Modeling transcriptional networks regulating secondary growth and wood formation in forest trees.
Identifieur interne : 002136 ( Main/Exploration ); précédent : 002135; suivant : 002137Modeling transcriptional networks regulating secondary growth and wood formation in forest trees.
Auteurs : Lijun Liu [États-Unis] ; Vladimir Filkov ; Andrew GrooverSource :
- Physiologia plantarum [ 1399-3054 ] ; 2014.
Descripteurs français
- KwdFr :
- Arbres (croissance et développement), Arbres (génétique), Arbres (physiologie), Biologie informatique (MeSH), Bois (croissance et développement), Bois (génétique), Bois (physiologie), Cambium (croissance et développement), Cambium (génétique), Cambium (physiologie), Forêts (MeSH), Génome végétal (génétique), Modèles génétiques (MeSH), Populus (croissance et développement), Populus (génétique), Populus (physiologie), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes au cours du développement (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Tiges de plante (croissance et développement), Tiges de plante (génétique), Tiges de plante (physiologie).
- MESH :
- croissance et développement : Arbres, Bois, Cambium, Populus, Tiges de plante.
- génétique : Arbres, Bois, Cambium, Génome végétal, Populus, Protéines végétales, Tiges de plante.
- métabolisme : Protéines végétales.
- physiologie : Arbres, Bois, Cambium, Populus, Tiges de plante.
- Biologie informatique, Forêts, Modèles génétiques, Régulation de l'expression des gènes au cours du développement, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique.
English descriptors
- KwdEn :
- Cambium (genetics), Cambium (growth & development), Cambium (physiology), Computational Biology (MeSH), Forests (MeSH), Gene Expression Regulation, Developmental (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genome, Plant (genetics), Models, Genetic (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plant Stems (genetics), Plant Stems (growth & development), Plant Stems (physiology), Populus (genetics), Populus (growth & development), Populus (physiology), Trees (genetics), Trees (growth & development), Trees (physiology), Wood (genetics), Wood (growth & development), Wood (physiology).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Cambium, Genome, Plant, Plant Stems, Populus, Trees, Wood.
- growth & development : Cambium, Plant Stems, Populus, Trees, Wood.
- chemical , metabolism : Plant Proteins.
- physiology : Cambium, Plant Stems, Populus, Trees, Wood.
- Computational Biology, Forests, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Regulatory Networks, Models, Genetic.
Abstract
The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary growth), but a comprehensive understanding of how these genes interact to influence woody growth is currently lacking. Modeling transcriptional networks has recently been made tractable by next-generation sequencing-based technologies that can comprehensively catalog gene expression and transcription factor-binding genome-wide, but has not yet been extensively applied to undomesticated tree species or woody growth. Here we discuss basic features of transcriptional networks, approaches for modeling biological networks, and examples of biological network models developed for forest trees to date. We discuss how transcriptional network research is being developed in the model forest tree genus, Populus, and how this research area can be further developed and applied. Transcriptional network models for forest tree secondary growth and wood formation could ultimately provide new predictive models to accelerate hypothesis-driven research and develop new breeding applications.
