Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
文献类型：期刊论文
| 作者 | Dong, Kangning ; Zhang, Shihua
|
| 刊名 | BRIEFINGS IN BIOINFORMATICS
 |
| 出版日期 | 2021-05-01 |
| 卷号 | 22期号:3页码:15 |
| 关键词 | cis-regulatory interaction networks single-cell ATAC-seq Gaussian graphical LASSO |
| ISSN号 | 1467-5463 |
| DOI | 10.1093/bib/bbaa120 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000709461300065 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/59474]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。