Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.
Identifieur interne : 002B33 ( PubMed/Corpus ); précédent : 002B32; suivant : 002B34Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.
Auteurs : David Secco ; Chuang Wang ; Huixia Shou ; Matthew D. Schultz ; Serge Chiarenza ; Laurent Nussaume ; Joseph R. Ecker ; James Whelan ; Ryan ListerSource :
- eLife [ 2050-084X ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : 5-Methylcytosine.
- chemical , chemistry : DNA, Plant.
- chemical , metabolism : DNA, Plant, Phosphates.
- physiology : Arabidopsis, Oryza.
- DNA Methylation, Gene Expression Regulation, Genome, Plant, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Stress, Physiological.
Abstract
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
DOI: 10.7554/eLife.09343
PubMed: 26196146
Links to Exploration step
pubmed:26196146Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.</title><author><name sortKey="Secco, David" sort="Secco, David" uniqKey="Secco D" first="David" last="Secco">David Secco</name><affiliation><nlm:affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chuang" sort="Wang, Chuang" uniqKey="Wang C" first="Chuang" last="Wang">Chuang Wang</name><affiliation><nlm:affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Shou, Huixia" sort="Shou, Huixia" uniqKey="Shou H" first="Huixia" last="Shou">Huixia Shou</name><affiliation><nlm:affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Schultz, Matthew D" sort="Schultz, Matthew D" uniqKey="Schultz M" first="Matthew D" last="Schultz">Matthew D. Schultz</name><affiliation><nlm:affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</nlm:affiliation></affiliation></author><author><name sortKey="Chiarenza, Serge" sort="Chiarenza, Serge" uniqKey="Chiarenza S" first="Serge" last="Chiarenza">Serge Chiarenza</name><affiliation><nlm:affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</nlm:affiliation></affiliation></author><author><name sortKey="Nussaume, Laurent" sort="Nussaume, Laurent" uniqKey="Nussaume L" first="Laurent" last="Nussaume">Laurent Nussaume</name><affiliation><nlm:affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ecker, Joseph R" sort="Ecker, Joseph R" uniqKey="Ecker J" first="Joseph R" last="Ecker">Joseph R. Ecker</name><affiliation><nlm:affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</nlm:affiliation></affiliation></author><author><name sortKey="Whelan, James" sort="Whelan, James" uniqKey="Whelan J" first="James" last="Whelan">James Whelan</name><affiliation><nlm:affiliation>Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lister, Ryan" sort="Lister, Ryan" uniqKey="Lister R" first="Ryan" last="Lister">Ryan Lister</name><affiliation><nlm:affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26196146</idno><idno type="pmid">26196146</idno><idno type="doi">10.7554/eLife.09343</idno><idno type="wicri:Area/PubMed/Corpus">002B33</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002B33</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.</title><author><name sortKey="Secco, David" sort="Secco, David" uniqKey="Secco D" first="David" last="Secco">David Secco</name><affiliation><nlm:affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chuang" sort="Wang, Chuang" uniqKey="Wang C" first="Chuang" last="Wang">Chuang Wang</name><affiliation><nlm:affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Shou, Huixia" sort="Shou, Huixia" uniqKey="Shou H" first="Huixia" last="Shou">Huixia Shou</name><affiliation><nlm:affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Schultz, Matthew D" sort="Schultz, Matthew D" uniqKey="Schultz M" first="Matthew D" last="Schultz">Matthew D. Schultz</name><affiliation><nlm:affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</nlm:affiliation></affiliation></author><author><name sortKey="Chiarenza, Serge" sort="Chiarenza, Serge" uniqKey="Chiarenza S" first="Serge" last="Chiarenza">Serge Chiarenza</name><affiliation><nlm:affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</nlm:affiliation></affiliation></author><author><name sortKey="Nussaume, Laurent" sort="Nussaume, Laurent" uniqKey="Nussaume L" first="Laurent" last="Nussaume">Laurent Nussaume</name><affiliation><nlm:affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ecker, Joseph R" sort="Ecker, Joseph R" uniqKey="Ecker J" first="Joseph R" last="Ecker">Joseph R. Ecker</name><affiliation><nlm:affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</nlm:affiliation></affiliation></author><author><name sortKey="Whelan, James" sort="Whelan, James" uniqKey="Whelan J" first="James" last="Whelan">James Whelan</name><affiliation><nlm:affiliation>Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lister, Ryan" sort="Lister, Ryan" uniqKey="Lister R" first="Ryan" last="Lister">Ryan Lister</name><affiliation><nlm:affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</nlm:affiliation></affiliation></author></analytic><series><title level="j">eLife</title><idno