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Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine

dc.rights.licenseopenen_US
dc.contributor.authorWONG, Darren Chern Jan
dc.contributor.authorLOPEZ GUTIERREZ, Rodrigo
hal.structure.identifierEcophysiologie et Génomique Fonctionnelle de la Vigne [UMR EGFV]
dc.contributor.authorGAMBETTA, Gregory
ORCID: 0000-0002-8838-5050
IDREF: 225449641
dc.contributor.authorCASTELLARIN, Simone Diego
dc.date.accessioned2020-04-01T14:57:27Z
dc.date.available2020-04-01T14:57:27Z
dc.date.issued2017
dc.identifier.issn1340-2838en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/4060
dc.description.abstractEnCoordinated transcriptional and metabolic reprogramming ensures a plant's continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.
dc.language.isoENen_US
dc.subjectAnalyse du transcriptome
dc.subjectFacteur de transcription
dc.subjectVitis Vinifera
dc.subjectexpression des gènes
dc.subject.enCis-Regulatory Element
dc.subject.enGene Co-Expression Network
dc.subject.enGrapevine
dc.subject.enPromoter
dc.subject.enTranscriptional Regulation
dc.title.enGenome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine
dc.title.alternativeDNA res.en_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1093/dnares/dsw061
dc.subject.halSciences du Vivant [q-bio]/Biologie végétaleen_US
dc.identifier.pubmed28119334en_US
bordeaux.journalDNA Researchen_US
bordeaux.page311-326en_US
bordeaux.volume24en_US
bordeaux.hal.laboratoriesEcophysiologie et Génomique Fonctionnelle de la Vigne (EGFV) - UMR 1287en_US
bordeaux.issue3en_US
bordeaux.institutionBordeaux Sciences Agroen_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
hal.identifierhal-03170549
hal.version1
hal.date.transferred2021-03-16T10:50:08Z
hal.exporttrue
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