OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
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13059_2019_Article_1893.pdf
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Author(s)
An, Lin
Yang, Tao
Yang, Jiahao
Nubler, Johannes
Xiang, Guanjue
Hardison, Ross C
Li, Qunhua
Zhang, Yu
Date Issued
December 18, 2019
Journal
Genome Biology
Publisher
BioMed Central
Citation
An, Lin et al. "OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries." Genome Biology 20 (Dec. 2019): no. 282 doi 10.1186/s13059-019-1893-y ©2019 Author(s)
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s13059-019-1893-y
