The translational landscape of ground state pluripotency

Yaser Atlasi,Michiel Vermeulen,Christos G Gkogkas,Nahum Sonenberg,Seyed Mehdi Jafarnejad,Hendrik G Stunnenberg

doi:10.1038/s41467-020-15449-9

Abstract

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 mRNA-transcription, translation and regulation of protein stability in controlling protein abundance.

Highlights

Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance
Ribosome profiling is a next-generation sequencing (NGS)-based method that accurately measures the abundance of ribosome footprints (RFPs; mRNA fragments protected from RNase by the translating ribosomes)
We verified the high quality of generated data using several parameters: (a) the data were highly reproducible among the biological replicates (r > 0.93 for RFP and r > 0.95 for RNA, Supplementary Fig. 1a, b, Supplementary Data 1), (b) the RFPs define the known coding sequences (CDS) with 12-nt offsets upstream of the translation start codons, (c) a high coverage of RFP reads within coding sequence but low coverage at untranslated regions (UTRs), which is specific for RFP but not RNA-seq libraries (Supplementary Fig 1c–e)

Summary

Introduction

Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. Quantitative measurements of RNA and protein levels revealed that for ~60% of genes, changes in mRNA abundance cannot accurately predict the variations in protein abundance in mammalian cells[6] Consistent with this notion, parallel measurements of mRNA expression and protein levels as well as mRNA and protein turnover suggest the major impact of translational control in regulating the proteome landscape[6,7,8]. The current knowledge on the translational control in mouse ESCs, is mainly based on conventional ESCs cultured in serum/LIF (SL) medium[10,12,16,17] These undifferentiated cells are metastable and show features of both pre-implantation and early post-implantation epiblast These cells are lineage-primed and strongly downregulate the pre-implantation transcription factors (TFs), show high expression of postimplantation markers, and do not contribute to chimera upon blastocyst complementation (reviewed in ref. 24)

Methods

Results

Conclusion