RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 or human embryonic kidney cell line HEK293 via the dTAG degron system

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 dTAGV-1-inducible UPF1 degron system in the human colorectal adenocarcinoma cell line HCT116 or human embryonic kidney cell line HEK293 by tagging UPF1 at the N-terminus with an Myc-FKBP-tag (FKBP = FKBP12-F36V). With these cell lines we wanted to explore the transcriptome-wide expression changes including the extent of NMD inhibition upon rapid depletion of UPF1. To this end, depletion of UPF1 was induced with 0.25 µM dTAGV-1 for 12h. As controls, the parental cell line or untreated cells were used.