Single cell RNA-seq reveals protracted germ line X chromosome reactivation dynamics directed by a PRC2 dependent mechanism

Abstract

Initiating soon after PGC specification, female germ cells undergo reactivation of the silenced X chromosome during genome wide reprogramming. However, the kinetics and dynamics of XCR in vivo have remained poorly understood. To address this here we perform a global appraisal of XCR using high-dimensional techniques. Using F1 B6 v CAST mouse embryos, we perform a detailed assessment, applying single-cell RNA-seq and chromatin profiling on germ cells purified from E10.5 to E16.5. While scRNA-seq profile showed that male and female germ cells are transcriptionally indistinct at E11.5, they are sexually dimorphic by E12.5, diverging further through development to E16.5. With allelic resolution, we show that the reactivating X chromosome is only partly active at E10.5, then reactivates gradually and reaches near parity in output to the constitutively active X chromosome at [~]E16.5 when developing oogonia are meiosis prophase I. Crucially, we show that sexually dimorphic dosage compensation patterns observed in germ cells, occur in tandem with an increase in the allelic proportion from the reactivating X chromosome. While Xist is extinguished from E10.5, the epigenetic memory of earlier XCI in female cells persists much longer, likely from self-sustained PRC2 complex (Ezh2 / Eed / Suz12) function. The reactivating X chromosome is enriched in the epigenetic silencing mark H3K27me3 at E13.5, which is removed by E16.5 permitting gene expression. Our findings link XCR, along with functional regulation of PRC2 in promoting female meiosis.