Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy [dgcr8_RNA]

Dormancy is a key feature of stem cell function in adult tissues as well as embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state is not known. Here we show that microRNA activity, which is normally dispensable for pre-implantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in loss of pluripotency and embryo collapse. Through small RNA profiling of individual embryos and computational integration of miRNA targets, we identified the miRNA-protein network of diapause. Individual miRNA function contributes to combinatorial regulation by the network and the perturbation of the network reduces embryo survival. Without miRNAs, nuclear and cytoplasmic bodies show aberrant expression. We identified the nutrient-sensitive transcription factor TFE3 as an upstream regulator of miRNA biogenesis, linking mTOR activity to miRNA induction. Our results reveal that miRNAs are critical for the transcriptional and structural rewiring of early embryos to establish dormancy.