Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.
Identifieur interne : 002591 ( Main/Exploration ); précédent : 002590; suivant : 002592Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.
Auteurs : Clément Lafon-Placette [France] ; Patricia Faivre-Rampant ; Alain Delaunay ; Nathaniel Street ; Franck Brignolas ; Stéphane MaurySource :
- The New phytologist [ 1469-8137 ] ; 2013.
Descripteurs français
- KwdFr :
- ARN messager (génétique), ARN messager (métabolisme), Analyse de séquence d'ADN (MeSH), Cartographie chromosomique (MeSH), Chromatine (métabolisme), Croisements génétiques (MeSH), Cytosine (métabolisme), Deoxyribonuclease I (métabolisme), Gènes de plante (génétique), Hybridation génétique (MeSH), Immunoprécipitation de la chromatine (MeSH), Modèles génétiques (MeSH), Méristème (cytologie), Méristème (génétique), Méthylation de l'ADN (génétique), Populus (cytologie), Populus (génétique), Reproductibilité des résultats (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Séquence nucléotidique (MeSH), Variation génétique (MeSH).
- MESH :
- cytologie : Méristème, Populus.
- génétique : ARN messager, Gènes de plante, Méristème, Méthylation de l'ADN, Populus.
- métabolisme : ARN messager, Chromatine, Cytosine, Deoxyribonuclease I.
- Analyse de séquence d'ADN, Cartographie chromosomique, Croisements génétiques, Hybridation génétique, Immunoprécipitation de la chromatine, Modèles génétiques, Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Séquence nucléotidique, Variation génétique.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Chromatin (metabolism), Chromatin Immunoprecipitation (MeSH), Chromosome Mapping (MeSH), Crosses, Genetic (MeSH), Cytosine (metabolism), DNA Methylation (genetics), Deoxyribonuclease I (metabolism), Gene Expression Regulation, Plant (MeSH), Genes, Plant (genetics), Genetic Variation (MeSH), Hybridization, Genetic (MeSH), Meristem (cytology), Meristem (genetics), Models, Genetic (MeSH), Populus (cytology), Populus (genetics), RNA, Messenger (genetics), RNA, Messenger (metabolism), Reproducibility of Results (MeSH), Sequence Analysis, DNA (MeSH).
- MESH :
- chemical , genetics : RNA, Messenger.
- chemical , metabolism : Chromatin, Cytosine, Deoxyribonuclease I, RNA, Messenger.
- cytology : Meristem, Populus.
- genetics : DNA Methylation, Genes, Plant, Meristem, Populus.
- Base Sequence, Chromatin Immunoprecipitation, Chromosome Mapping, Crosses, Genetic, Gene Expression Regulation, Plant, Genetic Variation, Hybridization, Genetic, Models, Genetic, Reproducibility of Results, Sequence Analysis, DNA.
Abstract
DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification. Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels. While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes. Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.
DOI: 10.1111/nph.12026
PubMed: 23253333
Affiliations:
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génétique</term><term>Immunoprécipitation de la chromatine</term><term>Modèles génétiques</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquence nucléotidique</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification. Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels. While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes. Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23253333</PMID><DateCompleted><Year>2013</Year><Month>05</Month><Day>21</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>197</Volume><Issue>2</Issue><PubDate><Year>2013</Year><Month>Jan</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.</ArticleTitle><Pagination><MedlinePgn>416-30</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.12026</ELocationID><Abstract><AbstractText>DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification. Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels. While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes. Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.</AbstractText><CopyrightInformation>© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lafon-Placette</LastName><ForeName>Clément</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures-LBLGC, UPRES EA 1207, Orléans 45067, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faivre-Rampant</LastName><ForeName>Patricia</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Delaunay</LastName><ForeName>Alain</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Brignolas</LastName><ForeName>Franck</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Maury</LastName><ForeName>Stéphane</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>12</Month><Day>17</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="D002843">Chromatin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>8J337D1HZY</RegistryNumber><NameOfSubstance UI="D003596">Cytosine</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.21.1</RegistryNumber><NameOfSubstance UI="D003850">Deoxyribonuclease I</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002843" MajorTopicYN="N">Chromatin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D047369" MajorTopicYN="N">Chromatin Immunoprecipitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003433" MajorTopicYN="N">Crosses, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003596" MajorTopicYN="N">Cytosine</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019175" MajorTopicYN="N">DNA Methylation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003850" MajorTopicYN="N">Deoxyribonuclease I</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="N">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018519" MajorTopicYN="N">Meristem</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>08</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>10</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>12</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>12</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>5</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23253333</ArticleId><ArticleId IdType="doi">10.1111/nph.12026</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Centre-Val de Loire</li><li>Région Centre</li></region><orgName><li>Université d'Orléans</li></orgName></list><tree><noCountry><name sortKey="Brignolas, Franck" sort="Brignolas, Franck" uniqKey="Brignolas F" first="Franck" last="Brignolas">Franck Brignolas</name><name sortKey="Delaunay, Alain" sort="Delaunay, Alain" uniqKey="Delaunay A" first="Alain" last="Delaunay">Alain Delaunay</name><name sortKey="Faivre Rampant, Patricia" sort="Faivre Rampant, Patricia" uniqKey="Faivre Rampant P" first="Patricia" last="Faivre-Rampant">Patricia Faivre-Rampant</name><name sortKey="Maury, Stephane" sort="Maury, Stephane" uniqKey="Maury S" first="Stéphane" last="Maury">Stéphane Maury</name><name sortKey="Street, Nathaniel" sort="Street, Nathaniel" uniqKey="Street N" first="Nathaniel" last="Street">Nathaniel Street</name></noCountry><country name="France"><region name="Centre-Val de Loire"><name sortKey="Lafon Placette, Clement" sort="Lafon Placette, Clement" uniqKey="Lafon Placette C" first="Clément" last="Lafon-Placette">Clément Lafon-Placette</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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