DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD‐Like Domains in the Single Cells

Author:

Li Angsheng12,Zeng Guangjie1,Wang Haoyu34,Li Xiao34,Zhang Zhihua34ORCID

Affiliation:

1. State Key Laboratory of Software Development Environment School of Computer Science Beihang University Beijing 100191 P. R. China

2. Zhongguancun Laboratory Beijing 100094 P. R. China

3. CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for Bioinformation Beijing 100101 China

4. School of Life Science University of Chinese Academy of Sciences Beijing 101408 P. R. China

Abstract

AbstractTopologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD‐like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state‐of‐the‐art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.

Funder

Natural Science Foundation of Beijing Municipality

Publisher

Wiley

Subject

General Physics and Astronomy,General Engineering,Biochemistry, Genetics and Molecular Biology (miscellaneous),General Materials Science,General Chemical Engineering,Medicine (miscellaneous)

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