KMS Of Academy of mathematics and systems sciences, CAS
| Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data | |
Dong, Kangning ; Zhang, Shihua
| |
| 2021-05-01 | |
| Source Publication | BRIEFINGS IN BIOINFORMATICS
 |
| ISSN | 1467-5463 |
| Volume | 22Issue:3Pages:15 |
| Abstract | 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. |
| Keyword | cis-regulatory interaction networks single-cell ATAC-seq Gaussian graphical LASSO |
| DOI | 10.1093/bib/bbaa120 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Biochemistry & Molecular Biology ; Mathematical & Computational Biology |
| WOS Subject | Biochemical Research Methods ; Mathematical & Computational Biology |
| WOS ID | WOS:000709461300065 |
| Publisher | OXFORD UNIV PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/59475 |
| Collection | 应用数学研究所 |
| Corresponding Author | Zhang, Shihua |
| Affiliation | Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China |
| Recommended Citation 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. |
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