The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function.
Identifieur interne : 001B15 ( Main/Exploration ); précédent : 001B14; suivant : 001B16The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function.
Auteurs : Lijun Liu [États-Unis] ; Matthew Zinkgraf ; H Earl Petzold ; Eric P. Beers ; Vladimir Filkov ; Andrew GrooverSource :
- The New phytologist [ 1469-8137 ] ; 2015.
Descripteurs français
- KwdFr :
- Bois (croissance et développement), Bois (génétique), Données de séquences moléculaires (MeSH), Facteurs de transcription (génétique), Facteurs de transcription (métabolisme), Immunoprécipitation de la chromatine (MeSH), Populus (croissance et développement), Populus (génétique), Protéines végétales (génétique), Protéines végétales (métabolisme), Protéines à homéodomaine (génétique), Protéines à homéodomaine (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Sites de fixation (MeSH), Séquence d'acides aminés (MeSH), Zea mays (génétique), Zea mays (métabolisme), Étude d'association pangénomique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- croissance et développement : Bois, Populus.
- génétique : Bois, Facteurs de transcription, Populus, Protéines végétales, Protéines à homéodomaine, Zea mays.
- métabolisme : Facteurs de transcription, Protéines végétales, Protéines à homéodomaine, Zea mays.
- Données de séquences moléculaires, Immunoprécipitation de la chromatine, Régulation de l'expression des gènes végétaux, Sites de fixation, Séquence d'acides aminés, Étude d'association pangénomique, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Binding Sites (MeSH), Chromatin Immunoprecipitation (MeSH), Evolution, Molecular (MeSH), Gene Expression Regulation, Plant (MeSH), Genome-Wide Association Study (MeSH), Homeodomain Proteins (genetics), Homeodomain Proteins (metabolism), Molecular Sequence Data (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (genetics), Populus (growth & development), Transcription Factors (genetics), Transcription Factors (metabolism), Wood (genetics), Wood (growth & development), Zea mays (genetics), Zea mays (metabolism).
- MESH :
- chemical , genetics : Homeodomain Proteins, Plant Proteins, Transcription Factors.
- chemical , metabolism : Homeodomain Proteins, Plant Proteins, Transcription Factors.
- genetics : Populus, Wood, Zea mays.
- growth & development : Populus, Wood.
- metabolism : Zea mays.
- Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Evolution, Molecular, Gene Expression Regulation, Plant, Genome-Wide Association Study, Molecular Sequence Data.
Abstract
The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) technology to identify ARK1 binding loci genome-wide in Populus. Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole-genome salicoid duplication event. Both ARK1 and a maize (Zea mays) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over-expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species.
DOI: 10.1111/nph.13151
PubMed: 25377848
Affiliations:
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Beers</name></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">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Binding Sites (MeSH)</term><term>Chromatin Immunoprecipitation (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Homeodomain Proteins (genetics)</term><term>Homeodomain Proteins (metabolism)</term><term>Molecular Sequence Data (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</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><term>Zea mays (genetics)</term><term>Zea mays (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bois (croissance et développement)</term><term>Bois (génétique)</term><term>Données de séquences moléculaires (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>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Protéines à homéodomaine (génétique)</term><term>Protéines à homéodomaine (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Sites de fixation (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term><term>Zea mays (génétique)</term><term>Zea mays (métabolisme)</term><term>Étude d'association pangénomique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Homeodomain Proteins</term><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Homeodomain Proteins</term><term>Plant Proteins</term><term>Transcription Factors</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>Populus</term><term>Wood</term><term>Zea mays</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>Bois</term><term>Facteurs de transcription</term><term>Populus</term><term>Protéines végétales</term><term>Protéines à homéodomaine</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term><term>Protéines végétales</term><term>Protéines à homéodomaine</term><term>Zea mays</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Chromatin Immunoprecipitation</term><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Genome-Wide Association Study</term><term>Molecular Sequence Data</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Immunoprécipitation de la chromatine</term><term>Régulation de l'expression des gènes végétaux</term><term>Sites de fixation</term><term>Séquence d'acides aminés</term><term>Étude d'association pangénomique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) technology to identify ARK1 binding loci genome-wide in Populus. Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole-genome salicoid duplication event. Both ARK1 and a maize (Zea mays) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over-expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25377848</PMID><DateCompleted><Year>2015</Year><Month>08</Month><Day>24</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>205</Volume><Issue>2</Issue><PubDate><Year>2015</Year><Month>Jan</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function.</ArticleTitle><Pagination><MedlinePgn>682-94</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.13151</ELocationID><Abstract><AbstractText>The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) technology to identify ARK1 binding loci genome-wide in Populus. Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole-genome salicoid duplication event. Both ARK1 and a maize (Zea mays) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over-expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species. </AbstractText><CopyrightInformation>No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Lijun</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Pacific Southwest Research Station, USDA Forest Service, Davis, CA, 95618, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zinkgraf</LastName><ForeName>Matthew</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Petzold</LastName><ForeName>H Earl</ForeName><Initials>HE</Initials></Author><Author ValidYN="Y"><LastName>Beers</LastName><ForeName>Eric P</ForeName><Initials>EP</Initials></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><DataBankList CompleteYN="Y"><DataBank><DataBankName>SRA</DataBankName><AccessionNumberList><AccessionNumber>SRP042635</AccessionNumber></AccessionNumberList></DataBank></DataBankList><GrantList CompleteYN="Y"><Grant><GrantID>S10RR027303</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>S10RR029668</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>11</Month><Day>07</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="D018398">Homeodomain Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D047369" MajorTopicYN="N">Chromatin Immunoprecipitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018398" MajorTopicYN="N">Homeodomain Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</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="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</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></MeshHeading><MeshHeading><DescriptorName UI="D003313" MajorTopicYN="N">Zea mays</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">chromatin immunoprecipitation sequencing (ChIP-seq)</Keyword><Keyword MajorTopicYN="N">forest tree</Keyword><Keyword MajorTopicYN="N">transcriptional regulation</Keyword><Keyword MajorTopicYN="N">wood formation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>08</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>10</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>11</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>11</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25377848</ArticleId><ArticleId IdType="doi">10.1111/nph.13151</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P" last="Beers">Eric P. Beers</name><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="Petzold, H Earl" sort="Petzold, H Earl" uniqKey="Petzold H" first="H Earl" last="Petzold">H Earl Petzold</name><name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Liu, Lijun" sort="Liu, Lijun" uniqKey="Liu L" first="Lijun" last="Liu">Lijun Liu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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