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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid38755928,
year = {2024},
author = {Yuan, T and Yan, H and Bailey, MLP and Williams, JF and Surovtsev, I and King, MC and Mochrie, SGJ},
title = {Effect of loops on the mean-square displacement of Rouse-model chromatin.},
journal = {Physical review. E},
volume = {109},
number = {4-1},
pages = {044502},
doi = {10.1103/PhysRevE.109.044502},
pmid = {38755928},
issn = {2470-0053},
mesh = {*Chromatin/metabolism/genetics/chemistry ; Models, Molecular ; },
abstract = {Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.},
}

*Chromatin/metabolism/genetics/chemistry
Models, Molecular

@article {pmid38753319,
year = {2024},
author = {Barozzi, I and Slaven, N and Canale, E and Lopes, R and Amorim Monteiro Barbosa, I and Bleu, M and Ivanoiu, D and Pacini, C and Mensa, E and Chambers, A and Bravaccini, S and Ravaioli, S and Gyorffy, B and Dieci, MV and Pruneri, G and Galli, GG and Magnani, L},
title = {A functional survey of the regulatory landscape of estrogen-receptor-positive breast cancer evolution.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-23-1157},
pmid = {38753319},
issn = {2159-8290},
abstract = {Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer (HDBC), potentially explaining ~40% of relapses. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of non-coding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies triggers the emergence of transient features which could ultimately be exploited to hinder the adaptive process.},
}

@article {pmid38743310,
year = {2024},
author = {Semeigazin, A and Iida, S and Minami, K and Tamura, S and Ide, S and Higashi, K and Toyoda, A and Kurokawa, K and Maeshima, K},
title = {Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells.},
journal = {Histochemistry and cell biology},
volume = {},
number = {},
pages = {},
pmid = {38743310},
issn = {1432-119X},
support = {JP23KJ0996//Japan Society for the Promotion of Science/ ; JP23KJ0998//Japan Society for the Promotion of Science/ ; JP22H05606//Japan Society for the Promotion of Science/ ; JP23K17398//Japan Society for the Promotion of Science/ ; JPMJSP2104//Japan Science and Technology Agency/ ; JPMJSP2104//Japan Science and Technology Agency/ ; },
abstract = {Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs) with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.},
}

@article {pmid38712032,
year = {2024},
author = {Loke, P and Zhao, M and Jankovic, D and Hornick, K and Link, V and Souza, COS and Belkaid, Y and Lack, J},
title = {Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3759654/v1},
pmid = {38712032},
abstract = {How macrophages in the tissue environment integrate multiple stimuli will depend on the genetic background of the host, but this is poorly understood. Here, we investigated C57BL/6 and BALB/c strain specific in vivo IL-4 activation of tissue-resident macrophages (TRMs) from the peritoneal cavity. C57BL/6 TRMs are more transcriptionally responsive to IL-4 stimulation, with a greater association of induced genes with super enhancers, induced enhancers, and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling revealed BL/6 specific enrichment of NF-κB, IRF, and STAT motifs. Additionally, IL-4-activated BL/6 TRMs demonstrated an augmented synergistic response upon in vitro lipopolysaccharide (LPS) exposure compared to BALB/c TRMs, despite naïve BALB/c TRMs displaying a more robust transcriptional response to LPS than naïve BL/6 TRMs. Single-cell RNA sequencing (scRNA-seq) analysis of mixed bone marrow chimeric mice indicated that transcriptional differences between BL/6 and BALB/c TRMs, and synergy between IL-4 and LPS, are cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming resulting in strain specific synergistic responses to LPS exposure.},
}

@article {pmid38705995,
year = {2024},
author = {Afanasyev, AY and Kim, Y and Tolokh, IS and Sharakhov, IV and Onufriev, AV},
title = {The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.},
journal = {Epigenetics & chromatin},
volume = {17},
number = {1},
pages = {13},
pmid = {38705995},
issn = {1756-8935},
support = {MCB-1715207//Directorate for Biological Sciences/ ; GM14459//Office of Extramural Research, National Institutes of Health/ ; },
mesh = {Animals ; *Nuclear Lamina/metabolism ; *Drosophila melanogaster/metabolism ; *Chromatin/metabolism ; *Transcription, Genetic ; },
abstract = {BACKGROUND: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE.

RESULTS: In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase.

CONCLUSIONS: At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.},
}

Animals
*Nuclear Lamina/metabolism
*Drosophila melanogaster/metabolism
*Chromatin/metabolism
*Transcription, Genetic

@article {pmid38697116,
year = {2024},
author = {Liu, C and Nagashima, H and Fernando, N and Bass, V and Gopalakrishnan, J and Signorella, S and Montgomery, W and Lim, AI and Harrison, O and Reich, L and Yao, C and Sun, HW and Brooks, SR and Jiang, K and Nagarajan, V and Zhao, Y and Jung, S and Phillips, R and Mikami, Y and Lareau, CA and Kanno, Y and Jankovic, D and Aryee, MJ and Pękowska, A and Belkaid, Y and O'Shea, J and Shih, HY},
title = {A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2024.04.007},
pmid = {38697116},
issn = {1097-4180},
abstract = {Cytokine expression during T cell differentiation is a highly regulated process that involves long-range promoter-enhancer and CTCF-CTCF contacts at cytokine loci. Here, we investigated the impact of dynamic chromatin loop formation within the topologically associating domain (TAD) in regulating the expression of interferon gamma (IFN-γ) and interleukin-22 (IL-22); these cytokine loci are closely located in the genome and are associated with complex enhancer landscapes, which are selectively active in type 1 and type 3 lymphocytes. In situ Hi-C analyses revealed inducible TADs that insulated Ifng and Il22 enhancers during Th1 cell differentiation. Targeted deletion of a 17 bp boundary motif of these TADs imbalanced Th1- and Th17-associated immunity, both in vitro and in vivo, upon Toxoplasma gondii infection. In contrast, this boundary element was dispensable for cytokine regulation in natural killer cells. Our findings suggest that precise cytokine regulation relies on lineage- and developmental stage-specific interactions of 3D chromatin architectures and enhancer landscapes.},
}

@article {pmid38696651,
year = {2024},
author = {Daly, AF and Beckers, A},
title = {The Genetic Pathophysiology and Clinical Management of the TADopathy, X-Linked Acrogigantism.},
journal = {Endocrine reviews},
volume = {},
number = {},
pages = {},
doi = {10.1210/endrev/bnae014},
pmid = {38696651},
issn = {1945-7189},
abstract = {Pituitary gigantism is a rare manifestation of chronic growth hormone (GH) excess that begins before closure of the growth plates. Nearly half of pituitary gigantism patients have an identifiable genetic cause. X-linked acrogigantism (X-LAG; 10% of pituitary gigantism) typically begins during infancy and can lead to the tallest individuals described. In the 10 years since its discovery, about 40 patients have been identified. Patients with X-LAG usually develop mixed GH and prolactin macroadenomas with occasional hyperplasia that secrete copious amounts of GH, and frequently prolactin. Circulating GH releasing hormone (GHRH) is also elevated in a proportion of patients. X-LAG is caused by constitutive or sporadic mosaic duplications at chromosome Xq26.3 that disrupt the normal chromatin architecture of a topologically associating domain (TAD) around the orphan G protein coupled receptor (GPCR), GPR101. This leads to the formation of a neoTAD in which GPR101 over-expression is driven by ectopic enhancers ("TADopathy"). X-LAG has been seen in three families due to transmission of the duplication from affected mothers to sons. GPR101 is a constitutively active receptor with an unknown natural ligand that signals via multiple G proteins and protein kinases A and C to promote GH/prolactin hypersecretion. Treatment of X-LAG is challenging due to the young patient population and resistance to somatostatin analogs; the GH receptor antagonist pegvisomant is often an effective option. GH, insulin-like growth factor 1 (IGF-1) and prolactin hypersecretion and physical overgrowth can be controlled before definitive adult gigantism occurs, often at the cost of permanent hypopituitarism.},
}