DOI: 10.1111/ppl.12113
PubMed: 24117954
Affiliations:
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Le document en format XML
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xml:lang="fr">États-Unis</country><wicri:regionArea>US Forest Service, Pacific Southwest Research Station, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Filkov, Vladimir" sort="Filkov, Vladimir" uniqKey="Filkov V" first="Vladimir" last="Filkov">Vladimir Filkov</name></author><author><name sortKey="Groover, Andrew" sort="Groover, Andrew" uniqKey="Groover A" first="Andrew" last="Groover">Andrew Groover</name></author></analytic><series><title level="j">Physiologia plantarum</title><idno type="eISSN">1399-3054</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cambium (genetics)</term><term>Cambium (growth & development)</term><term>Cambium (physiology)</term><term>Computational Biology (MeSH)</term><term>Forests (MeSH)</term><term>Gene Expression Regulation, Developmental (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genome, Plant (genetics)</term><term>Models, Genetic (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Plant Stems (genetics)</term><term>Plant Stems (growth & development)</term><term>Plant Stems (physiology)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Populus (physiology)</term><term>Trees (genetics)</term><term>Trees (growth & development)</term><term>Trees (physiology)</term><term>Wood (genetics)</term><term>Wood (growth & development)</term><term>Wood (physiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arbres (croissance et développement)</term><term>Arbres (génétique)</term><term>Arbres (physiologie)</term><term>Biologie informatique (MeSH)</term><term>Bois (croissance et développement)</term><term>Bois (génétique)</term><term>Bois (physiologie)</term><term>Cambium (croissance et développement)</term><term>Cambium (génétique)</term><term>Cambium (physiologie)</term><term>Forêts (MeSH)</term><term>Génome végétal (génétique)</term><term>Modèles génétiques (MeSH)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Régulation de l'expression des gènes au cours du développement (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Tiges de plante (croissance et développement)</term><term>Tiges de plante (génétique)</term><term>Tiges de plante (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" 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qualifier="physiologie" xml:lang="fr"><term>Arbres</term><term>Bois</term><term>Cambium</term><term>Populus</term><term>Tiges de plante</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Cambium</term><term>Plant Stems</term><term>Populus</term><term>Trees</term><term>Wood</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Forests</term><term>Gene Expression Regulation, Developmental</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Models, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term><term>Forêts</term><term>Modèles génétiques</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary growth), but a comprehensive understanding of how these genes interact to influence woody growth is currently lacking. Modeling transcriptional networks has recently been made tractable by next-generation sequencing-based technologies that can comprehensively catalog gene expression and transcription factor-binding genome-wide, but has not yet been extensively applied to undomesticated tree species or woody growth. Here we discuss basic features of transcriptional networks, approaches for modeling biological networks, and examples of biological network models developed for forest trees to date. We discuss how transcriptional network research is being developed in the model forest tree genus, Populus, and how this research area can be further developed and applied. Transcriptional network models for forest tree secondary growth and wood formation could ultimately provide new predictive models to accelerate hypothesis-driven research and develop new breeding applications. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24117954</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>14</Day></DateCompleted><DateRevised><Year>2014</Year><Month>05</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1399-3054</ISSN><JournalIssue CitedMedium="Internet"><Volume>151</Volume><Issue>2</Issue><PubDate><Year>2014</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Physiologia plantarum</Title><ISOAbbreviation>Physiol Plant</ISOAbbreviation></Journal><ArticleTitle>Modeling transcriptional networks regulating secondary growth and wood formation in forest trees.</ArticleTitle><Pagination><MedlinePgn>156-63</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/ppl.12113</ELocationID><Abstract><AbstractText>The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary growth), but a comprehensive understanding of how these genes interact to influence woody growth is currently lacking. Modeling transcriptional networks has recently been made tractable by next-generation sequencing-based technologies that can comprehensively catalog gene expression and transcription factor-binding genome-wide, but has not yet been extensively applied to undomesticated tree species or woody growth. Here we discuss basic features of transcriptional networks, approaches for modeling biological networks, and examples of biological network models developed for forest trees to date. We discuss how transcriptional network research is being developed in the model forest tree genus, Populus, and how this research area can be further developed and applied. Transcriptional network models for forest tree secondary growth and wood formation could ultimately provide new predictive models to accelerate hypothesis-driven research and develop new breeding applications. </AbstractText><CopyrightInformation>© 2013 Scandinavian Plant Physiology Society.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Lijun</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>US Forest Service, Pacific Southwest Research Station, Davis, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Filkov</LastName><ForeName>Vladimir</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Groover</LastName><ForeName>Andrew</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>10</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>Denmark</Country><MedlineTA>Physiol Plant</MedlineTA><NlmUniqueID>1256322</NlmUniqueID><ISSNLinking>0031-9317</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D058506" MajorTopicYN="N">Cambium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D065928" MajorTopicYN="N">Forests</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018507" MajorTopicYN="N">Gene Expression Regulation, Developmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="Y">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>07</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2013</Year><Month>08</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>09</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>10</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>10</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24117954</ArticleId><ArticleId IdType="doi">10.1111/ppl.12113</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><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></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Liu, Lijun" sort="Liu, Lijun" uniqKey="Liu L" first="Lijun" last="Liu">Lijun Liu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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