Comparison of computational methods for the identification of topologically associating domains [PDF]
Genome Biology, 2018 Background Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs).
Marie Zufferey +3 more
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TADKB: Family classification and a knowledge base of topologically associating domains [PDF]
BMC Genomics, 2019 Background Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications and ...
Tong Liu +7 more
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Topologically associating domains and the evolution of three-dimensional genome architecture in rice. [PDF]
Plant JSUMMARY: We examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genus Oryza.
Kurbidaeva A +7 more
europepmc +9 more sources
Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test [PDF]
Nature Communications, 2017 Spatial organization of the genome plays a crucial role in regulating gene expression. Here the authors introduce GMAP, the Gaussian Mixture model And Proportion test, to identify topologically associating domains and subdomains in Hi-C data.
Wenbao Yu, Bing He, Kai Tan
doaj +3 more sources
Exploring the 2D and 3D structural properties of topologically associating domains [PDF]
BMC Bioinformatics, 2019 Background Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs.
Tong Liu, Zheng Wang
doaj +6 more sources
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains [PDF]
Genome Biology, 2020 Background CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs).
Elissavet Kentepozidou +7 more
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A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains [PDF]
Nature CommunicationsTopologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy.
Jingxuan Xu +13 more
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On the existence and functionality of topologically associating domains. [PDF]
Nat Genet, 2020 Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin domains. Topologically associating domains (TADs) were originally discovered empirically in low-resolution Hi-C heat maps representing ensemble average interaction frequencies from millions of cells. Here, we discuss recent advances in high-resolution Hi-C, single-cell
Beagan JA, Phillips-Cremins JE.
europepmc +5 more sources
Structural and functional diversity of Topologically Associating Domains. [PDF]
FEBS Lett, 2015 Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the ...
Dekker J, Heard E.
europepmc +6 more sources
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin. [PDF]
J Virol, 2022 Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a
Campbell M +8 more
europepmc +6 more sources