PXD061797-1

PXD061797 is an original dataset announced via ProteomeXchange.

Title	Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome
Description	UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation-coupled mechanism that targets mRNAs harboring a premature stop codon (PTC) for degradation, thereby serving as a quality control and gene regulatory pathway ensuring transcriptome integrity. The UPF1 gene is essential in cultured human cells and previous studies relied mostly on RNA interference to downregulate UPF1. Here we established an auxin-inducible UPF1 degron system in the human colorectal adenocarcinoma cell line HCT116 by first inserting the auxin receptor F-box protein-encoding AtAFB2-mCherry in the AAVS1 locus, followed by tagging UPF1 at the N-terminus with an V5-AID-tag (AID = miniIAA7 = AtIAA7 amino acids 37–104). With this cell line we wanted to explore the time-resolved proteomic changes upon rapid depletion of UPF1. To this end, depletion of UPF1 was induced with 500 µM indole-3-acetic acid (IAA) for various time periods (0-24h). As controls, the cells were treated for the same time with DMSO.
HostingRepository	PRIDE
AnnounceDate	2025-09-03
AnnouncementXML	Submission_2025-09-03_07:03:04.541.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Oliver Popp
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-13 08:30:37	ID requested
⏵ 1	2025-09-03 07:03:04	announced

10.1016/J.MOLCEL.2025.08.015;

submitter keyword: mRNA degradation, NMD, gene expression,Nonsense-mediated mRNA decay, UPF1, translation

Volker Boehm
contact affiliation	Volker Boehm Gehring Lab, Institute for Genetics, University of Cologne, 50674 Cologne, Germany
contact email	boehmv@uni-koeln.de
lab head
Oliver Popp
contact affiliation	MDC Berlin
contact email	oliver.popp@mdc-berlin.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/2025/09/PXD061797

PRIDE project URI

• PRIDE
  1. PXD061797
     1. Label: PRIDE project
     2. Name: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome