OnTAD: Hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Lin An, Tao Yang, Jiahao Yang, Johannes Nuebler, Guanjue Xiang, Ross C. Hardison, Qunhua Li, Yu Zhang

Research output: Contribution to journalArticle

Abstract

The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.

Original languageEnglish (US)
Article number282
JournalGenome biology
Volume20
Issue number1
DOIs
StatePublished - Dec 18 2019

Fingerprint

domain structure
extrusion
Chromatin
gene expression
chromatin
divergence
gene
Gene Expression
Genes
genes
regulation

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

An, Lin ; Yang, Tao ; Yang, Jiahao ; Nuebler, Johannes ; Xiang, Guanjue ; Hardison, Ross C. ; Li, Qunhua ; Zhang, Yu. / OnTAD : Hierarchical domain structure reveals the divergence of activity among TADs and boundaries. In: Genome biology. 2019 ; Vol. 20, No. 1.
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OnTAD : Hierarchical domain structure reveals the divergence of activity among TADs and boundaries. / An, Lin; Yang, Tao; Yang, Jiahao; Nuebler, Johannes; Xiang, Guanjue; Hardison, Ross C.; Li, Qunhua; Zhang, Yu.

In: Genome biology, Vol. 20, No. 1, 282, 18.12.2019.

Research output: Contribution to journalArticle

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AU - Zhang, Yu

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