Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.
Identifieur interne : 002590 ( Main/Exploration ); précédent : 002589; suivant : 002591Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.
Auteurs : Kelly Vining [États-Unis] ; Kyle R. Pomraning ; Larry J. Wilhelm ; Cathleen Ma ; Matteo Pellegrini ; Yanming Di ; Todd C. Mockler ; Michael Freitag ; Steven H. StraussSource :
- BMC plant biology [ 1471-2229 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- cytologie : Populus.
- génétique : Populus.
- métabolisme : Cytosine.
- physiologie : Populus.
- Cellules cultivées, Dédifférenciation cellulaire, Méthylation de l'ADN, Techniques de culture cellulaire, Transformation génétique, Épigénomique.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Cytosine.
- cytology : Populus.
- genetics : Populus.
- physiology : Populus.
- Cell Culture Techniques, Cell Dedifferentiation, Cells, Cultured, DNA Methylation, Epigenomics, Transformation, Genetic.
Abstract
BACKGROUND
Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation.
RESULTS
We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes.
CONCLUSIONS
DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
DOI: 10.1186/1471-2229-13-92
PubMed: 23799904
PubMed Central: PMC3728041
Affiliations:
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Pomraning</name></author><author><name sortKey="Wilhelm, Larry J" sort="Wilhelm, Larry J" uniqKey="Wilhelm L" first="Larry J" last="Wilhelm">Larry J. Wilhelm</name></author><author><name sortKey="Ma, Cathleen" sort="Ma, Cathleen" uniqKey="Ma C" first="Cathleen" last="Ma">Cathleen Ma</name></author><author><name sortKey="Pellegrini, Matteo" sort="Pellegrini, Matteo" uniqKey="Pellegrini M" first="Matteo" last="Pellegrini">Matteo Pellegrini</name></author><author><name sortKey="Di, Yanming" sort="Di, Yanming" uniqKey="Di Y" first="Yanming" last="Di">Yanming Di</name></author><author><name sortKey="Mockler, Todd C" sort="Mockler, Todd C" uniqKey="Mockler T" first="Todd C" last="Mockler">Todd C. Mockler</name></author><author><name sortKey="Freitag, Michael" sort="Freitag, Michael" uniqKey="Freitag M" first="Michael" last="Freitag">Michael Freitag</name></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cell Culture Techniques (MeSH)</term><term>Cell Dedifferentiation (MeSH)</term><term>Cells, Cultured (MeSH)</term><term>Cytosine (metabolism)</term><term>DNA Methylation (MeSH)</term><term>Epigenomics (MeSH)</term><term>Populus (cytology)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Transformation, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cellules cultivées (MeSH)</term><term>Cytosine (métabolisme)</term><term>Dédifférenciation cellulaire (MeSH)</term><term>Méthylation de l'ADN (MeSH)</term><term>Populus (cytologie)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Techniques de culture cellulaire (MeSH)</term><term>Transformation génétique (MeSH)</term><term>Épigénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cytosine</term></keywords><keywords scheme="MESH" qualifier="cytologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cytosine</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cell Culture Techniques</term><term>Cell Dedifferentiation</term><term>Cells, Cultured</term><term>DNA Methylation</term><term>Epigenomics</term><term>Transformation, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cellules cultivées</term><term>Dédifférenciation cellulaire</term><term>Méthylation de l'ADN</term><term>Techniques de culture cellulaire</term><term>Transformation génétique</term><term>Épigénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23799904</PMID><DateCompleted><Year>2013</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><PubDate><Year>2013</Year><Month>Jun</Month><Day>25</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>92</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-13-92</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vining</LastName><ForeName>Kelly</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA. kelly.vining@oregonstate.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pomraning</LastName><ForeName>Kyle R</ForeName><Initials>KR</Initials></Author><Author ValidYN="Y"><LastName>Wilhelm</LastName><ForeName>Larry J</ForeName><Initials>LJ</Initials></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Cathleen</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Pellegrini</LastName><ForeName>Matteo</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Di</LastName><ForeName>Yanming</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Mockler</LastName><ForeName>Todd C</ForeName><Initials>TC</Initials></Author><Author ValidYN="Y"><LastName>Freitag</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Strauss</LastName><ForeName>Steven H</ForeName><Initials>SH</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></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>06</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>8J337D1HZY</RegistryNumber><NameOfSubstance UI="D003596">Cytosine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018929" MajorTopicYN="N">Cell Culture Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054337" MajorTopicYN="Y">Cell Dedifferentiation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002478" MajorTopicYN="N">Cells, Cultured</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></MeshHeading><MeshHeading><DescriptorName UI="D057890" 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IdType="pubmed">15108305</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Oregon</li></region></list><tree><noCountry><name sortKey="Di, Yanming" sort="Di, Yanming" uniqKey="Di Y" first="Yanming" last="Di">Yanming Di</name><name sortKey="Freitag, Michael" sort="Freitag, Michael" uniqKey="Freitag M" first="Michael" last="Freitag">Michael Freitag</name><name sortKey="Ma, Cathleen" sort="Ma, Cathleen" uniqKey="Ma C" first="Cathleen" last="Ma">Cathleen Ma</name><name sortKey="Mockler, Todd C" sort="Mockler, Todd C" uniqKey="Mockler T" first="Todd C" last="Mockler">Todd C. Mockler</name><name sortKey="Pellegrini, Matteo" sort="Pellegrini, Matteo" uniqKey="Pellegrini M" first="Matteo" last="Pellegrini">Matteo Pellegrini</name><name sortKey="Pomraning, Kyle R" sort="Pomraning, Kyle R" uniqKey="Pomraning K" first="Kyle R" last="Pomraning">Kyle R. Pomraning</name><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name><name sortKey="Wilhelm, Larry J" sort="Wilhelm, Larry J" uniqKey="Wilhelm L" first="Larry J" last="Wilhelm">Larry J. Wilhelm</name></noCountry><country name="États-Unis"><region name="Oregon"><name sortKey="Vining, Kelly" sort="Vining, Kelly" uniqKey="Vining K" first="Kelly" last="Vining">Kelly Vining</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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