Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [ChIP-Seq]

Exposure of unicellular or multicellular organisms to adverse environmental conditions, including nutrient deprivation, may induce a state of suspended animation or diapause. We here report that broad repression of RNA Pol II-driven gene expression by inhibiting the BET family's bromodomain-containing proteins (BET) triggers diapause in mouse embryonic stem (ES) cells. The diapause ES cells upregulate a functionally linked group of genes encoding negative regulators of MAP kinase signaling (NRMKS), which play a crucial role in ES cell differentiation. The elevated NRMKS expression is a hallmark of cells exposed to distinct diapause-inducing conditions, including mTOR inhibition, and are required for the pluripotency maintenance during diapause. Mechanistically, inhibition of mTORC1/2 leads to rapid decline of the Capicua transcriptional repressor (CIC) at the NRMKS gene promoters, followed by rapid transcriptional NRMKS gene upregulation. The mTOR and BET-dependent transcriptional switch supporting the undifferentiated state of the diapause ES cells suggests a broader usage of this mechanism in maintaining the undifferentiated state of metabolically dormant stem- or stem-like cells in different tissues. To reveal the mechanism of elevated NRMKS expression in distinct diapause-inducing conditions, we focused on the Capicua transcriptional repressor (CIC) binding patterns at the NRMKS gene promoters. We performed the CIC chromatin binding profiling analysis using data from CIC ChIP-seq in control and Torin1 treated ES cells for 60min and 2 weeks. Two biological replicates of ChIP samples and one replicate of input sample were included in each condition of the assay. To investigate the acute effects of mTORi on BRD4 and Histone acetylation levels, we also performed the BRD4 and Histone H4 acetylation chromatin binding profiling analysis using data from BRD4 and pan-H4Ac ChIP-seq in control and Torin1 treated ES cells for 15min and 30min.