UPF1 regulates mRNA stability by sensing poorly translated coding sequences - HITS-CLIP.

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 strength of translation initiation, uORF content, codon optimality, AU-rich elements, microRNA binding sites, and 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 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 EJC-independent NMD pathway that we term ORF-Mediated Decay (OMD).