Identification of cis-regulatory elements within UPF1 target transcripts

UPF1 have RNA helicase domain associated with its RNA targets. UPF1 plays the central role in nonsense-mediated mRNA decay (NMD), which eliminates aberrant mRNAs harboring premature termination codon. Recent studies revealed that UPF1 is also involved in STAU1-mediated mRNA decay (SMD) to regulate RNA expression level. We recently developed 5''-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq) to determine genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs. In this work, we used the combined analysis of RNA stability (BRIC-seq) and RNA-UPF1 protein interaction (RIP-seq) to discover bona-fide UPF1 target genes.