and Hickey, G and Hiller, M and Hindle, AG and Hubley, RM and Hughes, GM and Johnson, J and Juan, D and Kaplow, IM and Karlsson, EK and Keough, KC and Kirilenko, B and Koepfli, KP and Korstian, JM and Kowalczyk, A and Kozyrev, SV and Lawler, AJ and Lawless, C and Lehmann, T and Levesque, DL and Lewin, HA and Li, X and Lind, A and Lindblad-Toh, K and Mackay-Smith, A and Marinescu, VD and Marques-Bonet, T and Mason, VC and Meadows, JRS and Meyer, WK and Moore, JE and Moreira, LR and Moreno-Santillan, DD and Morrill, KM and Muntané, G and Murphy, WJ and Navarro, A and Nweeia, M and Ortmann, S and Osmanski, A and Paten, B and Paulat, NS and Pfenning, AR and Phan, BN and Pollard, KS and Pratt, HE and Ray, DA and Reilly, SK and Rosen, JR and Ruf, I and Ryan, L and Ryder, OA and Sabeti, PC and Schäffer, DE and Serres, A and Shapiro, B and Smit, AFA and Springer, M and Srinivasan, C and Steiner, C and Storer, JM and Sullivan, KAM and Sullivan, PF and Sundström, E and Supple, MA and Swofford, R and Talbot, JE and Teeling, E and Turner-Maier, J and Valenzuela, A and Wagner, F and Wallerman, O and Wang, C and Wang, J and Weng, Z and Wilder, AP and Wirthlin, ME and Xue, JR and Zhang, X},
title = {Three-dimensional genome rewiring in loci with human accelerated regions.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6643},
pages = {eabm1696},
doi = {10.1126/science.abm1696},
pmid = {37104607},
issn = {1095-9203},
abstract = {Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.},
}

@article {pmid37099832,
year = {2023},
author = {Zhang, H and Blobel, GA},
title = {Genome folding dynamics during the M-to-G1-phase transition.},
journal = {Current opinion in genetics & development},
volume = {80},
number = {},
pages = {102036},
doi = {10.1016/j.gde.2023.102036},
pmid = {37099832},
issn = {1879-0380},
abstract = {All measurable features of higher-order chromosomal architecture undergo drastic reorganization as cells enter and exit mitosis. During mitosis, gene transcription is temporarily halted, the nuclear envelope is dismantled, and chromosomes undergo condensation. At this time, chromatin compartments, topologically associating domains (TADs), and loops that connect enhancers with promoters as well as CTCF/cohesin loops are dissolved. Upon G1 entry, genome organization is rebuilt in the daughter nuclei to resemble that of the mother nucleus. We survey recent studies that traced these features in relation to gene expression during the mitosis-to-G1-phase transition at high temporal resolution. Dissection of fluctuating architectural features informed the hierarchical relationships of chromosomal organization, the mechanisms by which they are formed, and their mutual (in-) dependence. These studies highlight the importance of considering the cell cycle dynamics for studies of chromosomal organization.},
}

@article {pmid37084258,
year = {2023},
author = {Wang, B and Liu, K and Li, Y and Wang, J},
title = {DFHiC: A dilated full convolution model to enhance the resolution of Hi-C data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad211},
pmid = {37084258},
issn = {1367-4811},
abstract = {MOTIVATION: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

RESULTS: In this work, we propose a novel method, so-called DFHiC, which generates the high-resolution Hi-C matrix from the low-resolution Hi-C matrix in the framework of the dilated convolutional neural network. The dilated convolution is able to effectively explore the global patterns in the overall Hi-C matrix by taking advantage of the information of the Hi-C matrix in a way of the longer genomic distance. Consequently, DFHiC can improve the resolution of the Hi-C matrix reliably and accurately. More importantly, the super-resolution Hi-C data enhanced by DFHiC is more in line with the real high-resolution Hi-C data than those done by the other existing methods, in terms of both chromatin significant interactions and identifying topologically associating domains (TADs).

AVAILABILITY: https://github.com/BinWangCSU/DFHiC.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid37081156,
year = {2023},
author = {Rajderkar, S and Barozzi, I and Zhu, Y and Hu, R and Zhang, Y and Li, B and Alcaina Caro, A and Fukuda-Yuzawa, Y and Kelman, G and Akeza, A and Blow, MJ and Pham, Q and Harrington, AN and Godoy, J and Meky, EM and von Maydell, K and Hunter, RD and Akiyama, JA and Novak, CS and Plajzer-Frick, I and Afzal, V and Tran, S and Lopez-Rios, J and Talkowski, ME and Lloyd, KCK and Ren, B and Dickel, DE and Visel, A and Pennacchio, LA},
title = {Topologically associating domain boundaries are required for normal genome function.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {435},
pmid = {37081156},
issn = {2399-3642},
abstract = {Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes[1-3], but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.},
}

@article {pmid37076620,
year = {2023},
author = {Davidson, IF and Barth, R and Zaczek, M and van der Torre, J and Tang, W and Nagasaka, K and Janissen, R and Kerssemakers, J and Wutz, G and Dekker, C and Peters, JM},
title = {CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37076620},
issn = {1476-4687},
abstract = {In eukaryotes, genomic DNA is extruded into loops by cohesin[1]. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)[2,3] that have important roles in gene regulation and recombination during development and disease[1,4-7]. How CTCF establishes TAD boundaries and to what extent these are permeable to cohesin is unclear[8]. Here, to address these questions, we visualize interactions of single CTCF and cohesin molecules on DNA in vitro. We show that CTCF is sufficient to block diffusing cohesin, possibly reflecting how cohesive cohesin accumulates at TAD boundaries, and is also sufficient to block loop-extruding cohesin, reflecting how CTCF establishes TAD boundaries. CTCF functions asymmetrically, as predicted; however, CTCF is dependent on DNA tension. Moreover, CTCF regulates cohesin's loop-extrusion activity by changing its direction and by inducing loop shrinkage. Our data indicate that CTCF is not, as previously assumed, simply a barrier to cohesin-mediated loop extrusion but is an active regulator of this process, whereby the permeability of TAD boundaries can be modulated by DNA tension. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.},
}

@article {pmid37070946,
year = {2023},
author = {Yin, X and Romero-Campero, FJ and Yang, M and Baile, F and Cao, Y and Shu, J and Luo, L and Wang, D and Sun, S and Yan, P and Gong, Z and Mo, X and Qin, G and Calonje, M and Zhou, Y},
title = {Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koad112},
pmid = {37070946},
issn = {1532-298X},
abstract = {Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.},
}

@article {pmid37063858,
year = {2023},
author = {Guo, M and Yao, Z and Jiang, C and Songyang, Z and Gan, L and Xiong, Y},
title = {Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1161522},
pmid = {37063858},
issn = {1664-3224},
abstract = {BACKGROUNDS: Hepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive.

METHODS: We applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization.

RESULTS: We found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure.

CONCLUSION: Our work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.},
}

@article {pmid37055796,
year = {2023},
author = {Cheng, J and Cao, X and Wang, X and Wang, J and Yue, B and Sun, W and Huang, Y and Lan, X and Ren, G and Lei, C and Chen, H},
title = {Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.},
journal = {Journal of animal science and biotechnology},
volume = {14},
number = {1},
pages = {59},
pmid = {37055796},
issn = {1674-9782},
abstract = {BACKGROUND: Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China. Three-dimensional genome structure is confirmed to be an important layer of transcription regulation. Although genome-wide interaction data of several livestock species have already been produced, the genome structure states and its regulatory rules in cattle muscle are still limited.

