AUTHOR=Deng Qiuting , Wang Shengpeng , Huang Zijie , Lan Qing , Lai Guangyao , Xu Jiangshan , Yuan Yue , Liu Chang , Lin Xiumei , Feng Weimin , Ma Wen , Cheng Mengnan , Hao Shijie , Duan Shanshan , Zheng Huiwen , Chen Xiaoyan , Hou Yong , Luo Yingjie , Liu Longqi , Liu Chuanyu TITLE=Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesis JOURNAL=Frontiers in Neuroscience VOLUME=17 YEAR=2023 URL=https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2023.1170355 DOI=10.3389/fnins.2023.1170355 ISSN=1662-453X 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.