1. Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution
- Author
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Pengcheng Ma, Xingyan Liu, Zaoxu Xu, Huimin Liu, Xiangning Ding, Zhen Huang, Chenggang Shi, Langchao Liang, Luohao Xu, Xiaolu Li, Guimei Li, Yuqi He, Zhaoli Ding, Chaochao Chai, Haoyu Wang, Jiaying Qiu, Jiacheng Zhu, Xiaoling Wang, Peiwen Ding, Si Zhou, Yuting Yuan, Wendi Wu, Cen Wan, Yanan Yan, Yitao Zhou, Qi-Jun Zhou, Guo-Dong Wang, Qiujin Zhang, Xun Xu, Guang Li, Shihua Zhang, Bingyu Mao, and Dongsheng Chen
- Subjects
Mice ,Genome ,Animals ,Gene Expression ,General Biochemistry, Genetics and Molecular Biology ,Chromatin ,Zebrafish ,Lancelets - Abstract
Vertebrate evolution was accompanied by two rounds of whole-genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single-cell sequencing has been widely used to construct the developmental cell atlas of several representative species of vertebrates (human, mouse, zebrafish, and frog) and tunicates (sea squirts). Here, we perform single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated, we constructed a developmental tree for amphioxus cell fate commitment and lineage specification and characterize the underlying key regulators and genetic regulatory networks. The data are publicly available on the online platform AmphioxusAtlas.
- Published
- 2021