@article {pmid38685685,
year = {2024},
author = {Liu, H and Pan, Z and Lin, X and Chen, L and Yang, Q and Zhang, W and Dai, L and Zhang, Y and Li, W and Chen, Y and Peng, K and Wanggou, S and Zeng, F and Li, X},
title = {A potassium-chloride co-transporter with altered genome architecture functions as a suppressor in glioma.},
journal = {Journal of cellular and molecular medicine},
volume = {28},
number = {9},
pages = {e18352},
doi = {10.1111/jcmm.18352},
pmid = {38685685},
issn = {1582-4934},
support = {82270825//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Glioma/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; *Cell Proliferation/genetics ; Cell Line, Tumor ; *Brain Neoplasms/genetics/pathology/metabolism ; *Symporters/genetics/metabolism ; Cell Movement/genetics ; Prognosis ; Receptors, GABA-A/metabolism/genetics ; *K Cl- Cotransporters ; },
abstract = {Gliomas, the most lethal tumours in brain, have a poor prognosis despite accepting standard treatment. Limited benefits from current therapies can be attributed to genetic, epigenetic and microenvironmental cues that affect cell programming and drive tumour heterogeneity. Through the analysis of Hi-C data, we identified a potassium-chloride co-transporter SLC12A5 associated with disrupted topologically associating domain which was downregulated in tumour tissues. Multiple independent glioma cohorts were included to analyse the characterization of SLC12A5 and found it was significantly associated with pathological features, prognostic value, genomic alterations, transcriptional landscape and drug response. We constructed two SLC12A5 overexpression cell lines to verify the function of SLC12A5 that suppressed tumour cell proliferation and migration in vitro. In addition, SLC12A5 was also positively associated with GABAA receptor activity and negatively associated with pro-tumour immune signatures and immunotherapy response. Collectively, our study provides a comprehensive characterization of SLC12A5 in glioma and supports SLC12A5 as a potential suppressor of disease progression.},
}

Humans
*Glioma/genetics/pathology/metabolism
*Gene Expression Regulation, Neoplastic
*Cell Proliferation/genetics
Cell Line, Tumor
*Brain Neoplasms/genetics/pathology/metabolism
*Symporters/genetics/metabolism
Cell Movement/genetics
Prognosis
Receptors, GABA-A/metabolism/genetics
*K Cl- Cotransporters

@article {pmid38669773,
year = {2024},
author = {Wang, X and Yue, F},
title = {Hijacked enhancer-promoter and silencer-promoter loops in cancer.},
journal = {Current opinion in genetics & development},
volume = {86},
number = {},
pages = {102199},
doi = {10.1016/j.gde.2024.102199},
pmid = {38669773},
issn = {1879-0380},
abstract = {Recent work has shown that besides inducing fusion genes, structural variations (SVs) can also contribute to oncogenesis by disrupting the three-dimensional genome organization and dysregulating gene expression. At the chromatin-loop level, SVs can relocate enhancers or silencers from their original genomic loci to activate oncogenes or repress tumor suppressor genes. On a larger scale, different types of alterations in topologically associating domains (TADs) have been reported in cancer, such as TAD expansion, shuffling, and SV-induced neo-TADs. Furthermore, the transformation from normal cells to cancerous cells is usually coupled with active or repressive compartmental switches, and cancer-specific compartments have been proposed. This review discusses the sites, and the other latest advances in studying how SVs disrupt higher-order genome structure in cancer, which in turn leads to oncogene dysregulation. We also highlight the clinical implications of these changes and the challenges ahead in this field.},
}

@article {pmid38669177,
year = {2024},
author = {Kuffler, L and Skelly, DA and Czechanski, A and Fortin, HJ and Munger, SC and Baker, CL and Reinholdt, LG and Carter, GW},
title = {Imputation of 3D genome structure by genetic-epigenetic interaction modeling in mice.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.88222},
pmid = {38669177},
issn = {2050-084X},
support = {R01GM115518/GM/NIGMS NIH HHS/United States ; R35GM133724/GM/NIGMS NIH HHS/United States ; P40OD011102/NH/NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Epigenesis, Genetic ; *Chromatin/metabolism/genetics ; *Genome ; Genetic Variation ; Embryonic Stem Cells/metabolism ; },
abstract = {Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. Analyses of these interactions have previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. Here, we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. We establish the extent and structure of genotype-by-epigenotype interaction using embryonic stem cells derived from Diversity Outbred mice. This mouse population segregates millions of variants from eight inbred founders, enabling precision genetic mapping with extensive genotypic and phenotypic diversity. With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. Our results demonstrate that statistical interactions between genetic variants and chromatin accessibility are common throughout the genome. We found that these interactions occur within the local area of the affected gene, and that this locality corresponds to topologically associated domains (TADs). The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. We confirmed this finding with CTCF ChIP-seq that revealed strain-specific binding in the inbred founder mice. In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF-binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. These findings provide evidence that genetic and epigenetic factors operate within the context of 3D chromatin structure.},
}

Animals
Mice
*Epigenesis, Genetic
*Chromatin/metabolism/genetics
*Genome
Genetic Variation
Embryonic Stem Cells/metabolism

@article {pmid38663040,
year = {2024},
author = {Martitz, A and Schulz, EG},
title = {Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation.},
journal = {Current opinion in genetics & development},
volume = {86},
number = {},
pages = {102198},
doi = {10.1016/j.gde.2024.102198},
pmid = {38663040},
issn = {1879-0380},
abstract = {Genomes are organised through hierarchical structures, ranging from local kilobase-scale cis-regulatory contacts to large chromosome territories. Most notably, (sub)-compartments partition chromosomes according to transcriptional activity, while topologically associating domains (TADs) define cis-regulatory landscapes. The inactive X chromosome in mammals has provided unique insights into the regulation and function of the three-dimensional (3D) genome. Concurrent with silencing of the majority of genes and major alterations of its chromatin state, the X chromosome undergoes profound spatial rearrangements at multiple scales. These include the emergence of megadomains, alterations of the compartment structure and loss of the majority of TADs. Moreover, the Xist locus, which orchestrates X-chromosome inactivation, has provided key insights into regulation and function of regulatory domains. This review provides an overview of recent insights into the control of these structural rearrangements and contextualises them within a broader understanding of 3D genome organisation.},
}

