Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development
Shangli Cheng,
Yu Pei,
Liqun He,
Guangdun Peng,
Björn Reinius,
Patrick P.L. Tam,
Naihe Jing,
Qiaolin Deng
Affiliations
Shangli Cheng
Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Solna, Sweden
Yu Pei
Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Solna, Sweden; Center for Molecular Medicine, Karolinska University Hospital, 17176 Solna, Sweden
Liqun He
Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, 300052 Tianjin, China
Guangdun Peng
State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031 Shanghai, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
Björn Reinius
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Solna, Sweden
Patrick P.L. Tam
Embryology Unit, Children’s Medical Research Institute, The University of Sydney and School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
Naihe Jing
State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031 Shanghai, China; School of Life Science and Technology, Shanghai Tech University, 201210 Shanghai, China
Qiaolin Deng
Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Solna, Sweden; Center for Molecular Medicine, Karolinska University Hospital, 17176 Solna, Sweden; School of Life Sciences and Technology, Tongji University, 200092 Shanghai, China; Corresponding author
Summary: Following implantation, the epiblast (EPI) cells transit from the naive to primed pluripotency, accompanied by dynamic changes in X chromosome activity in females. To investigate the molecular attributes of this process, we performed single-cell RNA-seq analysis of 1,724 cells of E5.25, E5.5, E6.25, and E6.5 mouse embryos. We identified three cellular states in the EPI cells that capture the transition along the pluripotency continuum and the acquisition of primitive streak propensity. The transition of three EPI states was driven by inductive signaling activity emanating from the visceral endoderm (VE). In the EPI of female embryos, X chromosome reactivation (XCR) was initiated prior to the completion of imprinted X chromosome inactivation (XCI), and the ensuing random XCI was highly asynchronous. Moreover, imprinted paternal XCI proceeded faster in the VE than the extraembryonic ectoderm. Our study has provided a detailed molecular roadmap of the emergent lineage commitment before gastrulation and characterized X chromosome dynamics during early mouse development. : Cheng et al. present a molecular roadmap at single-cell and allelic resolution that highlights the developmental process of epiblast cells transiting through pluripotency states and acquiring the primitive streak propensity ahead of gastrulation. In the epiblast of female embryos, the paternal X chromosome is reactivated before the completion of imprinted inactivation. Keywords: pluripotency transition, epiblast heterogeneity, pregastrula development, X chromosome inactivation dynamics
