Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.
Identifieur interne : 001348 ( Main/Exploration ); précédent : 001347; suivant : 001349Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.
Auteurs : Matthew Zinkgraf [États-Unis] ; Lijun Liu [États-Unis] ; Andrew Groover [États-Unis] ; Vladimir Filkov [États-Unis]Source :
- The New phytologist [ 1469-8137 ] ; 2017.
Descripteurs français
- KwdFr :
- ADN des plantes (MeSH), Adaptation biologique (génétique), Bois (croissance et développement), Bois (génétique), Environnement (MeSH), Facteurs de transcription (génétique), Facteurs de transcription (métabolisme), Immunoprécipitation de la chromatine (MeSH), Populus (croissance et développement), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Étude d'association pangénomique (MeSH).
- MESH :
- croissance et développement : Bois, Populus.
- génétique : Adaptation biologique, Bois, Facteurs de transcription, Populus.
- métabolisme : Facteurs de transcription.
- ADN des plantes, Environnement, Immunoprécipitation de la chromatine, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Étude d'association pangénomique.
English descriptors
- KwdEn :
- Adaptation, Biological (genetics), Chromatin Immunoprecipitation (MeSH), DNA, Plant (MeSH), Environment (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genome-Wide Association Study (MeSH), Populus (genetics), Populus (growth & development), Transcription Factors (genetics), Transcription Factors (metabolism), Wood (genetics), Wood (growth & development).
- MESH :
- chemical , genetics : Transcription Factors.
- chemical , metabolism : Transcription Factors.
- chemical : DNA, Plant.
- genetics : Adaptation, Biological, Populus, Wood.
- growth & development : Populus, Wood.
- Chromatin Immunoprecipitation, Environment, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome-Wide Association Study.
Abstract
Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies.
DOI: 10.1111/nph.14492
PubMed: 28248425
Affiliations:
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V" first="Vladimir" last="Filkov">Vladimir Filkov</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, University of California, Davis, CA, 95618, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, University of California, Davis, CA, 95618</wicri:regionArea><wicri:noRegion>95618</wicri:noRegion></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Biological (genetics)</term><term>Chromatin Immunoprecipitation (MeSH)</term><term>DNA, Plant (MeSH)</term><term>Environment (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Transcription Factors (genetics)</term><term>Transcription Factors (metabolism)</term><term>Wood (genetics)</term><term>Wood (growth & development)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (MeSH)</term><term>Adaptation biologique (génétique)</term><term>Bois (croissance et développement)</term><term>Bois (génétique)</term><term>Environnement (MeSH)</term><term>Facteurs de transcription (génétique)</term><term>Facteurs de transcription (métabolisme)</term><term>Immunoprécipitation de la chromatine (MeSH)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bois</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adaptation, Biological</term><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Adaptation biologique</term><term>Bois</term><term>Facteurs de transcription</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromatin Immunoprecipitation</term><term>Environment</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genome-Wide Association Study</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN des plantes</term><term>Environnement</term><term>Immunoprécipitation de la chromatine</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28248425</PMID><DateCompleted><Year>2018</Year><Month>02</Month><Day>22</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>214</Volume><Issue>4</Issue><PubDate><Year>2017</Year><Month>Jun</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.</ArticleTitle><Pagination><MedlinePgn>1464-1478</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.14492</ELocationID><Abstract><AbstractText>Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies.</AbstractText><CopyrightInformation>No claim to original US government works. New Phytologist © 2017 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zinkgraf</LastName><ForeName>Matthew</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, University of California, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Lijun</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Groover</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-6686-5774</Identifier><AffiliationInfo><Affiliation>USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, University of California, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Filkov</LastName><ForeName>Vladimir</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Computer Science, University of California, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>03</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000220" MajorTopicYN="N">Adaptation, Biological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D047369" MajorTopicYN="N">Chromatin Immunoprecipitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004777" MajorTopicYN="N">Environment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="Y">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus
</Keyword><Keyword MajorTopicYN="N">data integration</Keyword><Keyword MajorTopicYN="N">genomics</Keyword><Keyword MajorTopicYN="N">transcriptional networks</Keyword><Keyword MajorTopicYN="N">wood formation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>10</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>01</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28248425</ArticleId><ArticleId IdType="doi">10.1111/nph.14492</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name></noRegion><name sortKey="Filkov, Vladimir" sort="Filkov, Vladimir" uniqKey="Filkov V" first="Vladimir" last="Filkov">Vladimir Filkov</name><name sortKey="Groover, Andrew" sort="Groover, Andrew" uniqKey="Groover A" first="Andrew" last="Groover">Andrew Groover</name><name sortKey="Groover, Andrew" sort="Groover, Andrew" uniqKey="Groover A" first="Andrew" last="Groover">Andrew Groover</name><name sortKey="Liu, Lijun" sort="Liu, Lijun" uniqKey="Liu L" first="Lijun" last="Liu">Lijun Liu</name><name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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