@article {pmid38410476,
year = {2024},
author = {Martins, F and Machado, AL and Ribeiro, A and Oliveira, SM and Carvalho, J and Matthiesen, R and Backman, V and Velho, S},
title = {KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3752760/v2},
pmid = {38410476},
support = {R01 CA228272/CA/NCI NIH HHS/United States ; U54 CA261694/CA/NCI NIH HHS/United States ; U54 CA268084/CA/NCI NIH HHS/United States ; },
abstract = {Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity.},
}

@article {pmid38654598,
year = {2024},
author = {Banerjee, A and Zhang, S and Bahar, I},
title = {Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.},
journal = {Briefings in functional genomics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bfgp/elae014},
pmid = {38654598},
issn = {2041-2657},
support = {R01 GM139297/GF/NIH HHS/United States ; },
abstract = {Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.},
}

@article {pmid38643172,
year = {2024},
author = {Baudic, M and Murata, H and Bosada, FM and Melo, US and Aizawa, T and Lindenbaum, P and van der Maarel, LE and Guedon, A and Baron, E and Fremy, E and Foucal, A and Ishikawa, T and Ushinohama, H and Jurgens, SJ and Choi, SH and Kyndt, F and Le Scouarnec, S and Wakker, V and Thollet, A and Rajalu, A and Takaki, T and Ohno, S and Shimizu, W and Horie, M and Kimura, T and Ellinor, PT and Petit, F and Dulac, Y and Bru, P and Boland, A and Deleuze, JF and Redon, R and Le Marec, H and Le Tourneau, T and Gourraud, JB and Yoshida, Y and Makita, N and Vieyres, C and Makiyama, T and Mundlos, S and Christoffels, VM and Probst, V and Schott, JJ and Barc, J},
title = {TAD boundary deletion causes PITX2-related cardiac electrical and structural defects.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3380},
pmid = {38643172},
issn = {2041-1723},
support = {R21006NN, RPV21014NNA//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.},
}

@article {pmid38613389,
year = {2024},
author = {Farhadova, S and Ghousein, A and Charon, F and Surcis, C and Gomez-Velazques, M and Roidor, C and Di Michele, F and Borensztein, M and De Sario, A and Esnault, C and Noordermeer, D and Moindrot, B and Feil, R},
title = {The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae247},
pmid = {38613389},
issn = {1362-4962},
support = {ANR-18-CE12-0022-02//Agence National de Recherche/ ; ANR-10-LABX-12-01//LabEx EPIGENMED-an ANR 'Investissement d'avenir' programme/ ; EQU202103012763//Fondation pour la Recherche Médicale/ ; 19CS145-00//PlanCancer/ ; //CNRS-INSERM ATIP-Avenir Programme/ ; //Azerbaijan National Academy of Sciences/ ; //Ministry of Education/ ; //University of Montpellier/ ; //La Ligue Nationale Contre le Cancer/ ; },
abstract = {The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain's imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5'-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.},
}

@article {pmid38589516,
year = {2024},
author = {Xiong, K and Zhang, R and Ma, J},
title = {scGHOST: identifying single-cell 3D genome subcompartments.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {38589516},
issn = {1548-7105},
support = {UM1HG011593//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HG012303//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Single-cell Hi-C (scHi-C) technologies allow for probing of genome-wide cell-to-cell variability in three-dimensional (3D) genome organization from individual cells. Computational methods have been developed to reveal single-cell 3D genome features based on scHi-C, including A/B compartments, topologically associating domains and chromatin loops. However, no method exists for annotating single-cell subcompartments, which is important for understanding chromosome spatial localization in single cells. Here we present scGHOST, a single-cell subcompartment annotation method using graph embedding with constrained random walk sampling. Applications of scGHOST to scHi-C data and contact maps derived from single-cell 3D genome imaging demonstrate reliable identification of single-cell subcompartments, offering insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from complex tissues, scGHOST identifies cell-type-specific or allele-specific subcompartments linked to gene transcription across various cell types and developmental stages, suggesting functional implications of single-cell subcompartments. scGHOST is an effective method for annotating single-cell 3D genome subcompartments in a broad range of biological contexts.},
}

@article {pmid38567720,
year = {2024},
author = {Funaya, S and Takahashi, Y and Suzuki, MG and Suzuki, Y and Aoki, F},
title = {H3.1/3.2 regulate the initial progression of the gene expression program.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae214},
pmid = {38567720},
issn = {1362-4962},
support = {19H05752//Ministry of Education, Culture, Sports, Science and Technology/ ; },
abstract = {In mice, transcription from the zygotic genome is initiated at the mid-one-cell stage, and occurs promiscuously in many areas of the genome, including intergenic regions. Regulated transcription from selected genes is established during the two-cell stage. This dramatic change in the gene expression pattern marks the initiation of the gene expression program and is essential for early development. We investigated the involvement of the histone variants H3.1/3.2 in the regulation of changes in gene expression pattern during the two-cell stage. Immunocytochemistry analysis showed low nuclear deposition of H3.1/3.2 in the one-cell stage, followed by a rapid increase in the late two-cell stage. Where chromatin structure is normally closed between the one- and two-cell stages, it remained open until the late two-cell stage when H3.1/3.2 were knocked down by small interfering RNA. Hi-C analysis showed that the formation of the topologically associating domain was disrupted in H3.1/3.2 knockdown (KD) embryos. Promiscuous transcription was also maintained in the late two-cell stage in H3.1/3.2 KD embryos. These results demonstrate that H3.1/3.2 are involved in the initial process of the gene expression program after fertilization, through the formation of a closed chromatin structure to execute regulated gene expression during the two-cell stage.},
}

@article {pmid38565950,
year = {2024},
author = {Ramírez-Cuéllar, J and Ferrari, R and Sanz, RT and Valverde-Santiago, M and García-García, J and Nacht, AS and Castillo, D and Le Dily, F and Neguembor, MV and Malatesta, M and Bonnin, S and Marti-Renom, MA and Beato, M and Vicent, GP},
title = {LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {38565950},
issn = {1460-2075},
support = {PID2019-105173RB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2022-137045OB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2020-115696RB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; 4DGenome" nr: 609989//EC | European Research Council (ERC)/ ; 201820I131//MEC | Consejo Superior de Investigaciones Científicas (CSIC)/ ; MIUR: 2018-2022 MUR:2023-2027//Italian Ministry for University and Research/ ; 2013-2017//Centro de Excelencia Severo Ochoa/ ; },
abstract = {The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.},
}

@article {pmid38561401,
year = {2024},
author = {Serra, F and Nieto-Aliseda, A and Fanlo-Escudero, L and Rovirosa, L and Cabrera-Pasadas, M and Lazarenkov, A and Urmeneta, B and Alcalde-Merino, A and Nola, EM and Okorokov, AL and Fraser, P and Graupera, M and Castillo, SD and Sardina, JL and Valencia, A and Javierre, BM},
title = {p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2821},
pmid = {38561401},
issn = {2041-1723},
support = {CP22/00127//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 4823998//European Hematology Association (EHA)/ ; PID2021-125277OB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
abstract = {Activation of the p53 tumor suppressor triggers a transcriptional program to control cellular response to stress. However, the molecular mechanisms by which p53 controls gene transcription are not completely understood. Here, we uncover the critical role of spatio-temporal genome architecture in this process. We demonstrate that p53 drives direct and indirect changes in genome compartments, topologically associating domains, and DNA loops prior to one hour of its activation, which escort the p53 transcriptional program. Focusing on p53-bound enhancers, we report 340 genes directly regulated by p53 over a median distance of 116 kb, with 74% of these genes not previously identified. Finally, we showcase that p53 controls transcription of distal genes through newly formed and pre-existing enhancer-promoter loops in a cohesin dependent manner. Collectively, our findings demonstrate a previously unappreciated architectural role of p53 as regulator at distinct topological layers and provide a reliable set of new p53 direct target genes that may help designs of cancer therapies.},
}