RESULTS: Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle (Bos taurus). We showed that compartments, topologically associating domains (TADs), and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development. Furthermore, we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps. We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.

CONCLUSIONS: Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology, which will benefit the progress of genetic improvement of beef cattle.},
}

@article {pmid37047368,
year = {2023},
author = {Mao, A and Chen, C and Portillo-Ledesma, S and Schlick, T},
title = {Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations.},
journal = {International journal of molecular sciences},
volume = {24},
number = {7},
pages = {},
doi = {10.3390/ijms24076395},
pmid = {37047368},
issn = {1422-0067},
support = {R35-GM122562/NH/NIH HHS/United States ; },
abstract = {In humans and other eukaryotes, DNA is condensed into chromatin fibers that are further wound into chromosomes. This organization allows regulatory elements in the genome, often distant from each other in the linear DNA, to interact and facilitate gene expression through regions known as topologically associating domains (TADs). CCCTC-binding factor (CTCF) is one of the major components of TAD formation and is responsible for recruiting a partner protein, cohesin, to perform loop extrusion and facilitate proper gene expression within TADs. Because single-residue CTCF mutations have been linked to the development of a variety of cancers in humans, we aim to better understand how these mutations affect the CTCF structure and its interaction with DNA. To this end, we compare all-atom molecular dynamics simulations of a wildtype CTCF-DNA complex to those of eight different cancer-linked CTCF mutant sequences. We find that most mutants have lower binding energies compared to the wildtype protein, leading to the formation of less stable complexes. Depending on the type and position of the mutation, this loss of stability can be attributed to major changes in the electrostatic potential, loss of hydrogen bonds between the CTCF and DNA, and/or destabilization of specific zinc fingers. Interestingly, certain mutations in specific fingers can affect the interaction with the DNA of other fingers, explaining why mere single mutations can impair CTCF function. Overall, these results shed mechanistic insights into experimental observations and further underscore CTCF's importance in the regulation of chromatin architecture and gene expression.},
}

@article {pmid37041182,
year = {2023},
author = {Tan, ZW and Toong, PJ and Guarnera, E and Berezovsky, IN},
title = {Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {5906},
pmid = {37041182},
issn = {2045-2322},
abstract = {We tackle here genomic mechanisms of a rapid onset and recovery from anosmia-a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin structure in mice, we hypothesized that the disruption of the OR gene expression and, respectively, deficiency of the OR function can be caused by chromatin reorganization taking place upon SARS-CoV-2 infection. We obtained chromatin ensemble reconstructions from COVID-19 patients and control samples using our original computational framework for the whole-genome 3D chromatin ensemble reconstruction. Specifically, we used megabase-scale structural units and effective interactions between them obtained in the Markov State modelling of the Hi-C contact network as an unput in the stochastic embedding procedure of the whole-genome 3D chromatin ensemble reconstruction. We have also developed here a new procedure for analyzing fine structural hierarchy with (sub)TAD-size units in local chromatin regions, which we apply here to parts of chromosomes containing OR genes and corresponding regulatory elements. We observed structural modifications in COVID-19 patients on different levels of chromatin organization, from the alteration of whole genome structure and chromosomal intermingling to reorganization of contacts between chromatin loops at the level of topologically associating domains. While complementary data on known regulatory elements point to potential pathology-associated changes within the overall picture of chromatin alterations, further investigation using additional epigenetic factors mapped on 3D reconstructions with improved resolution will be required for better understanding of anosmia caused by SARS-CoV-2 infection.},
}

@article {pmid37041138,
year = {2023},
author = {Melo, US and Jatzlau, J and Prada-Medina, CA and Flex, E and Hartmann, S and Ali, S and Schöpflin, R and Bernardini, L and Ciolfi, A and Moeinzadeh, MH and Klever, MK and Altay, A and Vallecillo-García, P and Carpentieri, G and Delledonne, M and Ort, MJ and Schwestka, M and Ferrero, GB and Tartaglia, M and Brusco, A and Gossen, M and Strunk, D and Geißler, S and Mundlos, S and Stricker, S and Knaus, P and Giorgio, E and Spielmann, M},
title = {Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2034},
pmid = {37041138},
issn = {2041-1723},
abstract = {Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in which signaling pathways such as BMP, TGFβ and WNT are known key players in driving ectopic bone formation. Identifying novel genes and pathways related to the mineralization process are important steps for future gene therapy in bone disorders. In this study, we detect an inter-chromosomal insertional duplication in a female proband disrupting a topologically associating domain and causing an ultra-rare progressive form of heterotopic ossification. This structural variant lead to enhancer hijacking and misexpression of ARHGAP36 in fibroblasts, validated here by orthogonal in vitro studies. In addition, ARHGAP36 overexpression inhibits TGFβ, and activates hedgehog signaling and genes/proteins related to extracellular matrix production. Our work on the genetic cause of this heterotopic ossification case has revealed that ARHGAP36 plays a role in bone formation and metabolism, outlining first details of this gene contributing to bone-formation and -disease.},
}

@article {pmid37017672,
year = {2023},
author = {Fritz, AJ and Ghule, PN and Toor, R and Dillac, L and Perelman, J and Boyd, J and Lian, JB and Gordon, JAR and Frietze, S and Van Wijnen, A and Stein, JL and Stein, GS},
title = {Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle.},
journal = {Critical reviews in eukaryotic gene expression},
volume = {33},
number = {3},
pages = {85-97},
doi = {10.1615/CritRevEukaryotGeneExpr.2022046190},
pmid = {37017672},
issn = {1045-4403},
abstract = {Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.},
}

@article {pmid37016431,
year = {2023},
author = {Narang, S and Evensen, NA and Saliba, J and Pierro, J and Loh, ML and Brown, PA and Kolekar, P and Mulder, H and Shao, Y and Easton, J and Ma, X and Tsirigos, A and Carroll, WL},
title = {NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {64},
pmid = {37016431},
issn = {1474-760X},
abstract = {BACKGROUND: The NSD2 p.E1099K (EK) mutation is shown to be enriched in patients with relapsed acute lymphoblastic leukemia (ALL), indicating a role in clonal evolution and drug resistance.

RESULTS: To uncover 3D chromatin architecture-related mechanisms underlying drug resistance, we perform Hi-C on three B-ALL cell lines heterozygous for NSD2 EK. The NSD2 mutation leads to widespread remodeling of the 3D genome, most dramatically in terms of compartment changes with a strong bias towards A compartment shifts. Systematic integration of the Hi-C data with previously published ATAC-seq, RNA-seq, and ChIP-seq data show an expansion in H3K36me2 and a shrinkage in H3K27me3 within A compartments as well as increased gene expression and chromatin accessibility. These results suggest that NSD2 EK plays a prominent role in chromatin decompaction through enrichment of H3K36me2. In contrast, we identify few changes in intra-topologically associating domain activity. While compartment changes vary across cell lines, a common core of decompacting loci are shared, driving the expression of genes/pathways previously implicated in drug resistance. We further perform RNA sequencing on a cohort of matched diagnosis/relapse ALL patients harboring the relapse-specific NSD2 EK mutation. Changes in patient gene expression upon relapse significantly correlate with core compartment changes, further implicating the role of NSD2 EK in genome decompaction.

