Rules that govern UPF1 binding to mRNA 3′ UTRs

Abstract

Nonsense-mediated mRNA decay (NMD), which degrades transcripts harboring a premature termination codon (PTC), depends on the helicase up-frameshift 1 (UPF1). However, mRNAs that are not NMD targets also bind UPF1. What governs the timing, position, and function of UPF1 binding to mRNAs remains unclear. We provide evidence that (i) multiple UPF1 molecules accumulate on the 3′-untranslated region (3′ UTR) of PTC-containing mRNAs and to an extent that is greater per unit 3′ UTR length if the mRNA is an NMD target; (ii) UPF1 binding begins ≥35 nt downstream of the PTC; (iii) enhanced UPF1 binding to the 3′ UTR of PTC-containing mRNA relative to its PTC-free counterpart depends on translation; and (iv) the presence of a 3′ UTR exon-junction complex (EJC) further enhances UPF1 binding and/or affinity. Our data suggest that NMD involves UPF1 binding along a 3′ UTR whether the 3′ UTR contains an EJC. This binding explains how mRNAs without a 3′ UTR EJC but with an abnormally long 3′ UTR can be NMD targets, albeit not as efficiently as their counterparts that contain a 3′ UTR EJC.messenger ribonucleoprotein structure | RNA-binding protein | messenger RNA quality control I n mammalian cells, mRNAs and the pre-mRNAs from which they derive continually lose and acquire proteins in ways that reflect past and current metabolic states and influence future metabolic steps. For example, newly synthesized mRNAs, which support the pioneer round of translation, are bound by the capbinding protein (CBP) heterodimer CBP80−CBP20 and, provided they underwent splicing, exon-junction complexes (EJCs) (1). In contrast, the bulk of cellular mRNAs have lost CBP80−CBP20 and EJCs, have acquired eukaryotic translation initiation factor (eIF)4E in the place of CBP80−CBP20, and support most of cellular translation. CBP80 and EJCs are important for nonsensemediated mRNA decay (NMD), which down-regulates mRNAs that harbor either an exon-exon junction downstream of a termination codon (2, 3) and/or an abnormally long 3′ UTR (3-6). Thus, NMD targets newly synthesized mRNAs during the pioneer round of translation, whereas eIF4E-bound mRNAs appear to be immune to NMD (1, 3). This conclusion is supported by single-RNA fluorescent in situ-hybridization measurements of premature termination codon (PTC)-containing mRNAs in intact cells after the induction of mRNA synthesis (7).Messenger ribonucleoprotein (mRNP) remodeling also takes place during NMD. When translation terminates at a PTC and an EJC is situated sufficiently downstream of the PTC so as not to be displaced by the terminating ribosome (8, 9), a complex called suppressor with morphogenic effect on genitalia (SMG) 1−upframeshift 1 (UPF1)−eukaryotic release factor (eRF) 1−eRF3 (SURF) is thought to form at the PTC and, together with the downstream EJC, constitutes a decay-inducing complex (DECID) (10, 11). The transient and/or weak interaction of mRNA capbound CBP80 with UPF1, which occurs on mRNAs even if they are not NMD targets, promotes UPF1 binding to eRF1−eRF3 and, subsequently, to an EJC (12...

Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways

“…Consistent with previously observed preferential steady-state association of UPF1 with NMD targets (Johansson et al 2007;Johns et al 2007;Silva et al 2008;Hwang et al 2010;Kurosaki and Maquat 2013;Lee et al 2015), the top 1000 significant NMD targets are overall enriched in UPF1 CLIP tags (Supplemental Fig. S6), demonstrating a strong correlation between the two data sets.…”

Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit

“…Cryo-EM structures of the exon junction complex (EJC)-UPF complex have positioned Upf1 on the 3 ′ side of the EJC (Melero et al 2012), contradictory to the current notion of Upf1 localization at the 5 ′ side that is closer to the premature termination codon. It has also been reported that hUPF1 binds directly to mRNA, with binding varying as a function of mRNA 3 ′ -UTR length (Hogg and Goff 2010;Kurosaki and Maquat 2013).…”

Nonsense-mediated mRNA decay in humans at a glance

“…Although the premature termination of translation enhances the binding of steady-state UPF1, which is largely hypophosphorylated (i.e. yet to be activated by SMG1-mediated phosphorylation), to the downstream 3′UTR (Kurosaki and Maquat, 2013;Lee et al, 2015), recent biochemical and transcriptome analyses have revealed that steady-state UPF1 associates with regions of cellular RNAs that are physically accessible to its binding, independently of translation. These RNAs include canonically defined NMD targets and also non-NMD targets, including long non-coding RNAs (Gregersen et al, 2014;Hogg and Goff, 2010;Hurt et al, 2013;Kurosaki and Maquat, 2013;Lee et al, 2015;Zünd et al, 2013).…”