@article {pmid38553796,
year = {2024},
author = {Li, M and Yang, J and Xiao, R and Liu, Y and Hu, J and Li, T and Wu, P and Zhang, M and Huang, Y and Sun, Y and Li, C},
title = {The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells.},
journal = {Cell proliferation},
volume = {},
number = {},
pages = {e13639},
doi = {10.1111/cpr.13639},
pmid = {38553796},
issn = {1365-2184},
support = {2016YFA0100103//National Key Research and Development Program of China/ ; 2021YFA1100300//National Key Research and Development Program of China/ ; 2021-I2M-1-019//CAMS Innovation Fund for Medical Sciences/ ; 2016-I2M-3-002//CAMS Innovation Fund for Medical Sciences/ ; 32288102//National Natural Science Foundation of China/ ; 32025006//National Natural Science Foundation of China/ ; },
abstract = {Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.},
}

@article {pmid38502563,
year = {2024},
author = {Jeong, D and Shi, G and Li, X and Thirumalai, D},
title = {Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.88564},
pmid = {38502563},
issn = {2050-084X},
support = {CHE 2320256//National Science Foundation/ ; F-0019//Welch Foundation/ ; },
abstract = {Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.},
}

@article {pmid38495565,
year = {2024},
author = {Wall, BPG and Nguyen, M and Harrell, JC and Dozmorov, MG},
title = {Machine and deep learning methods for predicting 3D genome organization.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {38495565},
issn = {2331-8422},
abstract = {Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.},
}

@article {pmid38490101,
year = {2024},
author = {Mizokami, H and Okabe, A and Choudhary, R and Mima, M and Saeda, K and Fukuyo, M and Rahmutulla, B and Seki, M and Goh, BC and Kondo, S and Dochi, H and Moriyama-Kita, M and Misawa, K and Hanazawa, T and Tan, P and Yoshizaki, T and Fullwood, MJ and Kaneda, A},
title = {Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma.},
journal = {EBioMedicine},
volume = {102},
number = {},
pages = {105057},
doi = {10.1016/j.ebiom.2024.105057},
pmid = {38490101},
issn = {2352-3964},
abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor endemic to Southern China and Southeast Asia. While previous studies have revealed a low frequency of gene mutations in NPC, its epigenomic aberrations are not fully elucidated apart from DNA hypermethylation. Epigenomic rewiring and enhancer dysregulation, such as enhancer hijacking due to genomic structural changes or extrachromosomal DNA, drive cancer progression.

METHODS: We conducted Hi-C, 4C-seq, ChIP-seq, and RNA-seq analyses to comprehensively elucidate the epigenome and interactome of NPC using C666-1 EBV(+)-NPC cell lines, NP69T immortalized nasopharyngeal epithelial cells, clinical NPC biopsy samples, and in vitro EBV infection in HK1 and NPC-TW01 EBV(-) cell lines.

FINDINGS: In C666-1, the EBV genome significantly interacted with inactive B compartments of host cells; the significant association of EBV-interacting regions (EBVIRs) with B compartment was confirmed using clinical NPC and in vitro EBV infection model. EBVIRs in C666-1 showed significantly higher levels of active histone modifications compared with NP69T. Aberrant activation of EBVIRs after EBV infection was validated using in vitro EBV infection models. Within the EBVIR-overlapping topologically associating domains, 14 H3K4me3(+) genes were significantly upregulated in C666-1. Target genes of EBVIRs including PLA2G4A, PTGS2 and CITED2, interacted with the enhancers activated in EBVIRs and were highly expressed in NPC, and their knockdown significantly reduced cell proliferation.

INTERPRETATION: The EBV genome contributes to NPC tumorigenesis through "enhancer infestation" by interacting with the inactive B compartments of the host genome and aberrantly activating enhancers.

FUNDING: The funds are listed in the Acknowledgements section.},
}

@article {pmid38481440,
year = {2024},
author = {Caruso, M and Mazzatenta, D and Asioli, S and Costanza, G and Trivellin, G and Franke, M and Abboud, D and Hanson, J and Raverot, V and Pétrossians, P and Beckers, A and Cappa, M and Daly, AF},
title = {Case report: Management of pediatric gigantism caused by the TADopathy, X-linked acrogigantism.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1345363},
pmid = {38481440},
issn = {1664-2392},
abstract = {X-linked acrogigantism (X-LAG) is a rare form of pituitary gigantism that is associated with growth hormone (GH) and prolactin-secreting pituitary adenomas/pituitary neuroendocrine tumors (PitNETs) that develop in infancy. It is caused by a duplication on chromosome Xq26.3 that leads to the misexpression of the gene GPR101, a constitutively active stimulator of pituitary GH and prolactin secretion. GPR101 normally exists within its own topologically associating domain (TAD) and is insulated from surrounding regulatory elements. X-LAG is a TADopathy in which the duplication disrupts a conserved TAD border, leading to a neo-TAD in which ectopic enhancers drive GPR101 over-expression, thus causing gigantism. Here we trace the full diagnostic and therapeutic pathway of a female patient with X-LAG from 4C-seq studies demonstrating the neo-TAD through medical and surgical interventions and detailed tumor histopathology. The complex nature of treating young children with X-LAG is illustrated, including the achievement of hormonal control using a combination of neurosurgery and adult doses of first-generation somatostatin analogs.},
}

@article {pmid38473917,
year = {2024},
author = {Plaisancié, J and Chesneau, B and Fares-Taie, L and Rozet, JM and Pechmeja, J and Noero, J and Gaston, V and Bailleul-Forestier, I and Calvas, P and Chassaing, N},
title = {Structural Variant Disrupting the Expression of the Remote FOXC1 Gene in a Patient with Syndromic Complex Microphthalmia.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
doi = {10.3390/ijms25052669},
pmid = {38473917},
issn = {1422-0067},
abstract = {Ocular malformations (OMs) arise from early defects during embryonic eye development. Despite the identification of over 100 genes linked to this heterogeneous group of disorders, the genetic cause remains unknown for half of the individuals following Whole-Exome Sequencing. Diagnosis procedures are further hampered by the difficulty of studying samples from clinically relevant tissue, which is one of the main obstacles in OMs. Whole-Genome Sequencing (WGS) to screen for non-coding regions and structural variants may unveil new diagnoses for OM individuals. In this study, we report a patient exhibiting a syndromic OM with a de novo 3.15 Mb inversion in the 6p25 region identified by WGS. This balanced structural variant was located 100 kb away from the FOXC1 gene, previously associated with ocular defects in the literature. We hypothesized that the inversion disrupts the topologically associating domain of FOXC1 and impairs the expression of the gene. Using a new type of samples to study transcripts, we were able to show that the patient presented monoallelic expression of FOXC1 in conjunctival cells, consistent with the abolition of the expression of the inverted allele. This report underscores the importance of investigating structural variants, even in non-coding regions, in individuals affected by ocular malformations.},
}

