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Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

Calixto, Cristiane P.G.; Guo, Wenbin; James, Allan B.; Tzioutziou, Nikoleta A.; Entizne, Juan Carlos; Panter, Paige E.; Knight, Heather; Nimmo, Hugh G.; Zhang, Runxuan; Brown, John W.S.

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Authors

Cristiane P.G. Calixto

Wenbin Guo

Allan B. James

Nikoleta A. Tzioutziou

Juan Carlos Entizne

Paige E. Panter

Hugh G. Nimmo

Runxuan Zhang

John W.S. Brown



Abstract

Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming 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 that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.

Citation

Calixto, C. P., Guo, W., James, A. B., Tzioutziou, N. A., Entizne, J. C., Panter, P. E., …Brown, J. W. (2018). Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. The Plant Cell, 30, 1424-1444. https://doi.org/10.1105/tpc.18.00177

Journal Article Type Article
Acceptance Date May 10, 2018
Online Publication Date May 15, 2018
Publication Date May 15, 2018
Deposit Date Nov 8, 2018
Publicly Available Date Mar 29, 2024
Journal Plant Cell
Print ISSN 1040-4651
Electronic ISSN 1532-298X
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 30
Pages 1424-1444
DOI https://doi.org/10.1105/tpc.18.00177

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