Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

Nucleic Acids Res. 2012 Mar;40(6):2454-69. doi: 10.1093/nar/gkr932. Epub 2011 Nov 29.


Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5' or 3'UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3'-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions
  • Alternative Splicing*
  • Arabidopsis / drug effects
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Codon, Initiator
  • Codon, Nonsense
  • Cycloheximide / pharmacology
  • Gene Expression Regulation, Plant*
  • Genes, Plant
  • Genes, Regulator*
  • Introns
  • Nonsense Mediated mRNA Decay* / drug effects
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RNA Helicases / genetics
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction


  • 3' Untranslated Regions
  • Arabidopsis Proteins
  • Codon, Initiator
  • Codon, Nonsense
  • Protein Isoforms
  • RNA, Messenger
  • UPF3 protein, Arabidopsis
  • Cycloheximide
  • UPF1 protein, Arabidopsis
  • RNA Helicases