CONCLUSIONS: In spite of cell-context-dependent changes mediated by EK, there appears to be a shared transcriptional program dependent on compartment shifts which could explain phenotypic differences across EK cell lines. This core program is an attractive target for therapeutic intervention.},
}

@article {pmid37012431,
year = {2023},
author = {Dozmorov, MG and Marshall, MA and Rashid, NS and Grible, JM and Valentine, A and Olex, AL and Murthy, K and Chakraborty, A and Reyna, J and Figueroa, DS and Hinojosa-Gonzalez, L and Da-Inn Lee, E and Baur, BA and Roy, S and Ay, F and Harrell, JC},
title = {Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {5420},
pmid = {37012431},
issn = {2045-2322},
support = {R35-GM128938/GM/NIGMS NIH HHS/United States ; R35-GM128938/GM/NIGMS NIH HHS/United States ; 1R01CA246182-01A1/CA/NCI NIH HHS/United States ; CCR19608826/KOMEN/Susan G. Komen/United States ; },
abstract = {Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.},
}

@article {pmid37000624,
year = {2023},
author = {Wang, B and Ji, L and Bian, Q},
title = {SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.},
journal = {Cell reports},
volume = {42},
number = {4},
pages = {112323},
doi = {10.1016/j.celrep.2023.112323},
pmid = {37000624},
issn = {2211-1247},
abstract = {Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.},
}

@article {pmid36996812,
year = {2023},
author = {Chen, LF and Long, HK and Park, M and Swigut, T and Boettiger, AN and Wysocka, J},
title = {Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2023.03.009},
pmid = {36996812},
issn = {1097-4164},
abstract = {Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.},
}

@article {pmid36990727,
year = {2023},
author = {Aldersey, JE and Liu, N and Tearle, R and Low, WY and Breen, J and Williams, JL and Bottema, CDK},
title = {Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue.},
journal = {Animal genetics},
volume = {},
number = {},
pages = {},
doi = {10.1111/age.13322},
pmid = {36990727},
issn = {1365-2052},
abstract = {Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300-kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus- and Brahman-specific Hi-C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus- and Brahman-specific Hi-C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.},
}

@article {pmid36941615,
year = {2023},
author = {Li, X and Wang, J and Yu, Y and Li, G and Wang, J and Li, C and Zeng, Z and Li, N and Zhang, Z and Dong, Q and Yu, Y and Wang, X and Wang, T and Grover, CE and Wang, B and Liu, B and Wendel, JF and Gong, L},
title = {Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae).},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {56},
pmid = {36941615},
issn = {1741-7007},
abstract = {BACKGROUND: Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species.

RESULTS: Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), including Gossypium arboreum, Gossypium raimondii, and Gossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved in Gossypioides and Gossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestral in-cis interactions.

CONCLUSIONS: Our findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.},
}

@article {pmid36914797,
year = {2023},
author = {Li, D and Wu, F and Zhou, S and Huang, XJ and Lee, HY},
title = {Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
pmid = {36914797},
issn = {1545-9985},
abstract = {Mammalian erythropoiesis involves progressive chromatin compaction and subsequent enucleation in terminal differentiation, but the mechanisms underlying the three-dimensional chromatin reorganization remain obscure. Here, we systematically analyze the higher-order chromatin in purified populations of primary human erythroblasts. Our results reveal that heterochromatin regions undergo substantial compression, with H3K9me3 markers relocalizing to the nuclear periphery and forming a significant number of long-range interactions, and that ~58% of the topologically associating domain (TAD) boundaries are disrupted, while certain TADs enriched for markers of the active transcription state and erythroid master regulators, GATA1 and KLF1, are selectively maintained during terminal erythropoiesis. Finally, we demonstrate that GATA1 is involved in safeguarding selected essential chromatin domains during terminal erythropoiesis. Our study therefore delineates the molecular characteristics of a development-driven chromatin compaction process, which reveals transcription competence as a key indicator of the selected domain maintenance to ensure appropriate gene expression during the extreme compaction of chromatin.},
}

@article {pmid36894325,
year = {2023},
author = {Dang, D and Zhang, SW and Duan, R and Zhang, S},
title = {Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277187.122},
pmid = {36894325},
issn = {1549-5469},
abstract = {Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization, and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. Obvious inconsistencies among the TADs identified by different methods indeed make the statistical and biological properties of TADs overly depend on the method we chose rather than on the data. To this end, we employ the consensus structural information captured by these methods to define the TAD separation landscape for decoding the consensus domain organization of the 3D genome. We demonstrate that the TAD separation landscape could be used to compare domain boundaries across multiple cell types for discovering conserved and divergent topological structures, decipher three types of boundary regions with diverse biological features, and identify Consensus TADs (ConsTADs). We illustrate that these analyses could deepen our understanding of the relationships between the topological domains and chromatin states, gene expression, and DNA replication timing.},
}

@article {pmid36869353,
year = {2023},
author = {Richer, S and Tian, Y and Schoenfelder, S and Hurst, L and Murrell, A and Pisignano, G},
title = {Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {40},
pmid = {36869353},
issn = {1474-760X},
support = {MR/P000711/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available.

RESULTS: We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs).

CONCLUSIONS: This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.},
}

@article {pmid36842325,
year = {2023},
author = {Karpinska, MA and Oudelaar, AM},
title = {The role of loop extrusion in enhancer-mediated gene activation.},
journal = {Current opinion in genetics & development},
volume = {79},
number = {},
pages = {102022},
doi = {10.1016/j.gde.2023.102022},
pmid = {36842325},
issn = {1879-0380},
abstract = {Gene expression patterns in complex multicellular organisms are regulated by enhancers, which communicate with their target gene promoters in three-dimensional (3D) chromatin structures. Despite advances in our understanding of the mechanisms that organize mammalian genomes into compartments and topologically associating domains (TADs), it is not well understood how specific interactions between enhancers and promoters are controlled in this 3D context. In this review, we give an overview of recent evidence that shows that a process of loop extrusion plays an important role in the regulation of enhancer-promoter communication and discuss recent insights into the molecular mechanism by which loop extrusion contributes to enhancer-mediated gene activation.},
}

@article {pmid36800432,
year = {2023},
author = {Zhao, Y and Ding, Y and He, L and Zhou, Q and Chen, X and Li, Y and Alfonsi, MV and Wu, Z and Sun, H and Wang, H},
title = {Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging.},
journal = {Science advances},
volume = {9},
number = {7},
pages = {eabo1360},
doi = {10.1126/sciadv.abo1360},
pmid = {36800432},
issn = {2375-2548},
abstract = {Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounced when SCs become activated. Marked loss in topologically associating domain (TAD) border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can form TAD clusters and super-enhancer-containing TAD clusters orchestrate stage-specific gene expression. Furthermore, we uncover that transcription factor PAX7 is pivotal in enhancer-promoter (E-P) loop formation. We also identify cis-regulatory elements that are crucial for local chromatin organization at Pax7 locus and Pax7 expression. Lastly, we unveil that geriatric SC displays a prominent gain in long-range contacts and loss of TAD border insulation. Together, our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage development and SC aging.},
}

@article {pmid36759336,
year = {2023},
author = {Kobets, VA and Ulianov, SV and Galitsyna, AA and Doronin, SA and Mikhaleva, EA and Gelfand, MS and Shevelyov, YY and Razin, SV and Khrameeva, EE},
title = {HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbad044},
pmid = {36759336},
issn = {1477-4054},
abstract = {The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.},
}

@article {pmid36750787,
year = {2023},
author = {Maslova, A and Plotnikov, V and Nuriddinov, M and Gridina, M and Fishman, V and Krasikova, A},
title = {Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {66},
pmid = {36750787},
issn = {1471-2164},
mesh = {Animals ; *Chickens/genetics ; Karyotype ; *Genomics ; Sex Chromosomes ; Chromosome Aberrations ; Mammals/genetics ; },
abstract = {BACKGROUND: Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line.

