Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

Mol Cell. 2019 Mar 7;73(5):1066-1074.e3. doi: 10.1016/j.molcel.2018.12.005. Epub 2019 Jan 17.


Light makes carbon fixation possible, allowing plant and animal life on Earth. We have previously shown that light regulates alternative splicing in plants. Light initiates a chloroplast retrograde signaling that regulates nuclear alternative splicing of a subset of Arabidopsis thaliana transcripts. Here, we show that light promotes RNA polymerase II (Pol II) elongation in the affected genes, whereas in darkness, elongation is lower. These changes in transcription are consistent with elongation causing the observed changes in alternative splicing, as revealed by different drug treatments and genetic evidence. The light control of splicing and elongation is abolished in an Arabidopsis mutant defective in the transcription factor IIS (TFIIS). We report that the chloroplast control of nuclear alternative splicing in plants responds to the kinetic coupling mechanism found in mammalian cells, providing unique evidence that coupling is important for a whole organism to respond to environmental cues.

Keywords: alternative splicing; light control in plants; transcription elongation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Alternative Splicing / radiation effects*
  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis / radiation effects*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Darkness
  • Gene Expression Regulation, Plant / radiation effects*
  • Histones / genetics
  • Histones / metabolism
  • Kinetics
  • Light*
  • Mutation
  • Plants, Genetically Modified / genetics
  • Plants, Genetically Modified / metabolism
  • Plants, Genetically Modified / radiation effects*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Plant / biosynthesis
  • RNA, Plant / genetics
  • RNA, Plant / radiation effects*
  • Transcription Elongation, Genetic / radiation effects*
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / metabolism


  • Arabidopsis Proteins
  • Histones
  • RNA, Plant
  • Transcriptional Elongation Factors
  • transcription factor S-II
  • RNA Polymerase II