RNA-seq analysis of mouse embryonic stem cells cultured in medium containing MEK and Akt inhibitors

Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. To unbiasedly identify genes regulating the kinetic properties of transcriptional bursting, we performed large-scale CRISPR/-Cas9 based screening and functional analysis, and found that Akt/MAPK signaling pathways are involved in the regulation of the kinetic properties of transcriptional bursting. To further characterize how these pathways affect mESC gene expression programs, we performed RNA-Seq analysis of mESCs cultured in standard (Std), 2i and Akt/MAPK signal-inhibitor containing medium (PD-MK). We found that expression levels of some genes encoding transcription elongation related factors were upregulated in PD-MK condition. Overall design: Bulk RNA-Seq was performed by CEL-Seq2 method (Hashimshony et al., 2016) with total RNA amounts were used the range of 30-60 ng. Three biological replicates were prepared.