Frontiers in Neuroscience (Jun 2023)
Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesis
- Qiuting Deng,
- Qiuting Deng,
- Shengpeng Wang,
- Shengpeng Wang,
- Zijie Huang,
- Zijie Huang,
- Qing Lan,
- Guangyao Lai,
- Jiangshan Xu,
- Yue Yuan,
- Chang Liu,
- Xiumei Lin,
- Xiumei Lin,
- Weimin Feng,
- Weimin Feng,
- Wen Ma,
- Mengnan Cheng,
- Shijie Hao,
- Shijie Hao,
- Shanshan Duan,
- Shanshan Duan,
- Huiwen Zheng,
- Xiaoyan Chen,
- Yong Hou,
- Yong Hou,
- Yingjie Luo,
- Longqi Liu,
- Longqi Liu,
- Longqi Liu,
- Longqi Liu,
- Chuanyu Liu,
- Chuanyu Liu
Affiliations
- Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Qiuting Deng
- BGI-Hangzhou, Hangzhou, China
- Shengpeng Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shengpeng Wang
- BGI-Hangzhou, Hangzhou, China
- Zijie Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Zijie Huang
- BGI-Shenzhen, Shenzhen, China
- Qing Lan
- BGI-Shenzhen, Shenzhen, China
- Guangyao Lai
- BGI-Shenzhen, Shenzhen, China
- Jiangshan Xu
- BGI-Hangzhou, Hangzhou, China
- Yue Yuan
- BGI-Hangzhou, Hangzhou, China
- Chang Liu
- BGI-Hangzhou, Hangzhou, China
- Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Xiumei Lin
- BGI-Hangzhou, Hangzhou, China
- Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Weimin Feng
- BGI-Hangzhou, Hangzhou, China
- Wen Ma
- BGI-Shenzhen, Shenzhen, China
- Mengnan Cheng
- BGI-Hangzhou, Hangzhou, China
- Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shijie Hao
- BGI-Hangzhou, Hangzhou, China
- Shanshan Duan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shanshan Duan
- BGI-Hangzhou, Hangzhou, China
- Huiwen Zheng
- BGI-Hangzhou, Hangzhou, China
- Xiaoyan Chen
- BGI-Hangzhou, Hangzhou, China
- Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Yong Hou
- BGI-Shenzhen, Shenzhen, China
- Yingjie Luo
- BGI-Shenzhen, Shenzhen, China
- Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Longqi Liu
- BGI-Hangzhou, Hangzhou, China
- Longqi Liu
- BGI-Shenzhen, Shenzhen, China
- Longqi Liu
- Shenzhen Bay Laboratory, Shenzhen, China
- Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China
- Chuanyu Liu
- Shenzhen Bay Laboratory, Shenzhen, China
- DOI
- https://doi.org/10.3389/fnins.2023.1170355
- Journal volume & issue
-
Vol. 17
Abstract
In mammals, early organogenesis begins soon after gastrulation, accompanied by specification of various type of progenitor/precusor cells. In order to reveal dynamic chromatin landscape of precursor cells and decipher the underlying molecular mechanism driving early mouse organogenesis, we performed single-cell ATAC-seq of E8.5-E10.5 mouse embryos. We profiled a total of 101,599 single cells and identified 41 specific cell types at these stages. Besides, by performing integrated analysis of scATAC-seq and public scRNA-seq data, we identified the critical cis-regulatory elements and key transcription factors which drving development of spinal cord and somitogenesis. Furthermore, we intersected accessible peaks with human diseases/traits-related loci and found potential clinical associated single nucleotide variants (SNPs). Overall, our work provides a fundamental source for understanding cell fate determination and revealing the underlying mechanism during postimplantation embryonic development, and expand our knowledge of pathology for human developmental malformations.
Keywords
