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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Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]
BMC Biology, 2018 Background The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Jan Krefting +2 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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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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Structural and functional diversity of Topologically Associating Domains [PDF]
FEBS Letters, 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 ...
Job Dekker, Edith Heard
exaly +6 more sources
Principles of genome folding into topologically associating domains [PDF]
Science Advances, 2019 This review discusses the features of TADs across species, and their role in chromosome organization, genome function, and evolution.
Quentin SZABÓ +2 more
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Topologically associating domains and the evolution of three‐dimensional genome architecture in rice [PDF]
Plant JournalSUMMARYWe examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genus Oryza. These included three varieties from subspecies within domesticated Asian rice O. sativa as well as their closely related wild relatives O. rufipogon and O.
Yutaka Sato +2 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 ancient features that coincide with Metazoan clusters of extreme noncoding conservation [PDF]
Nature Communications, 2017 Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic ...
Nathan Harmston +5 more
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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
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