type="eISSN">2050-084X</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>5-Methylcytosine (analysis)</term><term>Arabidopsis (physiology)</term><term>DNA Methylation</term><term>DNA, Plant (chemistry)</term><term>DNA, Plant (metabolism)</term><term>Gene Expression Regulation</term><term>Genome, Plant</term><term>Oryza (physiology)</term><term>Phosphates (metabolism)</term><term>Regulatory Elements, Transcriptional</term><term>Sequence Analysis, DNA</term><term>Stress, Physiological</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>5-Methylcytosine</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Plant</term><term>Phosphates</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Arabidopsis</term><term>Oryza</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Methylation</term><term>Gene Expression Regulation</term><term>Genome, Plant</term><term>Regulatory Elements, Transcriptional</term><term>Sequence Analysis, DNA</term><term>Stress, Physiological</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26196146</PMID><DateCreated><Year>2015</Year><Month>08</Month><Day>18</Day></DateCreated><DateCompleted><Year>2016</Year><Month>05</Month><Day>18</Day></DateCompleted><DateRevised><Year>2015</Year><Month>08</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2050-084X</ISSN><JournalIssue CitedMedium="Internet"><Volume>4</Volume><PubDate><Year>2015</Year><Month>Jul</Month><Day>21</Day></PubDate></JournalIssue><Title>eLife</Title><ISOAbbreviation>Elife</ISOAbbreviation></Journal><ArticleTitle>Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.7554/eLife.09343</ELocationID><Abstract><AbstractText>Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Secco</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Chuang</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shou</LastName><ForeName>Huixia</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schultz</LastName><ForeName>Matthew D</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chiarenza</LastName><ForeName>Serge</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nussaume</LastName><ForeName>Laurent</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ecker</LastName><ForeName>Joseph R</ForeName><Initials>JR</Initials><AffiliationInfo><Affiliation>Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Whelan</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lister</LastName><ForeName>Ryan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>07</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Elife</MedlineTA><NlmUniqueID>101579614</NlmUniqueID><ISSNLinking>2050-084X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010710">Phosphates</NameOfSubstance></Chemical><Chemical><RegistryNumber>6R795CQT4H</RegistryNumber><NameOfSubstance UI="D044503">5-Methylcytosine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Plant Physiol. 2013 May;162(1):116-31</RefSource><PMID Version="1">23542151</PMID></CommentsCorrections><CommentsCorrections 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Feb;31(2):154-9</RefSource><PMID Version="1">23354102</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2013;8(2):e55772</RefSource><PMID Version="1">23418457</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cell. 2013 Mar 28;153(1):193-205</RefSource><PMID Version="1">23540698</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Biometrics. 2013 Mar;69(1):1-7</RefSource><PMID Version="1">23379645</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D044503" MajorTopicYN="N">5-Methylcytosine</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019175" MajorTopicYN="Y">DNA Methylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="Y">Gene Expression Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010710" MajorTopicYN="N">Phosphates</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D050436" MajorTopicYN="Y">Regulatory Elements, Transcriptional</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013312" MajorTopicYN="Y">Stress, Physiological</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4534844</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DNA methylation</Keyword><Keyword MajorTopicYN="N">arabidopsis</Keyword><Keyword MajorTopicYN="N">epigenome</Keyword><Keyword MajorTopicYN="N">evolutionary biology</Keyword><Keyword MajorTopicYN="N">genomics</Keyword><Keyword MajorTopicYN="N">nutrient stress</Keyword><Keyword MajorTopicYN="N">phosphate starvation</Keyword><Keyword MajorTopicYN="N">plant biology</Keyword><Keyword MajorTopicYN="N">rice</Keyword><Keyword MajorTopicYN="N">transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>06</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>5</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26196146</ArticleId><ArticleId IdType="doi">10.7554/eLife.09343</ArticleId><ArticleId IdType="pmc">PMC4534844</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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