PXD042395

PXD042395 is an original dataset announced via ProteomeXchange.

Title	PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress
Description	Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:12:52.116.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jakob Trendel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-22 07:17:44	ID requested
1	2023-10-24 13:41:33	announced
2	2023-11-14 09:12:39	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:12:52	announced	2024-10-22: Updated project metadata.

10.1093/nar/gkad557;

Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J, PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res, 51(14):e79(2023) [pubmed]

submitter keyword: nascent proteome enrichment,Protein-RNA crosslinking, AHA, protein occupancy on RNA, arsenite washout, recovery from translational arrest, SILAC

Proteomic of Stem Cells and Cancer
contact affiliation	DKFZ Heidelberg
contact email	j.krijgsveld@dkfz-heidelberg.de
lab head
Jakob Trendel
contact affiliation	TU Munich
contact email	jakob.trendel@tum.de
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/2023/10/PXD042395

PRIDE project URI

• PRIDE
  1. PXD042395
     1. Label: PRIDE project
     2. Name: PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress