Long open reading frame transcripts escape nonsense-mediated mRNA decay in yeast

Area of Science:

• Molecular Biology
• Gene Regulation
• Eukaryotic Transcription

Background:

• Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant eukaryotic transcripts.
• Long 3' untranslated regions (UTRs) are known features of NMD substrates.
• The influence of other transcript features on NMD efficiency remains incompletely understood.

Purpose of the Study:

• To investigate the impact of transcript features beyond 3' UTR length on NMD efficiency.
• To identify novel determinants of NMD substrate recognition in yeast.

Main Methods:

• Generation of yeast strains expressing 979 distinct reporter mRNAs with varying promoter and open reading frame (ORF) regions but a common destabilizing 3' UTR.
• Utilized a barcode-based DNA microarray to quantify reporter mRNA levels in the presence and absence of active NMD.

Main Results:

• Transcript open reading frame (ORF) length significantly influenced NMD efficiency, with shorter ORFs enhancing decay.
• This effect of ORF length on NMD sensitivity was independent of the specific 3' UTR tested.
• Increased ORF length did not result from reduced Upf1 binding to transcripts.

Conclusions:

• Short translation length, alongside long 3' UTRs, is a critical determinant for NMD substrate recognition in yeast.
• These findings expand the understanding of NMD regulation beyond 3' UTR length.
• Identified ORF length as a novel factor influencing mRNA decay pathways.