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

doi:10.1186/s13059-019-1893-y

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 journal › Article › peer-review

40 Scopus citations

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 language	English (US)
Article number	282
Journal	Genome biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1893-y
State	Published - Dec 18 2019

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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title = "OnTAD: Hierarchical domain structure reveals the divergence of activity among TADs and boundaries",

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.",

author = "Lin An and Tao Yang and Jiahao Yang and Johannes Nuebler and Guanjue Xiang and Hardison, {Ross C.} and Qunhua Li and Yu Zhang",

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T2 - Hierarchical domain structure reveals the divergence of activity among TADs and boundaries

AU - An, Lin

AU - Yang, Tao

AU - Yang, Jiahao

AU - Nuebler, Johannes

AU - Xiang, Guanjue

AU - Hardison, Ross C.

AU - Li, Qunhua

AU - Zhang, Yu

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AB - 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.

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

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