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Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Oliver Popp

LAB HEAD: Volker Boehm

PROVIDER: PXD061797 | Pride | 2025-09-03

REPOSITORIES: Pride

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			Action	DRS
	Elmo_20240122_OP_HSdia_Landthaler_A01_12h_DMSO_A.raw	Raw
	Elmo_20240122_OP_HSdia_Landthaler_A02_12h_DMSO_B.raw	Raw
	Elmo_20240122_OP_HSdia_Landthaler_A03_12h_DMSO_C.raw	Raw
	Elmo_20240122_OP_HSdia_Landthaler_A04_12h_DMSO_D.raw	Raw
	Elmo_20240122_OP_HSdia_Landthaler_A05_12h_Depl_A.raw	Raw

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