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Genome Biol. 2019 Dec 18;20(1):282. doi: 10.1186/s13059-019-1893-y.

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

Author information

1
Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA, USA.
2
Camp4 Therapeutics, Cambridge, MA, USA.
3
Department of Mathematics, Tsinghua University, Beijing, China.
4
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
5
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
6
Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA, USA. qunhua.li@psu.edu.
7
Department of Statistics, Pennsylvania State University, University Park, PA, USA. qunhua.li@psu.edu.
8
Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA, USA. yzz2@psu.edu.
9
Department of Statistics, Pennsylvania State University, University Park, PA, USA. yzz2@psu.edu.

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.

PMID:
31847870
PMCID:
PMC6918570
DOI:
10.1186/s13059-019-1893-y
[Indexed for MEDLINE]
Free PMC Article

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