Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

Calixto, C. P.G., Guo, W., James, A. B. , Tzioutziou, N. A., Entizne, J. C., Panter, P. E., Knight, H., Nimmo, H. , Zhang, R. and Brown, J. W.S. (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell, 30, pp. 1424-1444. (doi: 10.1105/tpc.18.00177) (PMID:29764987)

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Plants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction, and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA-binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four "early AS" splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE. Such factors likely drive cascades of AS of downstream genes which alongside transcription modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.

Item Type:Articles
Additional Information:This work was supported by funding from the Biotechnology and Biological Sciences Research Council (BB/K006568/1, BB/P009751/1, and BB/N022807/1 to J.W.S.B.; BB/K006835/1 to H.G.N.; and BB/ M010996/1-EASTBIO Doctoral Training Partnership to J.C.E.) and by the Scottish Government Rural and Environment Science and Analytical Services Division (to J.W.S.B. and R.Z.). We acknowledge the European Alternative Splicing Network of Excellence (EURASNET; LSHGCT-2005-518238) for catalyzing important collaborations.
Glasgow Author(s) Enlighten ID:Nimmo, Professor Hugh and James, Dr Allan
Authors: Calixto, C. P.G., Guo, W., James, A. B., Tzioutziou, N. A., Entizne, J. C., Panter, P. E., Knight, H., Nimmo, H., Zhang, R., and Brown, J. W.S.
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:Plant Cell
Publisher:American Society of Plant Biologists
ISSN (Online):1532-298X
Published Online:15 May 2018
Copyright Holders:Copyright © 2018 American Society of Plant Biologists
First Published:First published in Plant Cell 30: 1424-1444
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
607041Mechanisms and function of alternative splicing in the plant circadian clockHugh NimmoBiotechnology and Biological Sciences Research Council (BBSRC)BB/K006835/1RI MOLECULAR CELL & SYSTEMS BIOLOGY