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Nonsense-mediated mRNA decay (NMD) causes accelerated transcript degradation when a premature translation termination codon disrupts the open reading frame (ORF). Although endogenous transcripts that have uninterrupted ORFs are typically insensitive to NMD, some can nonetheless become prone to NMD when translation terminates at out-of-frame premature stop codons. This occurs when introns containing stop codons fail to be spliced, when translation of an upstream ORF (uORF) terminates in the 5′-untranslated region (5′-UTR) or the coding region, or when the 5′-proximal AUG initiation codon is bypassed and translation initiates at a downstream out-of-frame AUG followed by a stop codon. Some 3′-untranslated regions (3′-UTRs) are also known to trigger NMD, but the mechanism is less well understood. To further study the role of 3′-UTRs in NMD, a reporter system was designed to examine 3′-UTRs from candidate genes known to produce NMD-sensitive transcripts. Out of eight that were tested, the 3′-UTRs from  MSH4  and  SPO16  caused NMD-dependent mRNA destabilization. Both endogenous genes produce multiple transcripts that differ in length at the 3′ end. Detailed studies revealed that the longest of six reporter  MSH4-3 ′ -UTR  transcripts was NMD-sensitive but five shorter transcripts were insensitive. NMD-dependent degradation of the long transcript required Xrn1, which degrades mRNA from the 5′ end. Sensitivity to NMD was not associated with extensive translational read-through past the normal stop codon. To our knowledge, this is the first example where multiple transcripts containing the same ORF are differentially sensitive to NMD in  Saccharomyces cerevisiae . The results provide a proof of principle that long 3′-UTRs can trigger NMD, which suggests a potential link between errors in transcription termination or processing and mRNA decay.

Multiple Transcripts from a 3′-UTR Reporter Vary in Sensitivity to Nonsense-Mediated mRNA Decay in Saccharomyces cerevisiae