Identification of alternative splicing events regulated by an Arabidopsis serine/arginine-like protein, atSR45a, in response to high-light stress using a tiling array

Plant Cell Physiol. 2011 Oct;52(10):1786-805. doi: 10.1093/pcp/pcr115. Epub 2011 Aug 23.

Abstract

We have demonstrated that an Arabidopsis serine/arginine rich-like protein, atSR45a, interacts with other splicing factors and its expression is markedly induced by high-light stress, suggesting the involvement of atSR45a in the regulation of stress-responsive alternative splicing. A whole-genome tiling array identified the alternative splicing of genes regulated by atSR45a by comparing gene expression profiles in wild-type and knockout atSR45a (KO-sr45a) plants under high-light stress. The expression levels of genomic regions within 217 genes were significantly altered in the KO-sr45a plants compared with the wild-type plants. Many genes encoded factors involved in signal transduction, cell cycle and DNA processing, protein fate and transcription. A semi-quantitative reverse transcription-PCR (RT-PCR) analysis confirmed changes in the transcript levels and/or alternative splicing efficiency under high-light stress in 18 genes, suggesting that atSR45a affects directly or indirectly not only alternative splicing efficiency but also the transcription of these target genes. Changes in the expression of atSR45a in response to high-light stress temporally correlated with changes in the alternative splicing efficiency and transcript levels of three and one target genes, respectively. Sequencing of the alternatively spliced variants of three target genes showed that atSR45a suppresses the splicing efficiency of intron retention-type alternative splicing events. These findings indicated the importance of atSR45a to the diversification of the transcriptome under high-light stress.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / radiation effects
  • Alternative Splicing / genetics*
  • Alternative Splicing / radiation effects
  • Arabidopsis / genetics*
  • Arabidopsis / physiology*
  • Arabidopsis / radiation effects
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Gene Expression Regulation, Plant / radiation effects
  • Gene Knockout Techniques
  • Genes, Plant / genetics
  • Genetic Association Studies
  • Light*
  • Mutation / genetics
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction
  • Serine-Arginine Splicing Factors
  • Stress, Physiological / radiation effects*
  • Transcription, Genetic / radiation effects

Substances

  • Arabidopsis Proteins
  • Nuclear Proteins
  • RNA, Messenger
  • RNA-Binding Proteins
  • SR45a protein, Arabidopsis
  • Serine-Arginine Splicing Factors