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

Handle URI:
http://hdl.handle.net/10754/334585
Title:
Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis
Authors:
Ding, Feng ( 0000-0001-8237-4062 ) ; Cui, Peng ( 0000-0003-3076-0070 ) ; Wang, Zhenyu; Zhang, ShouDong; Ali, Shahjahan; Xiong, Liming ( 0000-0001-8099-0806 )
Abstract:
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. 2014 Ding et al.; licensee BioMed Central Ltd.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Ding F, Cui P, Wang Z, Zhang S, Ali S, et al. (2014) Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics 15: 431. doi:10.1186/1471-2164-15-431.
Publisher:
Springer Nature
Journal:
BMC Genomics
Issue Date:
4-Jun-2014
DOI:
10.1186/1471-2164-15-431
PubMed ID:
24897929
PubMed Central ID:
PMC4079960
Type:
Article
ISSN:
14712164
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorDing, Fengen
dc.contributor.authorCui, Pengen
dc.contributor.authorWang, Zhenyuen
dc.contributor.authorZhang, ShouDongen
dc.contributor.authorAli, Shahjahanen
dc.contributor.authorXiong, Limingen
dc.date.accessioned2014-11-11T14:30:55Z-
dc.date.available2014-11-11T14:30:55Z-
dc.date.issued2014-06-04en
dc.identifier.citationDing F, Cui P, Wang Z, Zhang S, Ali S, et al. (2014) Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics 15: 431. doi:10.1186/1471-2164-15-431.en
dc.identifier.issn14712164en
dc.identifier.pmid24897929en
dc.identifier.doi10.1186/1471-2164-15-431en
dc.identifier.urihttp://hdl.handle.net/10754/334585en
dc.description.abstractBackground: 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. 2014 Ding et al.; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rights© Ding et al.; licensee BioMed Central Ltd. 2014en
dc.rightsThis 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.en
dc.rightsArchived with thanks to BMC Genomicsen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectAlternative splicingen
dc.subjectArabidopsis thalianaen
dc.subjectPre-mRNAen
dc.subjectSalt stressen
dc.subjectSR proteinsen
dc.subjectarginineen
dc.subjectmessenger RNA precursoren
dc.subjectnucleotideen
dc.subjectserineen
dc.subjectsodium chlorideen
dc.subjectadaptationen
dc.subjectalternative RNA splicingen
dc.subjectarticleen
dc.subjectconcentration (parameters)en
dc.subjectcontrolled studyen
dc.subjectdifferential alternative splicingen
dc.subjectDNA flanking regionen
dc.subjectexon skippingen
dc.subjectgeneen
dc.subjectgene controlen
dc.subjectgenetic associationen
dc.subjectgenetic databaseen
dc.subjectgenetic parametersen
dc.subjectgenome analysisen
dc.subjectintronen
dc.subjectnonhumanen
dc.subjectplant genomeen
dc.subjectplant responseen
dc.subjectRNA sequenceen
dc.subjectsalt stressen
dc.subjectseedlingen
dc.subjectsite selectionen
dc.titleGenome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsisen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC4079960en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorDing, Fengen
kaust.authorCui, Pengen
kaust.authorWang, Zhenyuen
kaust.authorZhang, ShouDongen
kaust.authorAli, Shahjahanen
kaust.authorXiong, Limingen

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