Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Identifieur interne : 00F517 ( Main/Merge ); précédent : 00F516; suivant : 00F518Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Auteurs : David Secco [Australie] ; Chuang Wang [République populaire de Chine] ; Huixia Shou [République populaire de Chine] ; Matthew D. Schultz [États-Unis] ; Serge Chiarenza [France] ; Laurent Nussaume [France] ; Joseph R. Ecker [États-Unis] ; James Whelan [République populaire de Chine, Australie] ; Ryan Lister [Australie]Source :
- eLife [ 2050-084X ] ; ????.
Descripteurs français
- KwdFr :
- 5-Méthyl-cytosine (analyse), ADN des plantes (), ADN des plantes (métabolisme), Analyse de séquence d'ADN, Arabidopsis (physiologie), Génome végétal, Méthylation de l'ADN, Oryza (physiologie), Phosphates (métabolisme), Régulation de l'expression des gènes, Stress physiologique, Éléments de régulation transcriptionnelle.
- MESH :
- analyse : 5-Méthyl-cytosine.
- métabolisme : ADN des plantes, Phosphates.
- physiologie : Arabidopsis, Oryza.
- ADN des plantes, Analyse de séquence d'ADN, Génome végétal, Méthylation de l'ADN, Régulation de l'expression des gènes, Stress physiologique, Éléments de régulation transcriptionnelle.
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
Url:
DOI: 10.7554/eLife.09343
PubMed: 26196146
PubMed Central: 4534844
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PMC:4534844Le document en format XML
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Australia</institution>,<addr-line>Perth</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Chuang" sort="Wang, Chuang" uniqKey="Wang C" first="Chuang" last="Wang">Chuang Wang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution content-type="dept">State Key laboratory of Plant Physiology and Biochemistry, College of Life Science</institution>,<institution>Zhejiang University</institution>,<addr-line>Hangzhou</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution content-type="dept">Joint Research Laboratory in Genomics and Nutriomics</institution>,<institution>Zhejiang University</institution>,<addr-line>Hangzhou</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shou, Huixia" sort="Shou, Huixia" uniqKey="Shou H" first="Huixia" last="Shou">Huixia Shou</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution content-type="dept">State Key laboratory of Plant Physiology and Biochemistry, College of Life Science</institution>,<institution>Zhejiang University</institution>,<addr-line>Hangzhou</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution content-type="dept">Joint Research Laboratory in Genomics and Nutriomics</institution>,<institution>Zhejiang University</institution>,<addr-line>Hangzhou</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></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 wicri:level="1"><nlm:aff id="aff4"><institution content-type="dept">Genomic Analysis Laboratory</institution>, The<institution>Salk Institute for Biological Studies</institution>,<addr-line>La Jolla</addr-line>,<country>United States</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chiarenza, Serge" sort="Chiarenza, Serge" uniqKey="Chiarenza S" first="Serge" last="Chiarenza">Serge Chiarenza</name><affiliation wicri:level="1"><nlm:aff id="aff5"><institution content-type="dept">UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes</institution>,<institution>Université d'Aix-Marseille</institution>,<addr-line>Saint-Paul-lez-Durance</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nussaume, Laurent" sort="Nussaume, Laurent" uniqKey="Nussaume L" first="Laurent" last="Nussaume">Laurent Nussaume</name><affiliation wicri:level="1"><nlm:aff id="aff5"><institution content-type="dept">UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes</institution>,<institution>Université d'Aix-Marseille</institution>,<addr-line>Saint-Paul-lez-Durance</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></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 wicri:level="1"><nlm:aff id="aff4"><institution content-type="dept">Genomic Analysis Laboratory</institution>, The<institution>Salk Institute for Biological Studies</institution>,<addr-line>La Jolla</addr-line>,<country>United States</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Whelan, James" sort="Whelan, James" uniqKey="Whelan J" first="James" last="Whelan">James Whelan</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution content-type="dept">Joint Research Laboratory in Genomics and Nutriomics</institution>,<institution>Zhejiang University</institution>,<addr-line>Hangzhou</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><institution content-type="dept">Department of Animal, Plant and Soil Science, School of Life Science, ARC Centre of Excellence in Plant Energy Biology</institution>,<institution>La Trobe University</institution>,<addr-line>Bundoora</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lister, Ryan" sort="Lister, Ryan" uniqKey="Lister R" first="Ryan" last="Lister">Ryan Lister</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution content-type="dept">ARC Centre of Excellence in Plant Energy Biology</institution>,<institution>The University of Western Australia</institution>,<addr-line>Perth</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">eLife</title><idno type="ISSN">2050-084X</idno><idno type="eISSN">2050-084X</idno><imprint><date when="????">????</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="KwdFr" xml:lang="fr"><term>5-Méthyl-cytosine (analyse)</term><term>ADN des plantes ()</term><term>ADN des plantes (métabolisme)</term><term>Analyse de séquence d'ADN</term><term>Arabidopsis (physiologie)</term><term>Génome végétal</term><term>Méthylation de l'ADN</term><term>Oryza (physiologie)</term><term>Phosphates (métabolisme)</term><term>Régulation de l'expression des gènes</term><term>Stress physiologique</term><term>Éléments de régulation transcriptionnelle</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="analyse" xml:lang="fr"><term>5-Méthyl-cytosine</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN des plantes</term><term>Phosphates</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Arabidopsis</term><term>Oryza</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><keywords scheme="MESH" xml:lang="fr"><term>ADN des plantes</term><term>Analyse de séquence d'ADN</term><term>Génome végétal</term><term>Méthylation de l'ADN</term><term>Régulation de l'expression des gènes</term><term>Stress physiologique</term><term>Éléments de régulation transcriptionnelle</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>DCL3a</italic>-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in <italic>Arabidopsis</italic> 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.</p><p><bold>DOI:</bold><ext-link ext-link-type="doi" xlink:href="10.7554/eLife.09343.001">http://dx.doi.org/10.7554/eLife.09343.001</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ahmed, I" uniqKey="Ahmed I">I Ahmed</name></author><author><name sortKey="Sarazin, A" uniqKey="Sarazin A">A Sarazin</name></author><author><name sortKey="Bowler, C" uniqKey="Bowler C">C Bowler</name></author><author><name sortKey="Colot, V" uniqKey="Colot V">V Colot</name></author><author><name sortKey="Quesneville, H" uniqKey="Quesneville H">H Quesneville</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ames, B" uniqKey="Ames B">B 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sortKey="Giovannoni, Jj" uniqKey="Giovannoni J">JJ Giovannoni</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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