Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development

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. [Display omitted] •A comprehensive scRNA-seq roadmap of early mouse development before gastrulation•Three cellular states of the epiblast cells transit the pluripotency continuum•X-reactivation in the epiblast initiates before completion of imprinted X-inactivation•Faster X-inactivation in visceral endoderm than in the extraembryonic ectoderm 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.