@article {pmid38455359,
year = {2023},
author = {Pathak, RU and Phanindhar, K and Mishra, RK},
title = {Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1326933},
doi = {10.3389/fmolb.2023.1326933},
pmid = {38455359},
issn = {2296-889X},
abstract = {The hierarchical structure of eukaryotic genomes has regulatory layers, one of them being epigenetic "indexing" of the genome that leads to cell-type-specific patterns of gene expression. By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using scaffold/matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large-scale genome-wide mapping of S/MARs has begun to uncover these aspects of genome organization. A recent genome-wide study showed the association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that the multitude of TE-derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. In this study, we provide an insight that TE-driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs, as elements that can hop through the genome along with regulatory capabilities, may provide an active mechanism of genome evolution leading to the emergence of novel features in biological systems. The significance is that a genome-wide study mapping developmental S/MARs reveals an intriguing link between these elements and TEs. This article highlights the potential of the TE-S/MAR combination to drive evolution by restructuring and shaping the genome.},
}

@article {pmid38452764,
year = {2024},
author = {Kim, KL and Rahme, GJ and Goel, VY and El Farran, CA and Hansen, AS and Bernstein, BE},
title = {Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2024.02.007},
pmid = {38452764},
issn = {1097-4164},
abstract = {Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.},
}

@article {pmid38449288,
year = {2024},
author = {Liu, E and Lyu, H and Liu, Y and Fu, L and Cheng, X and Yin, X},
title = {Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae138},
pmid = {38449288},
issn = {1367-4811},
abstract = {MOTIVATION: Topologically associating domains (TADs) are fundamental building blocks of three-dimensional genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity.

RESULTS: We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels.

AVAILABILITY: scKTLD is freely available at https://github.com/lhqxinghun/scKTLD.

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

@article {pmid38448979,
year = {2024},
author = {Liu, Y and Zheng, Z and Wang, C and Wang, Y and Sun, X and Ren, Z and Yang, X and Yang, X},
title = {Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens.},
journal = {Journal of animal science and biotechnology},
volume = {15},
number = {1},
pages = {40},
pmid = {38448979},
issn = {1674-9782},
support = {32372910 and 32102567//the National Science Foundation of China/ ; 2022KJXX-13, 2023-YBNY-144 and K3031223077//Program for Shaanxi Science and Technology/ ; 2022GD-TSLD-46-0302//Program for Shaanxi Science and Technology/ ; },
abstract = {BACKGROUND: Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate. Three-dimensional (3D) chromatin architecture takes part in disease processing by regulating transcriptional reprogramming. The study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver (FLS) and reveal their effect on hepatic transcriptional reprogramming in laying hens.

RESULTS: Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposition as well as higher total triglyceride and cholesterol in serum. A/B compartment switching, topologically associating domain (TAD) and chromatin loop changes are identified by high-throughput/resolution chromosome conformation capture (HiC) technology. Targeted genes of these alternations in hepatic 3D genome organization significantly enrich pathways related to lipid metabolism and hepatic damage. H3K27ac differential peaks and differential expression genes (DEGs) identified through RNA-seq analysis are also enriched in these pathways. Notably, certain DEGs are found to correspond with changes in 3D chromatin structure and H3K27ac binding in their promoters. DNA motif analysis reveals that candidate transcription factors are implicated in regulating transcriptional reprogramming. Furthermore, disturbed folate metabolism is observed, as evidenced by lower folate levels and altered enzyme expression.

CONCLUSION: Our findings establish a link between transcriptional reprogramming changes and 3D chromatin structure variations during early FLS formation, which provides candidate transcription factors and folate as targets for FLS prevention or treatment.},
}

@article {pmid38432398,
year = {2024},
author = {Fraile, A and Cebrián, J and Thuissard-Vasallo, I and Pérez-Martín, S and Casado, R and Gil-Fournier, B and Alonso-Martín, J and Tamargo, J and Caballero, R and Delpón, E and Cosío, FG},
title = {Coexistent HCN4 and GATA5 rare variants and Atrial Fibrillation in a large Spanish Family.},
journal = {The Canadian journal of cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cjca.2024.02.024},
pmid = {38432398},
issn = {1916-7075},
abstract = {BACKGROUND: Familial association of atrial fibrillation (AF) can involve single gene variants related to known arrhythmogenic mechanisms; however, genome-wide association studies often disclose complex genetic variants in familial and non-familial AF, making it difficult to relate to known pathogenetic mechanisms.

METHODS: The finding of 4 siblings with AF led to studying 47 members of a family. Long-term Holter monitoring (298 hours average) ruled out silent AFWhole-exome sequencing was performed and variants shared by the index cases were filtered and prioritized according to current recommendations. HCN4 currents (IHCN4) were recorded in Chinese hamster ovary cells expressing human p.P1163H and/or native Hcn4 channels using the patch-clamp technique and topologically associated domain analysis of GATA5 variant carriers were performed.

RESULTS: The clinical study diagnosed 2 more AF cases. Five family members carried the heterozygous p.P1163H, HCN4 variant, 14 the intronic 20,61040536,G,A GATA5 rare variant, and 9 carried both variants (HCN4+GATA5). Five of the 6 AF cases (onset age ranging 33-70 years) carried both variants and one the GATA5 variant alone. Multivariate analysis showed that the presence of HCN4+GATA5 variants significantly and independently increased AF risk [OR=32.740 (1.812-591.408)] and not age, hypertension or overweight. Functional testing showed that IHcn4 generated by heterozygous p.P1163H were normal. Topologically associating domain analysis suggested that GATA5 could affect the expression of many genes, including those encoding microRNA-1.

CONCLUSION: The coincidence of two rare gene variants was independently associated with AF, but functional studies do not allow the postulation of the arrhythmogenic mechanism(s) involved.},
}

@article {pmid38402218,
year = {2024},
author = {Torres, DE and Kramer, HM and Tracanna, V and Fiorin, GL and Cook, DE and Seidl, MF and Thomma, BPHJ},
title = {Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1701},
pmid = {38402218},
issn = {2041-1723},
support = {project 831.15.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; LT000627/2014-L//Human Frontier Science Program (HFSP)/ ; 2018-67013-28492//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.},
}

@article {pmid38355805,
year = {2024},
author = {Patta, I and Zand, M and Lee, L and Mishra, S and Bortnick, A and Lu, H and Prusty, A and McArdle, S and Mikulski, Z and Wang, HY and Cheng, CS and Fisch, KM and Hu, M and Murre, C},
title = {Nuclear morphology is shaped by loop-extrusion programs.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38355805},
issn = {1476-4687},
abstract = {It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces[1-3]. However, how polymorphonuclear structures are assembled remains unknown[4]. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin[5]-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted in enrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.},
}

@article {pmid38346246,
year = {2024},
author = {Liu, S and Athreya, A and Lao, Z and Zhang, B},
title = {From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.},
journal = {Annual review of biophysics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biophys-030822-032650},
pmid = {38346246},
issn = {1936-1238},
abstract = {Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo. Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid38280381,
year = {2024},
author = {Nakamura, T and Ueda, J and Mizuno, S and Honda, K and Kazuno, AA and Yamamoto, H and Hara, T and Takata, A},
title = {Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100488},
doi = {10.1016/j.xgen.2024.100488},
pmid = {38280381},
issn = {2666-979X},
abstract = {Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.},
}

