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Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

BACKGROUND: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. RESULTS: To analyze global changes in AS under salt stress, we...

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Autores principales: Ding, Feng, Cui, Peng, Wang, Zhenyu, Zhang, Shoudong, Ali, Shahjahan, Xiong, Liming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079960/
https://www.ncbi.nlm.nih.gov/pubmed/24897929
http://dx.doi.org/10.1186/1471-2164-15-431
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author Ding, Feng
Cui, Peng
Wang, Zhenyu
Zhang, Shoudong
Ali, Shahjahan
Xiong, Liming
author_facet Ding, Feng
Cui, Peng
Wang, Zhenyu
Zhang, Shoudong
Ali, Shahjahan
Xiong, Liming
author_sort Ding, Feng
collection PubMed
description BACKGROUND: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. RESULTS: To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS. CONCLUSIONS: Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users.
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spelling pubmed-40799602014-09-19 Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis Ding, Feng Cui, Peng Wang, Zhenyu Zhang, Shoudong Ali, Shahjahan Xiong, Liming BMC Genomics Research Article BACKGROUND: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. RESULTS: To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS. CONCLUSIONS: Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users. BioMed Central 2014-06-04 /pmc/articles/PMC4079960/ /pubmed/24897929 http://dx.doi.org/10.1186/1471-2164-15-431 Text en © Ding et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. 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
Ding, Feng
Cui, Peng
Wang, Zhenyu
Zhang, Shoudong
Ali, Shahjahan
Xiong, Liming
Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title_full Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title_fullStr Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title_full_unstemmed Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title_short Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
title_sort genome-wide analysis of alternative splicing of pre-mrna under salt stress in arabidopsis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079960/
https://www.ncbi.nlm.nih.gov/pubmed/24897929
http://dx.doi.org/10.1186/1471-2164-15-431
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