Multiple Transcripts from a 39-UTR Reporter Vary in Sensitivity to Nonsense-Mediated mRNA Decay in

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 59-untranslated region (59-UTR) or the coding region, or when the 59-proximal AUG initiation codon is bypassed and translation initiates at a downstream out-of-frame AUG followed by a stop codon. Some 39-untranslated regions (39-UTRs) are also known to trigger NMD, but the mechanism is less well understood. To further study the role of 39-UTRs in NMD, a reporter system was designed to examine 39-UTRs from candidate genes known to produce NMD-sensitive transcripts. Out of eight that were tested, the 39-UTRs from MSH4 and SPO16 caused NMD-dependent mRNA destabilization. Both endogenous genes produce multiple transcripts that differ in length at the 39 end. Detailed studies revealed that the longest of six reporter MSH4-39-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 59 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 NM