Transcriptional and temporal response of Populus stems to gravi-stimulation.
Identifieur interne : 000C24 ( Main/Exploration ); précédent : 000C23; suivant : 000C25Transcriptional and temporal response of Populus stems to gravi-stimulation.
Auteurs : Matthew Zinkgraf [États-Unis] ; Suzanne Gerttula [États-Unis] ; Shutang Zhao [République populaire de Chine] ; Vladimir Filkov [États-Unis] ; Andrew Groover [États-Unis]Source :
- Journal of integrative plant biology [ 1744-7909 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Annotation de séquence moléculaire (MeSH), Bois (génétique), Facteurs temps (MeSH), Gene Ontology (MeSH), Gravitation (MeSH), Gènes de plante (MeSH), Populus (génétique), Populus (physiologie), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Spécificité d'organe (génétique), Tiges de plante (génétique), Tiges de plante (physiologie), Transcription génétique (MeSH).
- MESH :
- génétique : Bois, Populus, Spécificité d'organe, Tiges de plante.
- physiologie : Populus, Tiges de plante.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Annotation de séquence moléculaire, Facteurs temps, Gene Ontology, Gravitation, Gènes de plante, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Transcription génétique.
English descriptors
- KwdEn :
- Cluster Analysis (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Ontology (MeSH), Gene Regulatory Networks (MeSH), Genes, Plant (MeSH), Gravitation (MeSH), Molecular Sequence Annotation (MeSH), Organ Specificity (genetics), Plant Stems (genetics), Plant Stems (physiology), Populus (genetics), Populus (physiology), Time Factors (MeSH), Transcription, Genetic (MeSH), Wood (genetics).
- MESH :
- genetics : Organ Specificity, Plant Stems, Populus, Wood.
- physiology : Plant Stems, Populus.
- Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Ontology, Gene Regulatory Networks, Genes, Plant, Gravitation, Molecular Sequence Annotation, Time Factors, Transcription, Genetic.
Abstract
Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi-stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time-series analysis of seven time points over a 14-d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue-specific impulse responses that peaked at about 24-48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14-d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time-series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.
DOI: 10.1111/jipb.12645
PubMed: 29480544
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95618</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Journal of integrative plant biology</title><idno type="eISSN">1744-7909</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cluster Analysis (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Gravitation (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Organ Specificity (genetics)</term><term>Plant Stems (genetics)</term><term>Plant Stems (physiology)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Time Factors (MeSH)</term><term>Transcription, Genetic (MeSH)</term><term>Wood (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Bois (génétique)</term><term>Facteurs temps (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gravitation (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Spécificité d'organe (génétique)</term><term>Tiges de plante (génétique)</term><term>Tiges de plante (physiologie)</term><term>Transcription génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Organ Specificity</term><term>Plant Stems</term><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bois</term><term>Populus</term><term>Spécificité d'organe</term><term>Tiges de plante</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term><term>Tiges de plante</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Plant Stems</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>Gene Regulatory Networks</term><term>Genes, Plant</term><term>Gravitation</term><term>Molecular Sequence Annotation</term><term>Time Factors</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Annotation de séquence moléculaire</term><term>Facteurs temps</term><term>Gene Ontology</term><term>Gravitation</term><term>Gènes de plante</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi-stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time-series analysis of seven time points over a 14-d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue-specific impulse responses that peaked at about 24-48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14-d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time-series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29480544</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>10</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1744-7909</ISSN><JournalIssue CitedMedium="Internet"><Volume>60</Volume><Issue>7</Issue><PubDate><Year>2018</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Journal of integrative plant biology</Title><ISOAbbreviation>J Integr Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Transcriptional and temporal response of Populus stems to gravi-stimulation.</ArticleTitle><Pagination><MedlinePgn>578-590</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/jipb.12645</ELocationID><Abstract><AbstractText>Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi-stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time-series analysis of seven time points over a 14-d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue-specific impulse responses that peaked at about 24-48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14-d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time-series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.</AbstractText><CopyrightInformation>Published 2018. This article is a U.S. Government work and is in the public domain in the USA.</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, 1731 Research Park Drive, Davis, CA 95618, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gerttula</LastName><ForeName>Suzanne</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Shutang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</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, One Shields Avenue, Davis, CA 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Groover</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95618, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>05</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>China (Republic : 1949- )</Country><MedlineTA>J Integr Plant Biol</MedlineTA><NlmUniqueID>101250502</NlmUniqueID><ISSNLinking>1672-9072</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006112" MajorTopicYN="Y">Gravitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009928" MajorTopicYN="N">Organ Specificity</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="Y">Transcription, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>02</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>2</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>10</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>2</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29480544</ArticleId><ArticleId IdType="doi">10.1111/jipb.12645</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Californie</li></region><settlement><li>Pékin</li></settlement></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name></region><name sortKey="Filkov, Vladimir" sort="Filkov, Vladimir" uniqKey="Filkov V" first="Vladimir" last="Filkov">Vladimir Filkov</name><name sortKey="Gerttula, Suzanne" sort="Gerttula, Suzanne" uniqKey="Gerttula S" first="Suzanne" last="Gerttula">Suzanne Gerttula</name><name sortKey="Gerttula, Suzanne" sort="Gerttula, Suzanne" uniqKey="Gerttula S" first="Suzanne" last="Gerttula">Suzanne Gerttula</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="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Zhao, Shutang" sort="Zhao, Shutang" uniqKey="Zhao S" first="Shutang" last="Zhao">Shutang Zhao</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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