UPF1 regulates mRNA stability by sensing poorly translated coding sequences

Post-transcriptional mRNA regulation shapes gene expression, yet how cis-elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that the strength of translation initiation, upstream open reading frame (uORF) content, codon optimality, AU-rich elements, microRNA binding sites, and open reading frame (ORF) length function combinatorially to regulate mRNA stability. Machine-learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs, which are associated with a higher decay rate, including mRNAs with uORFs and those with exposed ORFs after stop codons. Our study emphasizes Upf1’s converging role in surveilling mRNAs with exposed ORFs that are poorly translated, such as mRNAs with long ORFs, ORF-like 3′ UTRs, and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an exon-junction complex (EJC)-independent nonsense-mediated decay (NMD) pathway that we term ORF-mediated decay (OMD). [Display omitted] •ORF length, uORFs, Kozak sequence, codon optimality are conserved mRNA regulatory cis-elements•mRNAs with long ORFs are poorly translated and unstable•Upf1 binds mRNAs with long ORFs, uORFs, untranslated ORFs, and GC-rich mRNA to promote decay•Upf1’s phosphorylation is critical for binding its targets Musaev et al. explore conserved regulatory mechanisms of mRNA. They report that mRNAs with long ORFs undergo accelerated decay and reduced translation. Upf1 is a key factor in recognizing mRNAs with long ORFs, uORFs, and poorly translated mRNAs, and its phosphorylation is critical for these binding preferences.