A single-cell transcriptome atlas of marsupial embryogenesis and Xinactivation.

Abstract

Single-cell RNA sequencing of embryos can resolve the transcriptional landscape of development at unprecedented resolution. To date, single-cell RNA-sequencing studies of mammalian embryos have focused exclusively on eutherian species. Analysis of mammalian outgroups has the potential to identify deeply conserved lineage specification and pluripotency factors, and can extend our understanding of Xdosage compensation. Metatherian (marsupial) mammals diverged from eutherians around 160million years ago. They exhibit distinctive developmental features, including late implantation1 and imprinted Xchromosome inactivation2, which is associated with expression of the XIST-like noncoding RNA RSX3. Here we perform a single-cell RNA-sequencing analysis of embryogenesis and Xchromosome inactivation in a marsupial, the grey short-tailed opossum (Monodelphis domestica). We resolve the developmental trajectory and transcriptional signatures of the epiblast, primitive endoderm and trophectoderm, and identify deeply conserved lineage-specific markers that pre-date the eutherian-marsupial divergence. RSX coating and inactivation of the Xchromosome occurs early and rapidly. This observation supports the hypothesis that-in organisms with early Xchromosome inactivation-imprinted Xchromosome inactivation prevents biallelic Xsilencing. We identify XSR, an RSXantisense transcript expressed from the active Xchromosome, as a candidate for the regulator of imprinted Xchromosome inactivation. Our datasets provide insights into the evolution of mammalian embryogenesis and Xdosage compensation.