RESULTS: We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH.

CONCLUSIONS: In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.},
}

Animals
*Chickens/genetics
Karyotype
*Genomics
Sex Chromosomes
Chromosome Aberrations
Mammals/genetics

@article {pmid36744801,
year = {2023},
author = {Yang, L and Akgol Oksuz, B and Dekker, J and Gibcus, JH},
title = {Capturing Chromosome Conformation Across Length Scales.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {191},
pages = {},
doi = {10.3791/64001},
pmid = {36744801},
issn = {1940-087X},
mesh = {*Chromosomes/genetics/metabolism ; *Chromatin/genetics ; DNA/genetics/chemistry ; Cell Nucleus/metabolism ; DNA Restriction Enzymes/metabolism ; Formaldehyde/chemistry ; Nucleic Acid Conformation ; },
abstract = {Chromosome conformation capture (3C) is used to detect three-dimensional chromatin interactions. Typically, chemical crosslinking with formaldehyde (FA) is used to fix chromatin interactions. Then, chromatin digestion with a restriction enzyme and subsequent religation of fragment ends converts three-dimensional (3D) proximity into unique ligation products. Finally, after reversal of crosslinks, protein removal, and DNA isolation, DNA is sheared and prepared for high-throughput sequencing. The frequency of proximity ligation of pairs of loci is a measure of the frequency of their colocalization in three-dimensional space in a cell population. A sequenced Hi-C library provides genome-wide information on interaction frequencies between all pairs of loci. The resolution and precision of Hi-C relies on efficient crosslinking that maintains chromatin contacts and frequent and uniform fragmentation of the chromatin. This paper describes an improved in situ Hi-C protocol, Hi-C 3.0, that increases the efficiency of crosslinking by combining two crosslinkers (formaldehyde [FA] and disuccinimidyl glutarate [DSG]), followed by finer digestion using two restriction enzymes (DpnII and DdeI). Hi-C 3.0 is a single protocol for the accurate quantification of genome folding features at smaller scales such as loops and topologically associating domains (TADs), as well as features at larger nucleus-wide scales such as compartments.},
}

*Chromosomes/genetics/metabolism
*Chromatin/genetics
DNA/genetics/chemistry
Cell Nucleus/metabolism
DNA Restriction Enzymes/metabolism
Formaldehyde/chemistry
Nucleic Acid Conformation

@article {pmid36740586,
year = {2023},
author = {Selcen, I and Prentice, E and Casaccia, P},
title = {The epigenetic landscape of oligodendrocyte lineage cells.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.14959},
pmid = {36740586},
issn = {1749-6632},
abstract = {The epigenetic landscape of oligodendrocyte lineage cells refers to the cell-specific modifications of DNA, chromatin, and RNA that define a unique gene expression pattern of functionally specialized cells. Here, we focus on the epigenetic changes occurring as progenitors differentiate into myelin-forming cells and respond to the local environment. First, modifications of DNA, RNA, nucleosomal histones, key principles of chromatin organization, topologically associating domains, and local remodeling will be reviewed. Then, the relationship between epigenetic modulators and RNA processing will be explored. Finally, the reciprocal relationship between the epigenome as a determinant of the mechanical properties of cell nuclei and the target of mechanotransduction will be discussed. The overall goal is to provide an interpretative key on how epigenetic changes may account for the heterogeneity of the transcriptional profiles identified in this lineage.},
}

@article {pmid36736317,
year = {2023},
author = {Costea, J and Schoeberl, UE and Malzl, D and von der Linde, M and Fitz, J and Gupta, A and Makharova, M and Goloborodko, A and Pavri, R},
title = {A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2023.01.014},
pmid = {36736317},
issn = {1097-4164},
abstract = {Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.},
}

@article {pmid36735786,
year = {2023},
author = {Cavalheiro, GR and Girardot, C and Viales, RR and Pollex, T and Cao, TBN and Lacour, P and Feng, S and Rabinowitz, A and Furlong, EEM},
title = {CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles.},
journal = {Science advances},
volume = {9},
number = {5},
pages = {eade1085},
pmid = {36735786},
issn = {2375-2548},
mesh = {Animals ; *Drosophila/genetics/metabolism ; *Drosophila Proteins/metabolism ; Genome ; Chromatin/genetics ; Chromosomes ; DNA-Binding Proteins/metabolism ; Eye Proteins/genetics/metabolism ; Microtubule-Associated Proteins/metabolism ; Nuclear Proteins/metabolism ; CCCTC-Binding Factor/genetics ; },
abstract = {The boundaries of topologically associating domains (TADs) are delimited by insulators and/or active promoters; however, how they are initially established during embryogenesis remains unclear. Here, we examined this during the first hours of Drosophila embryogenesis. DNA-FISH confirms that intra-TAD pairwise proximity is established during zygotic genome activation (ZGA) but with extensive cell-to-cell heterogeneity. Most newly formed boundaries are occupied by combinations of CTCF, BEAF-32, and/or CP190. Depleting each insulator individually from chromatin revealed that TADs can still establish, although with lower insulation, with a subset of boundaries (~10%) being more dependent on specific insulators. Some weakened boundaries have aberrant gene expression due to unconstrained enhancer activity. However, the majority of misexpressed genes have no obvious direct relationship to changes in domain-boundary insulation. Deletion of an active promoter (thereby blocking transcription) at one boundary had a greater impact than deleting the insulator-bound region itself. This suggests that cross-talk between insulators and active promoters and/or transcription might reinforce domain boundary insulation during embryogenesis.},
}

Animals
*Drosophila/genetics/metabolism
*Drosophila Proteins/metabolism
Genome
Chromatin/genetics
Chromosomes
DNA-Binding Proteins/metabolism
Eye Proteins/genetics/metabolism
Microtubule-Associated Proteins/metabolism
Nuclear Proteins/metabolism
CCCTC-Binding Factor/genetics

@article {pmid36719724,
year = {2023},
author = {Landshammer, A and Bolondi, A and Kretzmer, H and Much, C and Buschow, R and Rose, A and Wu, HJ and Mackowiak, SD and Braendl, B and Giesselmann, P and Tornisiello, R and Parsi, KM and Huey, J and Mielke, T and Meierhofer, D and Maehr, R and Hnisz, D and Michor, F and Rinn, JL and Meissner, A},
title = {T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {36719724},
issn = {2050-084X},
mesh = {Pregnancy ; Female ; Humans ; *RNA, Long Noncoding/genetics/metabolism ; Epithelial-Mesenchymal Transition ; Endoderm ; Gene Expression Regulation, Developmental ; SOXF Transcription Factors/genetics/metabolism ; Cell Differentiation/genetics ; },
abstract = {Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.},
}

Pregnancy
Female
Humans
*RNA, Long Noncoding/genetics/metabolism
Epithelial-Mesenchymal Transition
Endoderm
Gene Expression Regulation, Developmental
SOXF Transcription Factors/genetics/metabolism
Cell Differentiation/genetics

