Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes

  • Craig G. SimpsonEmail author
  • John Fuller
  • Cristiane P. G. Calixto
  • Jim McNicol
  • Clare Booth
  • John W. S. Brown
  • Dorothee Staiger
Part of the Methods in Molecular Biology book series (MIMB, volume 1398)


Posttranscriptional control makes an important contribution to circadian regulation of gene expression. In higher plants, alternative splicing is particularly prevalent upon abiotic and biotic stress and in the circadian system. Here we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) to monitor alternative splicing events. The use of the panel allows the quantification of changes in the proportion of splice isoforms between different samples, e.g., different time points, different tissues, genotypes, ecotypes, or treatments.

Key words

Alternative splicing Circadian rhythm RNA-binding proteins Splicing factors 



Work in our laboratories is supported by grants from the Biotechnology and Biological Sciences Research Council (BB/G024979/1, European Research Area network Plant Genomics [Plant Alternative Splicing and Abiotic Stress]) and the Scottish Government Rural and Environment Science and Analytical Services division (to J.W.S.B. and C.S.) and the DFG (STA 653 and SPP1530) (to D.S.).


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Craig G. Simpson
    • 1
    Email author
  • John Fuller
    • 1
  • Cristiane P. G. Calixto
    • 2
  • Jim McNicol
    • 3
  • Clare Booth
    • 1
  • John W. S. Brown
    • 1
    • 2
  • Dorothee Staiger
    • 4
  1. 1.Cell and Molecular SciencesThe James Hutton InstituteInvergowrieUK
  2. 2.Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteDundeeUK
  3. 3.Biomathematics and Statistics ScotlandInvergowrieUK
  4. 4.Molecular Cell Physiology, Faculty of BiologyBielefeld UniversityBielefeldGermany

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