Single-cell chromatin accessibility and transcriptome atlas of mouse embryos
Shan Jiang,
Zheng Huang,
Yun Li,
Chengwei Yu,
Hao Yu,
Yuwen Ke,
Lan Jiang,
Jiang Liu
Affiliations
Shan Jiang
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
Zheng Huang
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
Yun Li
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
Chengwei Yu
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology College, University of Chinese Academy of Sciences, Beijing 100049, China
Hao Yu
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology College, University of Chinese Academy of Sciences, Beijing 100049, China
Yuwen Ke
College of Biological Science, China Agricultural University, Beijing 100193, China
Lan Jiang
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology College, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding author
Jiang Liu
China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology College, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Corresponding author
Summary: Cis-regulatory elements regulate gene expression and lineage specification. However, the potential regulation of cis-elements on mammalian embryogenesis remains largely unexplored. To address this question, we perform single-cell assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA-seq in embryonic day 7.5 (E7.5) and E13.5 mouse embryos. We construct the chromatin accessibility landscapes with cell spatial information in E7.5 embryos, showing the spatial patterns of cis-elements and the spatial distribution of potentially functional transcription factors (TFs). We further show that many germ-layer-specific cis-elements and TFs in E7.5 embryos are maintained in the cell types derived from the corresponding germ layers at later stages, suggesting that these cis-elements and TFs are important during cell differentiation. We also find a potential progenitor for Sertoli and granulosa cells in gonads. Interestingly, both Sertoli and granulosa cells exist in male gonads and female gonads during gonad development. Collectively, we provide a valuable resource to understand organogenesis in mammals.