@article {pmid36717722,
year = {2023},
author = {Barajas-Mora, EM and Lee, L and Lu, H and Valderrama, JA and Bjanes, E and Nizet, V and Feeney, AJ and Hu, M and Murre, C},
title = {Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens.},
journal = {Nature immunology},
volume = {24},
number = {2},
pages = {320-336},
pmid = {36717722},
issn = {1529-2916},
mesh = {Mice ; Animals ; *Chromatin/genetics ; Immunoglobulin Variable Region/genetics ; Immunoglobulin kappa-Chains/genetics ; *Methicillin-Resistant Staphylococcus aureus/genetics ; B-Lymphocytes ; Epigenesis, Genetic ; },
abstract = {Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene segments that rearrange to generate antigen receptor repertoires. Here, we identified an enhancer (E34) in the murine immunoglobulin kappa (Igk) locus that instructed rearrangement of Vκ genes located in a sub-topologically associating domain, including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. We show that E34 instructs the nuclear repositioning of the E34 sub-topologically associating domain from a recombination-repressive compartment to a recombination-permissive compartment that is marked by equivalent activating histone modifications. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. We propose that the merging of Vκ genes with Jκ elements is instructed by one-dimensional epigenetic information imposed by enhancers across Vκ and Jκ genomic regions. The data also reveal how enhancers generate distinct antibody repertoires that provide protection against lethal bacterial infection.},
}

Mice
Animals
*Chromatin/genetics
Immunoglobulin Variable Region/genetics
Immunoglobulin kappa-Chains/genetics
*Methicillin-Resistant Staphylococcus aureus/genetics
B-Lymphocytes
Epigenesis, Genetic

@article {pmid36708949,
year = {2023},
author = {Nayak, S and Jiang, K and Hope, E and Cross, M and Overmiller, A and Naz, F and Worrell, S and Bajpai, D and Hasneen, K and Brooks, SR and Dell'Orso, S and Morasso, MI},
title = {Chromatin landscape governing murine epidermal differentiation.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2022.12.020},
pmid = {36708949},
issn = {1523-1747},
abstract = {Chromatin landscape and regulatory networks are determinant in lineage specification and differentiation. To define the temporospatial differentiation axis in murine epidermal cells in vivo, we generated datasets profiling expression dynamics (RNA-Seq), chromatin accessibility (ATAC-Seq), architecture (Hi-C), and histone modifications (ChIP-Seq) in the epidermis. We show that many differentially regulated genes are suppressed during the differentiation process, with super-enhancers (SEs) controlling differentiation-specific epigenomic changes. Our data shows the relevance of the Dlx/Klf/Grhl combinatorial regulatory network in maintaining correct temporospatial gene expression during epidermal differentiation. We determined differential open compartments, topologically associating domain (TAD) score and looping in the Basal cell (B) and Suprabasal cell (SB) epidermal fractions, with the evolutionarily conserved Epidermal Differentiation Complex (EDC) region showing distinct SB-specific TAD and loop formation that coincided with SE sites. Overall, our study provides a global genome-wide resource of chromatin dynamics that define unrecognized regulatory networks and the epigenetic control of Dlx3-bound SE elements during epidermal differentiation.},
}

@article {pmid36708167,
year = {2023},
author = {Fan, S and Dang, D and Ye, Y and Zhang, SW and Gao, L and Zhang, S},
title = {scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.},
journal = {Journal of molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jmcb/mjad003},
pmid = {36708167},
issn = {1759-4685},
abstract = {Single-cell Hi-C technology provides an unprecedented opportunity to reveal chromatin structure in individual cells. However, high sequencing cost impedes the generation of biological Hi-C data with high sequencing depths and multiple replicates for downstream analysis. Here we developed a single-cell Hi-C simulator (scHi-CSim) that generates high-fidelity data for benchmarking. scHi-CSim merges neighboring cells to overcome the sparseness of data, samples interactions in distance-stratified chromosomes to maintain the heterogeneity of single cells, and estimates the empirical distribution of restriction fragments to generate simulated data. We demonstrated that scHi-CSim can generate high-fidelity data by comparing the performance of single-cell clustering and detection of chromosomal high-order structures with raw data. Furthermore, scHi-CSim is flexible to change sequencing depths and the number of simulated replicates. We showed that increasing sequencing depths could improve the accuracy of detecting topologically associating domains. We also used scHi-CSim to generate a series of simulated datasets with different sequencing depths to benchmark single-cell Hi-C clustering methods.},
}

@article {pmid36693380,
year = {2023},
author = {Kim, S and Wysocka, J},
title = {Deciphering the multi-scale, quantitative cis-regulatory code.},
journal = {Molecular cell},
volume = {83},
number = {3},
pages = {373-392},
pmid = {36693380},
issn = {1097-4164},
support = {R35 GM131757/GM/NIGMS NIH HHS/United States ; },
mesh = {*Enhancer Elements, Genetic ; *Transcription Factors/genetics/metabolism ; Promoter Regions, Genetic ; Gene Expression Regulation ; Base Sequence ; Chromatin/genetics ; },
abstract = {Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.},
}

*Enhancer Elements, Genetic
*Transcription Factors/genetics/metabolism
Promoter Regions, Genetic
Gene Expression Regulation
Base Sequence
Chromatin/genetics

@article {pmid36658660,
year = {2023},
author = {Ni, L and Liu, Y and Ma, X and Liu, T and Yang, X and Wang, Z and Liang, Q and Liu, S and Zhang, M and Wang, Z and Shen, Y and Tian, Z},
title = {Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {12},
pmid = {36658660},
issn = {1474-760X},
mesh = {*Soybeans/genetics ; *Genome ; Gene Expression Regulation ; Retroelements ; Genome, Plant ; Chromatin ; },
abstract = {BACKGROUND: High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.

RESULTS: Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.

CONCLUSION: Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.},
}

*Soybeans/genetics
*Genome
Gene Expression Regulation
Retroelements
Genome, Plant
Chromatin

@article {pmid36650052,
year = {2023},
author = {Islam, Z and Saravanan, B and Walavalkar, K and Farooq, U and Singh, AK and Radhakrishnan, S and Thakur, J and Pandit, A and Henikoff, S and Notani, D},
title = {Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.},
journal = {Genome research},
volume = {33},
number = {1},
pages = {1-17},
doi = {10.1101/gr.276643.122},
pmid = {36650052},
issn = {1549-5469},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {*Chromatin/genetics ; CCCTC-Binding Factor/metabolism ; Binding Sites ; Promoter Regions, Genetic ; *RNA ; Enhancer Elements, Genetic ; },
abstract = {Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF and MYC TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.},
}

*Chromatin/genetics
CCCTC-Binding Factor/metabolism
Binding Sites
Promoter Regions, Genetic
*RNA
Enhancer Elements, Genetic

@article {pmid36642680,
year = {2023},
author = {Yeo, SJ and Ying, C and Fullwood, MJ and Tergaonkar, V},
title = {Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2022.12.003},
pmid = {36642680},
issn = {0168-9525},
abstract = {Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.},
}

@article {pmid36617663,
year = {2023},
author = {Mulhair, PO and Crowley, L and Boyes, DH and Harper, A and Lewis, OT and , and Holland, PWH},
title = {Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera.},
journal = {Genome research},
volume = {33},
number = {1},
pages = {32-44},
doi = {10.1101/gr.277118.122},
pmid = {36617663},
issn = {1549-5469},
support = {218328/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Genes, Homeobox ; *Butterflies ; Phylogeny ; Multigene Family ; Genomics ; Evolution, Molecular ; },
abstract = {Homeobox genes encode transcription factors with essential roles in patterning and cell fate in developing animal embryos. Many homeobox genes, including Hox and NK genes, are arranged in gene clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary genome assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large order of insects. Here we analyze an extensive data set of high-quality genomes to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which the lab gene is repositioned and the ro gene is next to pb A topologically associating domain spans much of the gene cluster, suggesting deep regulatory conservation of the Hox cluster arrangement in this insect order. Most Lepidoptera have four Shx genes, divergent zen-derived loci, but these loci underwent dramatic duplication in several lineages, with some moths having over 165 homeobox loci in the Hox gene cluster; this expansion is associated with local LINE element density. In contrast, the NK gene cluster content is more stable, although there are differences in organization compared with other insects, as well as major rearrangements within butterflies. Our analysis represents the first description of homeobox gene content across the order Lepidoptera, exemplifying the potential of newly generated genome assemblies for understanding genome and gene family evolution.},
}

