Intron splicing suppresses RNA silencing in Arabidopsis

Plant J. 2011 Oct;68(1):159-67. doi: 10.1111/j.1365-313X.2011.04676.x. Epub 2011 Aug 5.


Silencing of introduced transgenes constitutes a major bottleneck in the production of transgenic crops. Commonly, these transgenes contain no introns, a feature shared with transposons, which are also prime targets for gene silencing. Given that introns are very common in endogenous genes but are often lacking in transgenes and transposons, we hypothesised that introns may suppress gene silencing. To investigate this, we conducted a genome-wide analysis of small RNA densities in exons from intronless versus intron-containing genes in Arabidopsis thaliana. We found that small RNA libraries are strongly enriched for exon sequences derived from intronless genes. Small RNA densities in exons of intronless genes were comparable to exons of transposable elements. To test these findings in vivo we used a transgenic reporter system to determine whether introns are able to suppress gene silencing in Arabidopsis. Introducing an intron into a transgene reduced silencing by more than fourfold. Compared with intronless transcripts, the spliced transcripts were less effective substrates for RNA-dependent RNA polymerase 6-mediated gene silencing. This intron suppression of transgene silencing requires efficient intron splicing and is dependent on ABH1, the Arabidopsis orthologue of human cap-binding protein 80.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / enzymology
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • DNA Transposable Elements / genetics
  • Exons / genetics
  • Gene Expression Regulation, Plant / genetics
  • Genome, Plant / genetics
  • Green Fluorescent Proteins / genetics
  • Introns / genetics*
  • RNA Cap-Binding Proteins / genetics
  • RNA Cap-Binding Proteins / metabolism*
  • RNA Interference*
  • RNA Splicing*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • RNA, Small Interfering
  • RNA-Dependent RNA Polymerase / genetics*
  • RNA-Dependent RNA Polymerase / metabolism
  • Transcriptome
  • Transgenes


  • ABH1 protein, Arabidopsis
  • Arabidopsis Proteins
  • DNA Transposable Elements
  • RNA Cap-Binding Proteins
  • RNA, Messenger
  • RNA, Plant
  • RNA, Small Interfering
  • Green Fluorescent Proteins
  • RNA-Dependent RNA Polymerase