@article {pmid38254945,
year = {2023},
author = {Murtaza, G and Jain, A and Hughes, M and Wagner, J and Singh, R},
title = {A Comprehensive Evaluation of Generalizability of Deep Learning-Based Hi-C Resolution Improvement Methods.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/genes15010054},
pmid = {38254945},
issn = {2073-4425},
support = {1R35HG011939-01/NH/NIH HHS/United States ; GR5245041/NIST/NIST DOC/United States ; },
abstract = {Hi-C is a widely used technique to study the 3D organization of the genome. Due to its high sequencing cost, most of the generated datasets are of a coarse resolution, which makes it impractical to study finer chromatin features such as Topologically Associating Domains (TADs) and chromatin loops. Multiple deep learning-based methods have recently been proposed to increase the resolution of these datasets by imputing Hi-C reads (typically called upscaling). However, the existing works evaluate these methods on either synthetically downsampled datasets, or a small subset of experimentally generated sparse Hi-C datasets, making it hard to establish their generalizability in the real-world use case. We present our framework-Hi-CY-that compares existing Hi-C resolution upscaling methods on seven experimentally generated low-resolution Hi-C datasets belonging to various levels of read sparsities originating from three cell lines on a comprehensive set of evaluation metrics. Hi-CY also includes four downstream analysis tasks, such as TAD and chromatin loops recall, to provide a thorough report on the generalizability of these methods. We observe that existing deep learning methods fail to generalize to experimentally generated sparse Hi-C datasets, showing a performance reduction of up to 57%. As a potential solution, we find that retraining deep learning-based methods with experimentally generated Hi-C datasets improves performance by up to 31%. More importantly, Hi-CY shows that even with retraining, the existing deep learning-based methods struggle to recover biological features such as chromatin loops and TADs when provided with sparse Hi-C datasets. Our study, through the Hi-CY framework, highlights the need for rigorous evaluation in the future. We identify specific avenues for improvements in the current deep learning-based Hi-C upscaling methods, including but not limited to using experimentally generated datasets for training.},
}

@article {pmid38244545,
year = {2024},
author = {Wahl, N and Espeso-Gil, S and Chietera, P and Nagel, A and Laighneach, A and Morris, DW and Rajarajan, P and Akbarian, S and Dechant, G and Apostolova, G},
title = {SATB2 organizes the 3D genome architecture of cognition in cortical neurons.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2023.12.024},
pmid = {38244545},
issn = {1097-4164},
abstract = {The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.},
}

@article {pmid38238628,
year = {2024},
author = {Hung, TC and Kingsley, DM and Boettiger, AN},
title = {Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38238628},
issn = {1546-1718},
support = {DP2GM132935A//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01DK127419//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.},
}

@article {pmid38218905,
year = {2024},
author = {Hua, D and Gu, M and Zhang, X and Du, Y and Xie, H and Qi, L and Du, X and Bai, Z and Zhu, X and Tian, D},
title = {DiffDomain enables identification of structurally reorganized topologically associating domains.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {502},
pmid = {38218905},
issn = {2041-1723},
support = {2022A1515010043//Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province)/ ; KCXFZ20211020172545006//Shenzhen Science and Technology Innovation Commission/ ; 12171198//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20210101147JC//Department of Science and Technology of Jilin Province (Jilin Province Science and Technology Department)/ ; },
abstract = {Topologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the early stages of development. Here, we present DiffDomain, an algorithm leveraging high-dimensional random matrix theory to identify structurally reorganized TADs using high-throughput chromosome conformation capture (Hi-C) contact maps. Method comparison using multiple real Hi-C datasets reveals that DiffDomain outperforms alternative methods for false positive rates, true positive rates, and identifying a new subtype of reorganized TADs. Applying DiffDomain to Hi-C data from different cell types and disease states demonstrates its biological relevance. Identified reorganized TADs are associated with structural variations and epigenomic changes such as changes in CTCF binding sites. By applying to a single-cell Hi-C data from mouse neuronal development, DiffDomain can identify reorganized TADs between cell types with reasonable reproducibility using pseudo-bulk Hi-C data from as few as 100 cells per condition. Moreover, DiffDomain reveals differential cell-to-population variability and heterogeneous cell-to-cell variability in TADs. Therefore, DiffDomain is a statistically sound method for better comparative analysis of TADs using both Hi-C and single-cell Hi-C data.},
}

@article {pmid38213897,
year = {2023},
author = {Rosen, J and Lee, L and Abnousi, A and Chen, J and Wen, J and Hu, M and Li, Y},
title = {HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {931-939},
pmid = {38213897},
issn = {2001-0370},
abstract = {High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization. Most recently, Hi-C-derived enrichment-based technologies, including HiChIP and PLAC-seq, offer attractive alternatives due to their high signal-to-noise ratio and low cost. While a series of computational tools have been developed for Hi-C data, methods tailored for HiChIP and PLAC-seq data are still under development. Here we present HPTAD, a computational method to identify topologically associating domains (TADs) from HiChIP and PLAC-seq data. We performed comprehensive benchmark analysis to demonstrate its superior performance over existing TAD callers designed for Hi-C data. HPTAD is freely available at https://github.com/yunliUNC/HPTAD.},
}

@article {pmid38206813,
year = {2024},
author = {Zhang, M and Huang, H and Li, J and Wu, Q},
title = {ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry.},
journal = {Cell reports},
volume = {43},
number = {1},
pages = {113663},
doi = {10.1016/j.celrep.2023.113663},
pmid = {38206813},
issn = {2211-1247},
abstract = {The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.},
}

@article {pmid37748139,
year = {2024},
author = {Tang, B and Wang, X and He, H and Chen, R and Qiao, G and Yang, Y and Xu, Z and Wang, L and Dong, Q and Yu, J and Zhang, MQ and Shi, M and Wang, J},
title = {Aging-disturbed FUS phase transition impairs hematopoietic stem cells by altering chromatin structure.},
journal = {Blood},
volume = {143},
number = {2},
pages = {124-138},
doi = {10.1182/blood.2023020539},
pmid = {37748139},
issn = {1528-0020},
abstract = {Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity. The molecular mechanisms behind this phenomenon are not fully understood. Here, we observed that the expression of FUS is increased in aged HSCs, and enforced FUS recapitulates the phenotype of aged HSCs through arginine-glycine-glycine-mediated aberrant FUS phase transition. By using Fus-gfp mice, we observed that FUShigh HSCs exhibit compromised FUS mobility and resemble aged HSCs both functionally and transcriptionally. The percentage of FUShigh HSCs is increased upon physiological aging and replication stress, and FUSlow HSCs of aged mice exhibit youthful function. Mechanistically, FUShigh HSCs exhibit a different global chromatin organization compared with FUSlow HSCs, which is observed in aged HSCs. Many topologically associating domains (TADs) are merged in aged HSCs because of the compromised binding of CCCTC-binding factor with chromatin, which is invoked by aberrant FUS condensates. It is notable that the transcriptional alteration between FUShigh and FUSlow HSCs originates from the merged TADs and is enriched in HSC aging-related genes. Collectively, this study reveals for the first time that aberrant FUS mobility promotes HSC aging by altering chromatin structure.},
}

