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 : 002765 ( Main/Corpus ); précédent : 002764; suivant : 002766Methylome 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 ; Patricia Faivre-Rampant ; Alain Delaunay ; Nathaniel Street ; Franck Brignolas ; Stéphane MaurySource :
- The New phytologist [ 1469-8137 ] ; 2013.
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
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Delaunay</name></author><author><name sortKey="Street, Nathaniel" sort="Street, Nathaniel" uniqKey="Street N" first="Nathaniel" last="Street">Nathaniel Street</name></author><author><name sortKey="Brignolas, Franck" sort="Brignolas, Franck" uniqKey="Brignolas F" first="Franck" last="Brignolas">Franck Brignolas</name></author><author><name sortKey="Maury, Stephane" sort="Maury, Stephane" uniqKey="Maury S" first="Stéphane" last="Maury">Stéphane Maury</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23253333</idno><idno type="pmid">23253333</idno><idno type="doi">10.1111/nph.12026</idno><idno type="wicri:Area/Main/Corpus">002765</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002765</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">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.</title><author><name sortKey="Lafon Placette, Clement" sort="Lafon Placette, Clement" uniqKey="Lafon Placette C" first="Clément" last="Lafon-Placette">Clément Lafon-Placette</name><affiliation><nlm:affiliation>Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures-LBLGC, UPRES EA 1207, Orléans 45067, France.</nlm:affiliation></affiliation></author><author><name sortKey="Faivre Rampant, Patricia" sort="Faivre Rampant, Patricia" uniqKey="Faivre Rampant P" first="Patricia" last="Faivre-Rampant">Patricia Faivre-Rampant</name></author><author><name sortKey="Delaunay, Alain" sort="Delaunay, Alain" uniqKey="Delaunay A" first="Alain" last="Delaunay">Alain Delaunay</name></author><author><name sortKey="Street, Nathaniel" sort="Street, Nathaniel" uniqKey="Street N" first="Nathaniel" last="Street">Nathaniel Street</name></author><author><name sortKey="Brignolas, Franck" sort="Brignolas, Franck" uniqKey="Brignolas F" first="Franck" last="Brignolas">Franck Brignolas</name></author><author><name sortKey="Maury, Stephane" sort="Maury, Stephane" uniqKey="Maury S" first="Stéphane" last="Maury">Stéphane Maury</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Chromatin (metabolism)</term><term>Chromatin Immunoprecipitation (MeSH)</term><term>Chromosome Mapping (MeSH)</term><term>Crosses, Genetic (MeSH)</term><term>Cytosine (metabolism)</term><term>DNA Methylation (genetics)</term><term>Deoxyribonuclease I (metabolism)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (genetics)</term><term>Genetic Variation (MeSH)</term><term>Hybridization, Genetic (MeSH)</term><term>Meristem (cytology)</term><term>Meristem (genetics)</term><term>Models, Genetic (MeSH)</term><term>Populus (cytology)</term><term>Populus (genetics)</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (metabolism)</term><term>Reproducibility of Results (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Chromatin</term><term>Cytosine</term><term>Deoxyribonuclease I</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Meristem</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>DNA Methylation</term><term>Genes, Plant</term><term>Meristem</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Chromatin Immunoprecipitation</term><term>Chromosome Mapping</term><term>Crosses, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Genetic Variation</term><term>Hybridization, Genetic</term><term>Models, Genetic</term><term>Reproducibility of Results</term><term>Sequence Analysis, DNA</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 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