Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data

doi:10.1093/bib/bbaa120

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	Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
	Dong, Kangning; Zhang, Shihua
	2021-05-01
发表期刊	BRIEFINGS IN BIOINFORMATICS
ISSN	1467-5463
卷号	22 期号:3 页码:15
摘要	The rapid accumulation of single-cell chromatin accessibility data offers a unique opportunity to investigate common and specific regulatory mechanisms across different cell types. However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing -80 000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory networks show strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue-related TFs, and many of them may reveal novel regulatory mechanisms.
关键词	cis-regulatory interaction networks single-cell ATAC-seq Gaussian graphical LASSO
DOI	10.1093/bib/bbaa120
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2019YFA0709501] ; National Natural Science Foundation of China[11661141019] ; National Natural Science Foundation of China[61621003] ; National Ten Thousand Talent Program for Young Top-notch Talents ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008]
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:000709461300065
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/59475
专题	应用数学研究所
通讯作者	Zhang, Shihua
作者单位	Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Dong, Kangning,Zhang, Shihua. Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data[J]. BRIEFINGS IN BIOINFORMATICS,2021,22(3):15.
APA	Dong, Kangning,&Zhang, Shihua.(2021).Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.BRIEFINGS IN BIOINFORMATICS,22(3),15.
MLA	Dong, Kangning,et al."Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data".BRIEFINGS IN BIOINFORMATICS 22.3(2021):15.