@article {pmid38168424,
year = {2023},
author = {Li, Y and Xiao, P and Boadu, F and Goldkamp, AK and Nirgude, S and Cheng, J and Hagen, DE and Kalish, JM and Rivera, RM},
title = {The counterpart congenital overgrowth syndromes Beckwith-Wiedemann Syndrome in human and large offspring syndrome in bovine involve alterations in DNA methylation, transcription, and chromatin configuration.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.14.23299981},
pmid = {38168424},
abstract = {Beckwith-Wiedemann Syndrome (BWS, OMIM #130650) is a congenital epigenetic disorder in humans which affects approximately 1 in 10,340 children. The incidence is likely an underestimation as the condition is usually recognized based on observable phenotypes at birth. BWS children have up to a 28% risk of developing tumors and currently, only 80% of patients can be corroborated molecularly (epimutations/variants). It is unknown how the subtypes of this condition are molecularly similar/dissimilar globally, therefore there is a need to deeply characterize the syndrome at the molecular level. Here we characterize the methylome, transcriptome and chromatin configuration of 18 BWS individuals together with the animal model of the condition, the bovine large offspring syndrome (LOS). Sex specific comparisons are performed for a subset of the BWS patients and LOS. Given that this epigenetic overgrowth syndrome has been characterized as a loss-of-imprinting condition, parental allele-specific comparisons were performed using the bovine animal model. In general, the differentially methylated regions (DMRs) detected in BWS and LOS showed significant enrichment for CTCF binding sites. Altered chromosome compartments in BWS and LOS were positively correlated with gene expression changes, and the promoters of differentially expressed genes showed significant enrichment for DMRs, differential topologically associating domains, and differential A/B compartments in some comparisons of BWS subtypes and LOS. We show shared regions of dysregulation between BWS and LOS, including several HOX gene clusters, and also demonstrate that altered DNA methylation differs between the clinically epigenetically identified BWS patients and those identified as having DNA variants (i.e. CDKN1C microdeletion). Lastly, we highlight additional genes and genomic regions that have the potential to serve as targets for biomarker development to improve current molecular methodologies. In summary, our results suggest that genome-wide alternation of chromosome architecture, which is partially caused by DNA methylation changes, also contribute to the development of BWS and LOS.},
}

@article {pmid38167349,
year = {2024},
author = {Sun, L and Zhou, J and Xu, X and Liu, Y and Ma, N and Liu, Y and Nie, W and Zou, L and Deng, XW and He, H},
title = {Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {35},
pmid = {38167349},
issn = {2041-1723},
abstract = {Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.},
}

@article {pmid38134876,
year = {2023},
author = {Malachowski, T and Chandradoss, KR and Boya, R and Zhou, L and Cook, AL and Su, C and Pham, K and Haws, SA and Kim, JH and Ryu, HS and Ge, C and Luppino, JM and Nguyen, SC and Titus, KR and Gong, W and Wallace, O and Joyce, EF and Wu, H and Rojas, LA and Phillips-Cremins, JE},
title = {Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.},
journal = {Cell},
volume = {186},
number = {26},
pages = {5840-5858.e36},
doi = {10.1016/j.cell.2023.11.019},
pmid = {38134876},
issn = {1097-4172},
abstract = {Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.},
}

@article {pmid38129077,
year = {2023},
author = {Jessberger, G and Várnai, C and Stocsits, RR and Tang, W and Stary, G and Peters, JM},
title = {Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277865.123},
pmid = {38129077},
issn = {1549-5469},
abstract = {Paternal genomes are compacted during spermiogenesis and decompacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in Xenopus egg extracts. In pronuclei, chromatin compartmentalization increases, but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, and cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.},
}

@article {pmid38102116,
year = {2023},
author = {Xiao, M and Kondo, S and Nomura, M and Kato, S and Nishimura, K and Zang, W and Zhang, Y and Akashi, T and Viny, A and Shigehiro, T and Ikawa, T and Yamazaki, H and Fukumoto, M and Tanaka, A and Hayashi, Y and Koike, Y and Aoyama, Y and Ito, H and Nishikawa, H and Kitamura, T and Kanai, A and Yokoyama, A and Fujiwara, T and Goyama, S and Noguchi, H and Lee, SC and Toyoda, A and Hinohara, K and Abdel-Wahab, O and Inoue, D},
title = {BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8372},
pmid = {38102116},
issn = {2041-1723},
support = {21ck0106697h0001//Japan Agency for Medical Research and Development (AMED)/ ; JP20H00537//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20H03717//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF (ncBAF). While cBAF and PBAF regulate fates of multiple cell types, roles for ncBAF in hematopoietic stem cells (HSCs) have not been investigated. Motivated by recent discovery of disrupted expression of BRD9, an essential component of ncBAF, in multiple cancers, including clonal hematopoietic disorders, we evaluate here the role of BRD9 in normal and malignant HSCs. BRD9 loss enhances chromatin accessibility, promoting myeloid lineage skewing while impairing B cell development. BRD9 significantly colocalizes with CTCF, whose chromatin recruitment is augmented by BRD9 loss, leading to altered chromatin state and expression of myeloid-related genes within intact topologically associating domains. These data uncover ncBAF as critical for cell fate specification in HSCs via three-dimensional regulation of gene expression and illuminate roles for ncBAF in normal and malignant hematopoiesis.},
}

@article {pmid38092881,
year = {2023},
author = {Fok, ET and Moorlag, SJCFM and Negishi, Y and Groh, LA and Dos Santos, JC and Gräwe, C and Monge, VV and Craenmehr, DDD and van Roosmalen, M and da Cunha Jolvino, DP and Migliorini, LB and Neto, AS and Severino, P and Vermeulen, M and Joosten, LAB and Netea, MG and Fanucchi, S and Mhlanga, MM},
title = {A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38092881},
issn = {1546-1718},
abstract = {Inflammation is characterized by a biphasic cycle consisting initially of a proinflammatory phase that is subsequently resolved by anti-inflammatory processes. Interleukin-1β (IL-1β) is a master regulator of proinflammation and is encoded within the same topologically associating domain (TAD) as IL-37, which is an anti-inflammatory cytokine that opposes the function of IL-1β. Within this TAD, we identified a long noncoding RNA called AMANZI, which negatively regulates IL-1β expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced proinflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL-1β and IL-37, thereby regulating two functionally opposed states of inflammation from within a single TAD.},
}

@article {pmid38084924,
year = {2023},
author = {Balasubramanian, D and Borges Pinto, P and Grasso, A and Vincent, S and Tarayre, H and Lajoignie, D and Ghavi-Helm, Y},
title = {Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad1183},
pmid = {38084924},
issn = {1362-4962},
support = {Enhancer3D 759708/ERC_/European Research Council/International ; },
abstract = {Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.},
}

@article {pmid38076897,
year = {2023},
author = {Rossini, R and Oshaghi, M and Nekrasov, M and Bellanger, A and Domaschenz, R and Dijkwel, Y and Abdelhalim, M and Collas, P and Tremethick, D and Paulsen, J},
title = {Multi-level 3D genome organization deteriorates during breast cancer progression.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.26.568711},
pmid = {38076897},
abstract = {Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.},
}

