Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway known to degrade mRNAs containing premature termination codons (PTCs). mRNA recognition by the Upf1, Upf2 and Upf3 NMD factors is favoured by long distances between the stop codon and the poly(A)-binding protein (Pab1) binding site. Using Nanopore direct RNA sequencing, we now show that PTC-containing NMD targets account for only 6% of Upf1-associated RNA and have long poly(A) tails, indicating that Upf1-binding occurs prior to their deadenylation. Conversely, most Upf1-associated mRNAs have short poly(A) tails, lack a PTC and correspond to highly expressed genes. A short poly(A) tail is thus an important feature of a new class of Upf1 targets, redefining the scope of the NMD RNA degradation pathway. Recognition of short poly(A)-tailed mRNAs by Upf1, Upf2 and Upf3 (the NMD machinery) triggers their decapping, uncovering a hitherto unknown role of the NMD machinery in the degradation of these transcripts.