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

Abstract

Following implantation, the epiblast (EPI) cells transit from the naïve to the primed pluripotency state in preparation for gastrulation, a momentous developmental milestone of the formation of the three primary germ layers. To investigate the molecular attributes of this critical developmental process of lineage specification and the dynamic changes in X-chromosome activity, we performed Smart-seq2 single-cell RNA-seq analysis of 1724 mouse E5.25 to E6.5 embryonic cells. We identified three distinct cellular states in the EPI cells that mirrors the transition of postimplantation EPI along the continuum of naïve to primed pluripotency and the acquisition of primitive streak propensity over time. The transition of the EPI cellular state was accompanied by enhanced interaction with the visceral endoderm mediated by inductive signalling activity. By tracing X-chromosome activity at the allelic resolution, we discovered that X-chromosome reactivation (XCR) was initiated prior to the complete silencing of imprinted X-chromosome in the EPI, and followed by asynchronous random X-chromosome inactivation (XCI). Moreover, imprinted X-chromosome inactivation proceeded with a faster kinetics in the visceral endoderm compared to the extraembryonic ectoderm. Our study has outlined in detail a molecular roadmap of the emergent process of lineage specification and X-chromosome reprogramming during mouse pregastrulation development.