Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

Luíza L. B. Dantas, Cristiane P. G. Calixto, Maira M. Dourado, Monalisa S. Carneiro, John W. S. Brown (Lead / Corresponding author), Carlos T. Hotta

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Abstract

Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice, and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.

Original languageEnglish
Article number1614
Pages (from-to)1-15
Number of pages15
JournalFrontiers in Plant Science
Volume10
DOIs
Publication statusPublished - 23 Dec 2019

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alternative splicing
circadian rhythm
sugarcane
temperature
genes
C4 plants
introns
Arabidopsis
rice
environmental factors
genome
corn
winter
summer
crops

Keywords

  • alternative splicing
  • circadian clock
  • diel rhythms
  • field experiment
  • gene expression
  • sugarcane

Cite this

Dantas, Luíza L. B. ; Calixto, Cristiane P. G. ; Dourado, Maira M. ; Carneiro, Monalisa S. ; Brown, John W. S. ; Hotta, Carlos T. / Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. In: Frontiers in Plant Science. 2019 ; Vol. 10. pp. 1-15.
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title = "Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane",
abstract = "Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60{\%} of intron-containing genes in Arabidopsis, 46{\%} in rice, and 38{\%} in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.",
keywords = "alternative splicing, circadian clock, diel rhythms, field experiment, gene expression, sugarcane",
author = "Dantas, {Lu{\'i}za L. B.} and Calixto, {Cristiane P. G.} and Dourado, {Maira M.} and Carneiro, {Monalisa S.} and Brown, {John W. S.} and Hotta, {Carlos T.}",
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Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. / Dantas, Luíza L. B.; Calixto, Cristiane P. G.; Dourado, Maira M.; Carneiro, Monalisa S.; Brown, John W. S. (Lead / Corresponding author); Hotta, Carlos T.

In: Frontiers in Plant Science, Vol. 10, 1614, 23.12.2019, p. 1-15.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

AU - Dantas, Luíza L. B.

AU - Calixto, Cristiane P. G.

AU - Dourado, Maira M.

AU - Carneiro, Monalisa S.

AU - Brown, John W. S.

AU - Hotta, Carlos T.

N1 - The present study was supported by the São Paulo Research Foundation (FAPESP) [grant nos. 11/00818-8 and 15/06260-0; BIOEN Program], and by the Serrapilheira Institute (grant no. Serra-1708-16001). LD was supported by FAPESP scholarships [grants 11/08897-4 and 15/10220-3]. CC and JB were supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K006568/1 and BB/N022807/1] and the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to JB]. Copyright © 2019 Dantas, Calixto, Dourado, Carneiro, Brown and Hotta.

PY - 2019/12/23

Y1 - 2019/12/23

N2 - Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice, and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.

AB - Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice, and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.

KW - alternative splicing

KW - circadian clock

KW - diel rhythms

KW - field experiment

KW - gene expression

KW - sugarcane

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DO - 10.3389/fpls.2019.01614

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