Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs

The RNA helicase UPF1 has been implicated in various functions including nonsense-mediated decay (NMD). Transcriptome-wide analysis of UPF1-binding sites in translationally active versus inhibited cells provides evidence for translation-independent UPF1-RNA interactions and also suggests that UPF1 bound to coding sequence may be displaced by translating ribosomes and that NMD substrate selection may occur after UPF1-RNA interaction. Recruitment of the UPF1 nonsense-mediated mRNA decay (NMD) factor to target mRNAs was initially proposed to occur through interaction with release factors at terminating ribosomes. However, recently emerging evidence points toward translation-independent interaction with the 3′ untranslated region (UTR) of mRNAs. We mapped transcriptome-wide UPF1-binding sites by individual-nucleotide-resolution UV cross-linking and immunoprecipitation in human cells and found that UPF1 preferentially associated with 3′ UTRs in translationally active cells but underwent significant redistribution toward coding regions (CDS) upon translation inhibition, thus indicating that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. Corroborated by RNA immunoprecipitation and by UPF1 cross-linking to long noncoding RNAs, our evidence for translation-independent UPF1-RNA interaction suggests that the triggering of NMD occurs after UPF1 binding to mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination.