HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets [PDF]
Computational and Structural Biotechnology Journal, 2023 High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization.
Jonathan Rosen +6 more
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Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease [PDF]
Frontiers in Cell and Developmental Biology, 2021 Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as
Juan J. Tena, José M. Santos-Pereira
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Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains [PDF]
Frontiers in Genetics, 2023 Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response.
Christophe Tav +26 more
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Pattern recognition of topologically associating domains using deep learning [PDF]
BMC Bioinformatics, 2022 Background Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal ...
Jhen Yuan Yang, Jia-Ming Chang
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Identifying topologically associating domains using differential kernels. [PDF]
PLoS Computational BiologyChromatin 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.
Luka Maisuradze +5 more
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Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency [PDF]
Genome Biology, 2021 Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and
Yongzheng Li +13 more
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RobusTAD: reference panel based annotation of nested topologically associating domains [PDF]
Genome BiologyTopologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs.
Yanlin Zhang +2 more
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DiffDomain enables identification of structurally reorganized topologically associating domains [PDF]
Nature CommunicationsTopologically 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,
Dunming Hua +9 more
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Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish [PDF]
iScience, 2020 Summary: CCCTC-binding factor (CTCF) is a conserved architectural protein that plays crucial roles in gene regulation and three-dimensional (3D) chromatin organization.
Yuvia A. Pérez-Rico +2 more
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Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans [PDF]
Cell Reports, 2022 Summary: Distinguishing between conserved and divergent regulatory mechanisms is essential for translating preclinical research from mice to humans, yet there is a lack of information about how evolutionary genome rearrangements affect the regulation of ...
Sarah E. Gilbertson +5 more
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