Enhancer-promoter communication: unraveling enhancer strength and positioning within a given topologically associating domain (TAD) [PDF]
Signal Transduction and Targeted Therapy, 2022 Benedetto Daniele Giaimo +1 more
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Topologically associating domain boundaries are required for normal genome function [PDF]
Communications Biology, 2023 Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1–3, but the overall ...
Sudha Rajderkar +28 more
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A comparison of topologically associating domain callers over mammals at high resolution [PDF]
BMC Bioinformatics, 2022 Background Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over
Emre Sefer
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Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries [PDF]
Nature Communications, 2023 Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered ...
Li-Hsin Chang +14 more
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A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information [PDF]
BMC Genomics, 2019 Background The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures.
Wei Gan +5 more
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Topologically Associating Domain Boundaries That Are Stable Across Diverse Cell Types Are Evolutionarily Constrained and Enriched for Heritability [PDF]
American Journal of Human Genetics, 2021 John Anthony Capra, Evonne McArthur
exaly +2 more sources
Cross-Scale Convergence in Epigenetic Gene Regulation: A Perspective on Functional Enrichment Analytics for Cancer [PDF]
Current Issues in Molecular BiologyEpigenetic regulation of gene expression is studied at three physical scales: micro: DNA sequence-level methylation/demethylation; meso: nucleosome occupancy and remodeling; and macro: chromosomal domain silencing by Polycomb complexes, heterochromatin ...
Adam G. Marsh, Ashley S. Doane
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Nature Communications, 2021 Transcriptional state plays a role in genome organization, however factors that link these processes are not well known. Here, the authors show Drosophila transcription factor Motif 1-binding protein (M1BP) interacts with the insulator protein CP190 to ...
Indira Bag +6 more
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Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
Nature Communications, 2022 Here the authors applied their recently developed multiplexed DNA-FISH Hi-M method to dissect the sources of heterogeneity in topologically associating domain (TAD)-like organization during Drosophila embryogenesis.
Markus Götz +4 more
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Clinical and Translational Medicine, 2022 Background During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three‐dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.
Geng G. Tian +3 more
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