PXD014528

PXD014528 is an original dataset announced via ProteomeXchange.

Title	The translational landscape of naïve and primed state pluripotency
Description	Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. The translational landscape of early mammalian development and its impact on cellular proteome, however, remains largely un-explored. 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 into primed embryonic stem cells (ESCs). We found that the ground state ESCs cultured with GSK3- and MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. These mRNAs show reduced translation during the exit from ground state pluripotency and transition to serum/LIF (SL) culture or upon commitment to primed epiblast-like stem cells (EpiLSCs). Strikingly, integrative analysis with cellular proteome indicate a strong translational buffering of this set of mRNAs in 2iL-ESCs leading to stable protein expression levels. Our data reveal that the global alteration of cellular proteome is largely accompanied by transcriptional rewiring. Furthermore, we identified a set of genes (including UHRF1 and KRAS) that undergo selective post-translational regulation during the transition of naïve into primed pluripotency and linked the observed changes to upstream GSK- and MEK/MAPK-signaling pathways using single inhibitor treated ESCs. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression during the transition of naïve to primed pluripotency and dissect the relative contributions of RNA-transcription, translation and regulation of protein stability in controlling protein abundance.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:40.806.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yaser Atlasi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-09 02:49:29	ID requested
1	2020-04-03 00:56:07	announced
⏵ 2	2024-10-22 05:01:44	announced	2024-10-22: Updated project metadata.

10.1038/s41467-020-15449-9;

Atlasi Y, Jafarnejad SM, Gkogkas CG, Vermeulen M, Sonenberg N, Stunnenberg HG, The translational landscape of ground state pluripotency. Nat Commun, 11(1):1617(2020) [pubmed]

submitter keyword: Ribosome profiling, Proteome, Translation,Embryonic stem cells, Ground state pluripotency

Henk Stunnenberg
contact affiliation	Radboud University Nijmegen The Netherlands
contact email	h.stunnenberg@ncmls.ru.nl
lab head
Yaser Atlasi
contact affiliation	Radboud University
contact email	yaser.atlasi@ncmls.ru.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD014528

PRIDE project URI

• PRIDE
  1. PXD014528
     1. Label: PRIDE project
     2. Name: The translational landscape of naïve and primed state pluripotency