Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis...

Area of Science:

• Plant molecular biology
• RNA biology
• Gene regulation

Background:

• The nonsense-mediated decay (NMD) pathway is a crucial mRNA surveillance system.
• Alternative splicing (AS) generates diverse mRNA variants, some potentially recognized by NMD.
• The extent of coupled AS and NMD in plants is largely unknown.

Purpose of the Study:

• To investigate the global extent of AS-NMD coupling in Arabidopsis thaliana.
• To determine the roles of UPF1 and UPF3 in NMD-mediated regulation of AS variants.
• To characterize the features and functions of NMD-targeted AS variants.

Main Methods:

• Transcriptome-wide splicing analysis in Arabidopsis mutants (upf1, upf3) and wild-type samples.
• Treatment with cycloheximide to assess translation dependence.
• Bioinformatic analysis of NMD-responsive transcripts for NMD-eliciting features.

Main Results:

• At least 17.4% of multi-exon genes produce NMD-targeted AS variants.
• UPF1 and UPF3 function in a translation-independent NMD pathway.
• 92.3% of NMD-responsive mRNAs possess canonical NMD-triggering features.
• NMD-sensitive AS variants are involved in signaling, protein modification, and stress responses.
• Noncoding RNAs and intergenic transcripts are also NMD responsive.

Conclusions:

• AS-coupled NMD plays a significant role in shaping the Arabidopsis transcriptome.
• NMD contributes to transcript processing quality control and gene regulation in plants.
• This pathway impacts diverse biological processes, including stress responses.