Transcript-specific characteristics determine the contribution of endo- and exonucleolytic decay pathways during the...

Area of Science:

• Molecular Biology
• Gene Expression Regulation
• RNA Metabolism

Background:

• Nonsense-mediated mRNA decay (NMD) is a crucial surveillance pathway that eliminates faulty mRNAs.
• The central NMD factor UPF1 orchestrates the recruitment of downstream factors, including SMG6 and the SMG5/7 complex.
• The distinct roles of SMG6 and SMG5/7 in degrading specific NMD substrates remain incompletely understood.

Purpose of the Study:

• To investigate the transcriptome-wide cleavage sites mediated by SMG6.
• To elucidate the differential contributions of SMG6 and SMG5/7 to NMD substrate degradation.
• To understand how mRNA architecture influences the choice of NMD degradation pathways.

Main Methods:

• Transcriptome-wide mapping of SMG6-mediated endocleavage sites using 3' fragment capture and degradome sequencing.
• Analysis of NMD-eliciting features in endogenous transcripts, including upstream open reading frames (uORFs), premature termination codons (PTCs), and long 3' UTRs.
• Comparative analysis of degradation pathways for NMD substrates with different features.

Main Results:

• Identified diverse positions of NMD-eliciting features in endogenous transcripts.
• Demonstrated that NMD substrates with PTCs are primarily degraded via SMG6-dependent endocleavage.
• Revealed that NMD substrates with uORFs or long 3' UTRs are degraded through a combination of SMG6- and SMG7-dependent pathways.

Conclusions:

• The degradation mechanism for NMD substrates is determined by the specific mRNA features.
• SMG6 plays a constitutive role in degrading PTC-containing NMD targets.
• SMG5/7 and SMG6 act combinatorially to degrade NMD substrates with uORFs and long 3' UTRs, highlighting the role of mRNA architecture in pathway selection.