NCM 2021: Direct RNA sequencing reveals unusual NMD targets in plants

Nonsense-mediated decay controls the quality of the mRNAs in eukaryotes by degradation of transcripts containing a premature stop codon. Alternative splicing plays a crucial role in triggering NMD by switching between translational and NMD-targeted isoforms. Here, Anna used full-length transcriptome sequencing of plant Physcomitrium patens with SMG1 knockout to reveal the role of NMD in transcriptome formation. Our analysis revealed numerous new NMD targets. About 20% of upregulated mRNA isoforms had novel splice-sites. Surprisingly, nonsense-mediated decay also strongly affects the transcription of some transposons, suggesting that the role of NMD in shaping the plant transcriptomes can be underestimated. The reported study was funded by RFBR, project number 20-04-00938