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Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

BACKGROUND: The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrain...

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Autores principales: Kwon, Young-Ju, Park, Mi-Jeong, Kim, Sang-Gyu, Baldwin, Ian T, Park, Chung-Mo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035800/
https://www.ncbi.nlm.nih.gov/pubmed/24885185
http://dx.doi.org/10.1186/1471-2229-14-136
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author Kwon, Young-Ju
Park, Mi-Jeong
Kim, Sang-Gyu
Baldwin, Ian T
Park, Chung-Mo
author_facet Kwon, Young-Ju
Park, Mi-Jeong
Kim, Sang-Gyu
Baldwin, Ian T
Park, Chung-Mo
author_sort Kwon, Young-Ju
collection PubMed
description BACKGROUND: The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. RESULTS: We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. CONCLUSION: Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress adaptation in plants. It is also envisioned that alternative splicing of the clock genes plays more complex roles than previously expected.
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spelling pubmed-40358002014-05-29 Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis Kwon, Young-Ju Park, Mi-Jeong Kim, Sang-Gyu Baldwin, Ian T Park, Chung-Mo BMC Plant Biol Research Article BACKGROUND: The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. RESULTS: We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. CONCLUSION: Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress adaptation in plants. It is also envisioned that alternative splicing of the clock genes plays more complex roles than previously expected. BioMed Central 2014-05-19 /pmc/articles/PMC4035800/ /pubmed/24885185 http://dx.doi.org/10.1186/1471-2229-14-136 Text en Copyright © 2014 Kwon et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Kwon, Young-Ju
Park, Mi-Jeong
Kim, Sang-Gyu
Baldwin, Ian T
Park, Chung-Mo
Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title_full Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title_fullStr Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title_full_unstemmed Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title_short Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis
title_sort alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in arabidopsis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035800/
https://www.ncbi.nlm.nih.gov/pubmed/24885185
http://dx.doi.org/10.1186/1471-2229-14-136
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