RNA: The translational landscape of ground state pluripotency

Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. Here we used genome-wide approaches combined with time-course analysis to measure the mRNA-abundance, mRNA-translation rate and protein expression during the transition of naïve-to-primed mouse embryonic stem cells (ESCs). We find that the ground state ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. This set of mRNAs undergo strong translational buffering to maintain stable protein expression levels in 2iL-ESCs. Importantly, we show that the global alteration of cellular proteome during the transition of naïve to primed pluripotency is largely accompanied by transcriptional rewiring. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression in different states of ESCs and dissect the relative contributions of RNA-transcription, translation and regulation of protein stability in controlling protein abundance. Analysis of genome wide mRNA translation by ribosome profiling and mRNA expression by RNA-seq. 9-conditions were used that include: 2iL, 2iLday1, 2iLday3, 2iLday7, SL, SLday1, SLday3, SLday7, EpiLSCs. Biological duplicates were used per condition; they are indicated as Rep1 and Rep2. In total 18 samples for RNA-seq and 18-samples for Ribosome profiling were generated.