Animals
*Genes, Homeobox
*Butterflies
Phylogeny
Multigene Family
Genomics
Evolution, Molecular

@article {pmid36609218,
year = {2023},
author = {Zhang, L and Xu, M and Zhang, W and Zhu, C and Cui, Z and Fu, H and Ma, Y and Huang, S and Cui, J and Liang, S and Huang, L and Wang, H},
title = {Three-dimensional genome landscape comprehensively reveals patterns of spatial gene regulation in papillary and anaplastic thyroid cancers: a study using representative cell lines for each cancer type.},
journal = {Cellular & molecular biology letters},
volume = {28},
number = {1},
pages = {1},
pmid = {36609218},
issn = {1689-1392},
mesh = {Humans ; Cell Line ; Chromatin/genetics ; DNA Copy Number Variations/genetics ; Homeodomain Proteins/genetics ; Methyltransferases/genetics ; *Thyroid Carcinoma, Anaplastic/genetics ; *Thyroid Neoplasms/genetics ; Transcription Factors/genetics ; Genome ; },
abstract = {BACKGROUND: Spatial chromatin structure is intricately linked with somatic aberrations, and somatic mutations of various cancer-related genes, termed co-mutations (CoMuts), occur in certain patterns during cancer initiation and progression. The functional mechanisms underlying these genetic events remain largely unclear in thyroid cancer (TC). With discrepant differentiation, papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) differ greatly in characteristics and prognosis. We aimed to reveal the spatial gene alterations and regulations between the two TC subtypes.

METHODS: We systematically investigated and compared the spatial co-mutations between ATC (8305C), PTC (BCPAP and TPC-1), and normal thyroid cells (Nthy-ori-3-1). We constructed a framework integrating whole-genome sequencing (WGS), high-throughput chromosome conformation capture (Hi-C), and transcriptome sequencing, to systematically detect the associations between the somatic co-mutations of cancer-related genes, structural variations (SVs), copy number variations (CNVs), and high-order chromatin conformation.

RESULTS: Spatial co-mutation hotspots were enriched around topologically associating domains (TADs) in TC. A common set of 227 boundaries were identified in both ATC and PTC, with significant overlaps between them. The spatial proximities of the co-mutated gene pairs in the two TC types were significantly greater than in the gene-level and overall backgrounds, and ATC cells had higher TAD contact frequency with CoMuts > 10 compared with PTC cells. Compared with normal thyroid cells, in ATC the number of the created novel three-dimensional chromatin structural domains increased by 10%, and the number of shifted TADs decreased by 7%. We found five TAD blocks with CoMut genes/events specific to ATC with certain mutations in genes including MAST-NSUN4, AM129B/TRUB2, COL5A1/PPP1R26, PPP1R26/GPSM1/CCDC183, and PRAC2/DLX4. For the majority of ATC and PTC cells, the HOXA10 and HIF2α signals close to the transcription start sites of CoMut genes within TADs were significantly stronger than those at the background. CNV breakpoints significantly overlapped with TAD boundaries in both TC subtypes. ATCs had more CNV losses overlapping with TAD boundaries, and noncoding SVs involved in intrachromosomal SVs, amplified inversions, and tandem duplication differed between ATC and PTC. TADs with short range were more abundant in ATC than PTC. More switches of A/B compartment types existed in ATC cells compared with PTC. Gene expression was significantly synchronized, and orchestrated by complex epigenetics and regulatory elements.

CONCLUSION: Chromatin interactions and gene alterations and regulations are largely heterogeneous in TC. CNVs and complex SVs may function in the TC genome by interplaying with TADs, and are largely different between ATC and PTC. Complexity of TC genomes, which are highly organized by 3D genome-wide interactions mediating mutational and structural variations and gene activation, may have been largely underappreciated. Our comprehensive analysis may provide key evidence and targets for more customized diagnosis and treatment of TC.},
}

Humans
Cell Line
Chromatin/genetics
DNA Copy Number Variations/genetics
Homeodomain Proteins/genetics
Methyltransferases/genetics
*Thyroid Carcinoma, Anaplastic/genetics
*Thyroid Neoplasms/genetics
Transcription Factors/genetics
Genome

@article {pmid36549923,
year = {2023},
author = {van Mierlo, G and Pushkarev, O and Kribelbauer, JF and Deplancke, B},
title = {Chromatin modules and their implication in genomic organization and gene regulation.},
journal = {Trends in genetics : TIG},
volume = {39},
number = {2},
pages = {140-153},
doi = {10.1016/j.tig.2022.11.003},
pmid = {36549923},
issn = {0168-9525},
mesh = {*Chromatin/genetics ; *Gene Expression Regulation/genetics ; Genome/genetics ; Genomics ; Regulatory Sequences, Nucleic Acid/genetics ; },
abstract = {Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulating gene expression remains obscure. Recent complementary observations revealed that interactions between CREs frequently result in the formation of small-scale functional modules within topologically associating domains. Such chromatin modules likely emerge from a complex interplay between regulatory machineries assembled at CREs, including site-specific binding of transcription factors. Here, we review the methods that allow identifying chromatin modules, summarize possible mechanisms that steer CRE interactions within these modules, and discuss outstanding challenges to uncover how chromatin modules fit in our current understanding of the functional 3D genome.},
}

*Chromatin/genetics
*Gene Expression Regulation/genetics
Genome/genetics
Genomics
Regulatory Sequences, Nucleic Acid/genetics

@article {pmid36511816,
year = {2022},
author = {Kato, H and Tateishi, K and Iwadate, D and Yamamoto, K and Fujiwara, H and Nakatsuka, T and Kudo, Y and Hayakawa, Y and Ijichi, H and Otsuka, M and Kishikawa, T and Takahashi, R and Miyabayashi, K and Nakai, Y and Hirata, Y and Toyoda, A and Morishita, S and Fujishiro, M},
title = {HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.15690},
pmid = {36511816},
issn = {1349-7006},
abstract = {The molecular subtypes of pancreatic cancer (PC), either classical/progenitor-like or basal/squamous-like, are currently a major topic of research because of their direct association with clinical outcomes. Some transcription factors (TFs) have been reported to be associated with these subtypes. However, the mechanisms by which these molecular signatures of PCs are established remain unknown. Epigenetic regulatory processes, supported by dynamic changes in the chromatin structure, are essential for transcriptional profiles. Previously, we reported the importance of open chromatin profiles in the biological features and transcriptional status of PCs. Here, we aimed to analyze the relationships between three-dimensional (3D) genome structures and the molecular subtypes of human PCs using Hi-C analysis. We observed a correlation of the specific elements of 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops, with the expression of related genes. We focused on HNF1B, a TF that is implicated in the progenitor subtype. Forced expression of HNF1B in squamous-type PC organoids induced the upregulation and downregulation of genes associated with progenitor and squamous subtypes, respectively. Long-range genomic interactions induced by HNF1B were accompanied by compartment modulation and H3K27ac redistribution. We also found that these HNF1B-induced changes in subtype-related gene expression required an intrinsically disordered region, suggesting a possible involvement of phase separation in compartment modulation. Thus, mapping of 3D structural changes induced by TFs, such as HNF1B, may become a useful resource for further understanding the molecular features of PCs.},
}

