Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [RNA-seq]. Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [RNA-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. Overall design: The exposure of ES cells to incrementally increased BET protein inhibitor (I-BET) concentration results in the generation of diapause ES cells, hereafter defined as I-BET resistant (I-BETR) ES cells. To investigate the gene expression patterns of I-BETR diapause ES cells, we performed the gene expression profiling analysis using data from bulk RNA-seq of 4 samples of control and 4 samples of I-BETR ES cells. To understand the similarity of gene expression patterns in the I-BETR ES cells and other models of diapause ES cells, we also carried out the gene expression profiling analysis using data from bulk RNA-seq of 3 samples EBSS starvation induced diapause ES cells, 3 samples of Leucine and serum withdraw induced diapause ES cells and 3 samples of mTOR inhibitor Torin1 induced diapause ES cells comparing with 3 samples of their own Control ES cells. Lastly, to understand the quick response in terms of gene expression changes upon mTOR inhibition in ES cells, we also performed gene expression profiling analysis using time course dependent samples in control and Torin1 treated ES cells including 30min, 60min, 120min and 360min.