title: Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs.
abstract: 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Zünd
authors.forename: Andreas R
authors.identifier: 0000000312194239
authors.initials: AR
authors.lastname: Gruber
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Oliver
authors.initials: O
authors.lastname: Mühlemann
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002874:Chromosome Mapping; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015151:Immunoblotting; D047468:Immunoprecipitation; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics / Q000502:physiology*; D020365:RNA Helicases; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015534:Trans-Activators / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D017931:DNA Primers; D018076:DNA, Complementary; D012333:RNA, Messenger; D015534:Trans-Activators; D020365:RNA Helicases; C101828:UPF1 protein, human