GSE127186
Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases
Pluripotent stem cells (PSCs) can transition between cell states in vitro, closely reflecting developmental changes in the early embryo. PSCs can be stabilized in their naive state by blocking extracellular differentiation stimuli, particularly FGF5 MEK signaling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK-signaling.  Mechanistically, chemical inhibition of CDK8 and CDK19 kinases (CDK8/19i) removes their ability to repress the Mediator complex at enhancers. Thus CDK8/19i increases Mediator-driven recruitment of RNA Pol II to promoters and enhancers.  This efficiently stabilizes the naive transcriptional program, and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with reduction in CDK8/19.  We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be captured in-vitro by inhibiting extracellular FGF-MEK-signaling, or downstream, by CDK8/19i. These principles may apply to other contexts of cellular plasticity. Overall design: Four human pluripotent stem cell lines (PSCs) were cultured in three conditions ("Primed" vs "CDK8/19i" vs "gr8i") for 16 days/3passages, and then transcriptomic differences between the three groups were assessed by RNAseq.  Culture conditions were either standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel), or including additional media supplementation with recombinant human LIF (10 mg/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i" or "8i"); or, for the "gr8i" condition: recombinant human LIF (10 mg/ml), CDK8/19-small molecule inhibitor at 0,4 mM, GSK3-inhibitor CHIR99021 at 1 mM, plus IWR1 at 5 mM.  The four cell lines were D2#2, D2#4, HERVH (HH), and H1.