@article {pmid36493778,
year = {2023},
author = {Alavattam, KG and Mitzelfelt, KA and Bonora, G and Fields, PA and Yang, X and Chiu, HS and Pabon, L and Bertero, A and Palpant, NJ and Noble, WS and Murry, CE},
title = {Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation.},
journal = {Stem cell reports},
volume = {18},
number = {1},
pages = {159-174},
pmid = {36493778},
issn = {2213-6711},
support = {U54 DK107979/DK/NIDDK NIH HHS/United States ; R01 HL146868/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Endothelial Cells ; *Chromatin ; Cell Differentiation/genetics ; Gene Expression Regulation ; },
abstract = {Vascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. The gene-regulatory mechanisms underpinning endothelial specialization are largely unknown, as are the roles of chromatin organization in regulating endothelial cell transcription. To investigate the relationships between chromatin organization and gene expression, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-sequencing assays at specific time points. Long-range intrachromosomal contacts increase over the course of differentiation, accompanied by widespread heteroeuchromatic compartment transitions that are tightly associated with transcription. Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene expression. Chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes essential to vascular biology. Chromatin dynamics guide transcription in endothelial cell development and promote the divergence of endothelial cells from cardiomyocytes.},
}

Humans
*Endothelial Cells
*Chromatin
Cell Differentiation/genetics
Gene Expression Regulation

@article {pmid36482308,
year = {2022},
author = {Yang, JY and Chang, JM},
title = {Pattern recognition of topologically associating domains using deep learning.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 10},
pages = {634},
pmid = {36482308},
issn = {1471-2105},
mesh = {Humans ; Animals ; Mice ; *Deep Learning ; Genomics ; },
abstract = {BACKGROUND: Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines?

RESULTS: To address the above question, we propose a novel task-TAD recognition-as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising, AUC > 0.80, through cross-species and cell-type validation.

CONCLUSIONS: TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable.},
}

Humans
Animals
Mice
*Deep Learning
Genomics

@article {pmid36471076,
year = {2022},
author = {Mach, P and Kos, PI and Zhan, Y and Cramard, J and Gaudin, S and Tünnermann, J and Marchi, E and Eglinger, J and Zuin, J and Kryzhanovska, M and Smallwood, S and Gelman, L and Roth, G and Nora, EP and Tiana, G and Giorgetti, L},
title = {Cohesin and CTCF control the dynamics of chromosome folding.},
journal = {Nature genetics},
volume = {54},
number = {12},
pages = {1907-1918},
pmid = {36471076},
issn = {1546-1718},
mesh = {*Chromosomes/genetics ; },
abstract = {In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.},
}

*Chromosomes/genetics

@article {pmid36469845,
year = {2022},
author = {Zhao, X and Zhu, S and Peng, W and Xue, HH},
title = {The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {209},
number = {12},
pages = {2269-2278},
pmid = {36469845},
issn = {1550-6606},
support = {I01 BX005771/BX/BLRD VA/United States ; R01 AI112579/AI/NIAID NIH HHS/United States ; R01 AI121080/AI/NIAID NIH HHS/United States ; R01 AI139874/AI/NIAID NIH HHS/United States ; },
mesh = {CCCTC-Binding Factor/genetics ; *Chromatin/genetics ; *Cell Cycle Proteins/metabolism ; Genome ; Chromosomes ; Cell Differentiation/genetics ; },
abstract = {T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.},
}

CCCTC-Binding Factor/genetics
*Chromatin/genetics
*Cell Cycle Proteins/metabolism
Genome
Chromosomes
Cell Differentiation/genetics

@article {pmid36466643,
year = {2022},
author = {Wang, X and Yang, B and Zhao, W and Cao, W and Shen, Y and Li, Z and Bao, X},
title = {Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1012377},
pmid = {36466643},
issn = {1664-302X},
abstract = {Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. A high vanillin-tolerant Saccharomyces cerevisiae strain EMV-8 carrying site mutations compared to its parent strain NAN-27 was selected for the analyses. The dynamics of the chromatin structure of eukaryotic cells play a critical role in transcription and the regulation of gene expression and thus the phenotype. Consequently, Hi-C and transcriptome analyses were conducted in EMV-8 and NAN-27 in the log phase with or without vanillin stress to determine the effects of mutations and vanillin disturbance on the dynamics of three-dimensional chromosome organization and the influence of the organization on the transcriptome. The outcomes indicated that the chromosome interaction pattern disturbed by vanillin stress or genetic mutations in the log phase was similar to that in mouse cells. The short chromosomes contact the short chromosomes, and the long chromosomes contact the long chromosomes. In response to vanillin stress, the boundaries of the topologically associating domain (TAD) in the vanillin-tolerant strain EMV-8 were more stable than those in its parent strain NAN-27. The motifs of SFL1, STB3, and NHP6A/B were enriched at TAD boundaries in both EMV-8 and NAN-27 with or without vanillin, indicating that these four genes were probably related to TAD formation. The Indel mutation of YRR1, whose absence was confirmed to benefit vanillin tolerance in EMV-8, caused two new interaction sites that contained three genes, WTM2, PUP1, and ALE1, whose overexpression did not affect vanillin resistance in yeast. Overall, our results revealed that in the log phase, genetic mutations and vanillin disturbance have a negligible effect on three-dimensional chromosome organization, and the reformation or disappearance of TAD boundaries did not show an association with gene expression, which provides an example for studying yeast chromatin structure during stress tolerance using Hi-C technology.},
}

@article {pmid36465116,
year = {2022},
author = {Bi, H and Hou, Y and Wang, J and Xia, Z and Wang, D and Liu, Y and Bao, H and Han, X and Ren, K and Li, E and Yue, F and Ji, P},
title = {Chromatin reconstruction during mouse terminal erythropoiesis.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105554},
pmid = {36465116},
issn = {2589-0042},
abstract = {Mammalian terminal erythropoiesis involves chromatin and nuclear condensation followed by enucleation. Late-stage erythroblasts undergo caspase-mediated nuclear opening that is important for nuclear condensation through partial histone release. It remains unknown the dynamic changes of three-dimensional (3D) genomic organization during terminal erythropoiesis. Here, we used Hi-C to determine the chromatin structural change during primary mouse erythroblast terminal differentiation. We also performed RNA-sequencing and ATAC-sequencing under the same experimental setting to further reveal the genome accessibility and gene expression changes during this process. We found that late-stage terminal erythropoiesis involves global loss of topologically associating domains and establishment of inter-chromosomal interactions of the heterochromatin regions, which are associated with globally increased chromatin accessibility and upregulation of erythroid-related genes.},
}

@article {pmid36460680,
year = {2022},
author = {Zhang, Y and Blanchette, M},
title = {Reference panel guided topological structure annotation of Hi-C data.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {7426},
pmid = {36460680},
issn = {2041-1723},
abstract = {Accurately annotating topological structures (e.g., loops and topologically associating domains) from Hi-C data is critical for understanding the role of 3D genome organization in gene regulation. This is a challenging task, especially at high resolution, in part due to the limited sequencing coverage of Hi-C data. Current approaches focus on the analysis of individual Hi-C data sets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available, and (ii) the vast majority of topological structures are conserved across multiple cell types. Here, we present RefHiC, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate topological structure annotation from a given study sample. We compare RefHiC against tools that do not use reference samples and find that RefHiC outperforms other programs at both topological associating domain and loop annotation across different cell types, species, and sequencing depths.},
}