@article {pmid38061928,
year = {2023},
author = {Long, Y and Wendel, JF and Zhang, X and Wang, M},
title = {Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.11.009},
pmid = {38061928},
issn = {1878-4372},
abstract = {Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.},
}

@article {pmid38049665,
year = {2023},
author = {Leeman-Neill, RJ and Song, D and Bizarro, J and Wacheul, L and Rothschild, G and Singh, S and Yang, Y and Sarode, AY and Gollapalli, K and Wu, L and Zhang, W and Chen, Y and Lauring, MC and Whisenant, DE and Bhavsar, S and Lim, J and Swerdlow, SH and Bhagat, G and Zhao, Q and Berchowitz, LE and Lafontaine, DLJ and Wang, J and Basu, U},
title = {Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38049665},
issn = {1546-1718},
support = {R01AI134988//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; RO1AI143897//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI099195//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; DOD W81XWH-18-1-0394//U.S. Department of Defense (United States Department of Defense)/ ; GM124633//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32CA265828//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Whole-genome sequencing of longitudinal tumor pairs representing transformation of follicular lymphoma to high-grade B cell lymphoma with MYC and BCL2 rearrangements (double-hit lymphoma) identified coding and noncoding genomic alterations acquired during lymphoma progression. Many of these transformation-associated alterations recurrently and focally occur at topologically associating domain resident regulatory DNA elements, including H3K4me3 promoter marks located within H3K27ac super-enhancer clusters in B cell non-Hodgkin lymphoma. One region found to undergo recurrent alteration upon transformation overlaps a super-enhancer affecting the expression of the PAX5/ZCCHC7 gene pair. ZCCHC7 encodes a subunit of the Trf4/5-Air1/2-Mtr4 polyadenylation-like complex and demonstrated copy number gain, chromosomal translocation and enhancer retargeting-mediated transcriptional upregulation upon lymphoma transformation. Consequently, lymphoma cells demonstrate nucleolar dysregulation via altered noncoding 5.8S ribosomal RNA processing. We find that a noncoding mutation acquired during lymphoma progression affects noncoding rRNA processing, thereby rewiring protein synthesis leading to oncogenic changes in the lymphoma proteome.},
}

@article {pmid38017545,
year = {2023},
author = {Llinàs-Arias, P and Ensenyat-Mendez, M and Íñiguez-Muñoz, S and Orozco, JIJ and Valdez, B and Salomon, MP and Matsuba, C and Solivellas-Pieras, M and Bedoya-López, AF and Sesé, B and Mezger, A and Ormestad, M and Unzueta, F and Strand, SH and Boiko, AD and Hwang, ES and Cortés, J and DiNome, ML and Esteller, M and Lupien, M and Marzese, DM},
title = {Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors.},
journal = {Molecular cancer},
volume = {22},
number = {1},
pages = {190},
pmid = {38017545},
issn = {1476-4598},
support = {CD22/00026//Instituto de Salud Carlos III/ ; CPII22/00004//Instituto de Salud Carlos III/ ; IMP21/10//IDISBA - Impetus Call/ ; Margalida Comas//Govern de les Illes Balears/ ; },
abstract = {BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive subtype that exhibits a high incidence of distant metastases and lacks targeted therapeutic options. Here we explored how the epigenome contributes to matrix metalloprotease (MMP) dysregulation impacting tumor invasion, which is the first step of the metastatic process.

METHODS: We combined RNA expression and chromatin interaction data to identify insulator elements potentially associated with MMP gene expression and invasion. We employed CRISPR/Cas9 to disrupt the CCCTC-Binding Factor (CTCF) binding site on an insulator element downstream of the MMP8 gene (IE8) in two TNBC cellular models. We characterized these models by combining Hi-C, ATAC-seq, and RNA-seq with functional experiments to determine invasive ability. The potential of our findings to predict the progression of ductal carcinoma in situ (DCIS), was tested in data from clinical specimens.

RESULTS: We explored the clinical relevance of an insulator element located within the Chr11q22.2 locus, downstream of the MMP8 gene (IE8). This regulatory element resulted in a topologically associating domain (TAD) boundary that isolated nine MMP genes into two anti-correlated expression clusters. This expression pattern was associated with worse relapse-free (HR = 1.57 [1.06 - 2.33]; p = 0.023) and overall (HR = 2.65 [1.31 - 5.37], p = 0.005) survival of TNBC patients. After CRISPR/Cas9-mediated disruption of IE8, cancer cells showed a switch in the MMP expression signature, specifically downregulating the pro-invasive MMP1 gene and upregulating the antitumorigenic MMP8 gene, resulting in reduced invasive ability and collagen degradation. We observed that the MMP expression pattern predicts DCIS that eventually progresses into invasive ductal carcinomas (AUC = 0.77, p < 0.01).

CONCLUSION: Our study demonstrates how the activation of an IE near the MMP8 gene determines the regional transcriptional regulation of MMP genes with opposing functional activity, ultimately influencing the invasive properties of aggressive forms of breast cancer.},
}

@article {pmid38017297,
year = {2023},
author = {Jehangir, M and Ahmad, SF and Singchat, W and Panthum, T and Thong, T and Aramsirirujiwet, P and Lisachov, A and Muangmai, N and Han, K and Koga, A and Duengkae, P and Srikulnath, K},
title = {Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome.},
journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology},
volume = {31},
number = {4},
pages = {34},
pmid = {38017297},
issn = {1573-6849},
support = {P-20-52605//National Science and Technology Development Agency (NSTDA)/ ; },
abstract = {Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.},
}

@article {pmid38014261,
year = {2023},
author = {Zhao, H and Lin, Y and Lin, E and Liu, F and Shu, L and Jing, D and Wang, B and Wang, M and Shan, F and Zhang, L and Lam, JC and Midla, SC and Giardine, BM and Keller, CA and Hardison, RC and Blobel, GA and Zhang, H},
title = {Genome folding principles revealed in condensin-depleted mitotic chromosomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.09.566494},
pmid = {38014261},
abstract = {During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co- depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1Π and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensin-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.},
}

@article {pmid38013620,
year = {2023},
author = {Singh, AK and Walavalkar, K and Tavernari, D and Ciriello, G and Notani, D and Sabarinathan, R},
title = {Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers.},
journal = {Molecular oncology},
volume = {},
number = {},
pages = {},
doi = {10.1002/1878-0261.13559},
pmid = {38013620},
issn = {1878-0261},
abstract = {HPV infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome-wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and TADs. HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long-range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi-C and 4C-seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~500kb apart), leading to allele-specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.},
}

@article {pmid37976174,
year = {2023},
author = {Siqueira, E and Kim, BH and Reser, L and Chow, R and Delaney, K and Esteller, M and Ross, MM and Shabanowitz, J and Hunt, DF and Guil, S and Ausiö, J},
title = {Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells.},
journal = {Epigenetics},
volume = {18},
number = {1},
pages = {2276425},
doi = {10.1080/15592294.2023.2276425},
pmid = {37976174},
issn = {1559-2308},
abstract = {An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.},
}