Cooperative molecular networks drive a mammalian cell state transition

In the mammalian embryo, epiblast cells must exit their naive state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. Here we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems-biology to delineate the regulatory circuits governing naive state exit. Transcriptome profiles for 73 knockouts (KOs) predominantly manifest delays on the trajectory from naive to formative epiblast. We identified 374 naive-associated genes (NAGs), which are tightly connected to the epiblast state and largely conserved in human stem cells and primate embryos. Integrated analysis of mutant transcriptomes revealed that the activity of multiple genes promoting pluripotency progression is funneled into discrete regulatory modules. We demonstrate that these modules are under control of five signaling pathways that operate in parallel to direct this pivotal mammalian cell state transition.