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

被引：47
作者：
An, Lin [1 ,2 ]
Yang, Tao [1 ]
Yang, Jiahao [3 ]
Nuebler, Johannes [4 ]
Xiang, Guanjue [1 ]
Hardison, Ross C. [5 ]
Li, Qunhua [1 ,6 ]
Zhang, Yu [1 ,6 ]
机构：
[1] Penn State Univ, Bioinformat & Genom Program, University Pk, PA 16802 USA
[2] Camp4 Therapeut, Cambridge, MA USA
[3] Tsinghua Univ, Dept Math, Beijing, Peoples R China
[4] MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA
[5] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA
[6] Penn State Univ, Dept Stat, University Pk, PA 16802 USA
来源：
GENOME BIOLOGY | 2019年 / 20卷 / 01期
关键词：
CHROMOSOME CONFORMATION CAPTURE; CHROMATIN; PRINCIPLES; GENOME; ARCHITECTURE; CONDENSIN; REGIONS;
D O I：
10.1186/s13059-019-1893-y
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
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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页数：16
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