@article {pmid36448318,
year = {2023},
author = {Miyata, M and Yoshida, J and Takagishi, I and Horie, K},
title = {Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {30},
number = {1},
pages = {},
pmid = {36448318},
issn = {1756-1663},
mesh = {Animals ; Mice ; *CRISPR-Cas Systems ; *Mouse Embryonic Stem Cells ; Gene Editing/methods ; Genome ; Recombinational DNA Repair ; DNA End-Joining Repair ; },
abstract = {The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters and topologically associating domains. To analyse these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster in mouse embryonic stem cells using CRISPR-Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN); and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. Inversion was also detected at similar efficiency. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31-63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.},
}

Animals
Mice
*CRISPR-Cas Systems
*Mouse Embryonic Stem Cells
Gene Editing/methods
Genome
Recombinational DNA Repair
DNA End-Joining Repair

@article {pmid36443333,
year = {2022},
author = {Wang, Y and Mak, TSH and Dattani, S and Garcia-Barcelo, MM and Fu, AX and Yip, KY and Ngan, ES and Tam, PK and Tang, CS and Sham, PC},
title = {Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20423},
pmid = {36443333},
issn = {2045-2322},
mesh = {Humans ; *Hirschsprung Disease/genetics ; Epistasis, Genetic ; Whole Genome Sequencing ; Alleles ; Asian People ; Proto-Oncogene Proteins c-ret/genetics ; },
abstract = {Common variants in RET and NRG1 have been associated with Hirschsprung disease (HSCR), a congenital disorder characterised by incomplete innervation of distal gut, in East Asian (EA) populations. However, the allelic effects so far identified do not fully explain its heritability, suggesting the presence of epistasis, where effect of one genetic variant differs depending on other (modifier) variants. Few instances of epistasis have been documented in complex diseases due to modelling complexity and data challenges. We proposed four epistasis models to comprehensively capture epistasis for HSCR between and within RET and NRG1 loci using whole genome sequencing (WGS) data in EA samples. 65 variants within the Topologically Associating Domain (TAD) of RET demonstrated significant epistasis with the lead enhancer variant (RET+3; rs2435357). These epistatic variants formed two linkage disequilibrium (LD) clusters represented by rs2506026 and rs2506028 that differed in minor allele frequency and the best-supported epistatic model. Intriguingly, rs2506028 is in high LD with one cis-regulatory variant (rs2506030) highlighted previously, suggesting that detected epistasis might be mediated through synergistic effects on transcription regulation of RET. Our findings demonstrated the advantages of WGS data for detecting epistasis, and support the presence of interactive effects of regulatory variants in RET for HSCR.},
}

Humans
*Hirschsprung Disease/genetics
Epistasis, Genetic
Whole Genome Sequencing
Alleles
Asian People
Proto-Oncogene Proteins c-ret/genetics

@article {pmid36409894,
year = {2022},
author = {Zhao, H and Yang, M and Bishop, J and Teng, Y and Cao, Y and Beall, BD and Li, S and Liu, T and Fang, Q and Fang, C and Xin, H and Nützmann, HW and Osbourn, A and Meng, F and Jiang, J},
title = {Identification and functional validation of super-enhancers in Arabidopsis thaliana.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {48},
pages = {e2215328119},
pmid = {36409894},
issn = {1091-6490},
support = {BBS/E/J/00PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Arabidopsis/genetics ; Regulatory Sequences, Nucleic Acid ; *Triterpenes ; Chromatin/genetics ; Mammals/genetics ; },
abstract = {Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131-157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.},
}

Animals
*Arabidopsis/genetics
Regulatory Sequences, Nucleic Acid
*Triterpenes
Chromatin/genetics
Mammals/genetics

@article {pmid36357311,
year = {2022},
author = {Yancoskie, MN and Maritz, C and van Eijk, P and Reed, SH and Naegeli, H},
title = {To incise or not and where: SET-domain methyltransferases know.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2022.10.003},
pmid = {36357311},
issn = {0968-0004},
abstract = {The concept of the histone code posits that histone modifications regulate gene functions once interpreted by epigenetic readers. A well-studied case is trimethylation of lysine 4 of histone H3 (H3K4me3), which is enriched at gene promoters. However, H3K4me3 marks are not needed for the expression of most genes, suggesting extra roles, such as influencing the 3D genome architecture. Here, we highlight an intriguing analogy between the H3K4me3-dependent induction of double-strand breaks in several recombination events and the impact of this same mark on DNA incisions for the repair of bulky lesions. We propose that Su(var)3-9, Enhancer-of-zeste and Trithorax (SET)-domain methyltransferases generate H3K4me3 to guide nucleases into chromatin spaces, the favorable accessibility of which ensures that DNA break intermediates are readily processed, thereby safeguarding genome stability.},
}

@article {pmid36331876,
year = {2022},
author = {Kim, J and Jimenez, DS and Ragipani, B and Zhang, B and Street, LA and Kramer, M and Albritton, SE and Winterkorn, LH and Morao, AK and Ercan, S},
title = {Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36331876},
issn = {2050-084X},
support = {R35 GM130311/GM/NIGMS NIH HHS/United States ; T32 HD007520/HD/NICHD NIH HHS/United States ; R33 EB019784/EB/NIBIB NIH HHS/United States ; R01 DC005991/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Gene Expression Regulation ; Dosage Compensation, Genetic ; X Chromosome/genetics ; },
abstract = {Condensins are molecular motors that compact DNA via linear translocation. In Caenorhabditis elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of recruitment elements on the X-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a 'super rex' composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to the formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.},
}

Animals
*Caenorhabditis elegans/genetics
*Gene Expression Regulation
Dosage Compensation, Genetic
X Chromosome/genetics

@article {pmid36325618,
year = {2022},
author = {Attou, A and Zülske, T and Wedemann, G},
title = {Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.},
journal = {Biophysical journal},
volume = {121},
number = {24},
pages = {4788-4799},
pmid = {36325618},
issn = {1542-0086},
mesh = {CCCTC-Binding Factor/chemistry/genetics/metabolism ; *Nucleosomes ; Protein Binding ; *Cell Cycle Proteins/metabolism ; Chromatin ; },
abstract = {The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.},
}

CCCTC-Binding Factor/chemistry/genetics/metabolism
*Nucleosomes
Protein Binding
*Cell Cycle Proteins/metabolism
Chromatin

@article {pmid36323253,
year = {2022},
author = {Zhu, X and Qi, C and Wang, R and Lee, JH and Shao, J and Bei, L and Xiong, F and Nguyen, PT and Li, G and Krakowiak, J and Koh, SP and Simon, LM and Han, L and Moore, TI and Li, W},
title = {Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization.},
journal = {Cell reports},
volume = {41},
number = {5},
pages = {111576},
pmid = {36323253},
issn = {2211-1247},
support = {R21 GM132778/GM/NIGMS NIH HHS/United States ; R01 HG011633/HG/NHGRI NIH HHS/United States ; R01 CA262623/CA/NCI NIH HHS/United States ; K01 HL143111/HL/NHLBI NIH HHS/United States ; U01 HL156059/HL/NHLBI NIH HHS/United States ; R01 GM136922/GM/NIGMS NIH HHS/United States ; K22 CA204468/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Nuclear Pore Complex Proteins/genetics ; *Nuclear Proteins/genetics ; Transcription Factors/genetics ; Nuclear Pore ; Genome ; Chromatin ; Cell Cycle Proteins/genetics ; },
abstract = {The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.},
}

Humans
*Nuclear Pore Complex Proteins/genetics
*Nuclear Proteins/genetics
Transcription Factors/genetics
Nuclear Pore
Genome
Chromatin
Cell Cycle Proteins/genetics