DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Identifieur interne : 000866 ( Main/Exploration ); précédent : 000865; suivant : 000867DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Auteurs : Manu J. Dubin ; Pei Zhang [République populaire de Chine] ; Dazhe Meng [République populaire de Chine] ; Marie-Stanislas Remigereau ; Edward J. Osborne ; Francesco Paolo Casale ; Philipp Drewe ; André Kahles ; Géraldine Jean [France] ; Bjarni Vilhjálmsson ; Joanna Jagoda ; Selen Irez ; Viktor Voronin [Autriche] ; Qiang Song [Canada] ; Quan Long [France] ; Gunnar R Tsch ; Oliver Stegle ; Richard M. Clark [États-Unis] ; Magnus NordborgSource :
Abstract
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.
Url:
Affiliations:
- Autriche, Canada, France, République populaire de Chine, États-Unis
- Pays de la Loire
- Nantes
- Université de Nantes
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Le document en format XML
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Dubin</name></author><author><name sortKey="Zhang, Pei" sort="Zhang, Pei" uniqKey="Zhang P" first="Pei" last="Zhang">Pei Zhang</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-230793" status="INCOMING"><orgName>Laboratory of Infrared Material and Devices</orgName><desc><address><addrLine>College of Information Science and Engineering, Ningbo University, Ningbo 31521, China</addrLine><country key="CN"></country></address></desc><listRelation><relation active="#struct-322379" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-322379" type="direct"><org type="institution" xml:id="struct-322379" status="INCOMING"><orgName>NINGBO UNIVERSITY</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>République populaire de Chine</country></affiliation></author><author><name sortKey="Meng, Dazhe" sort="Meng, Dazhe" uniqKey="Meng D" first="Dazhe" last="Meng">Dazhe Meng</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-263701" status="INCOMING"><orgName>Institute of Computing Technology</orgName><desc><address><country key="CN"></country></address></desc><listRelation><relation active="#struct-303369" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-303369" type="direct"><org type="institution" xml:id="struct-303369" status="VALID"><orgName>Chinese Academy of Sciences [Beijing]</orgName><desc><address><addrLine>52 Sanlihe Rd., Beijing, 100864</addrLine><country key="CN"></country></address><ref type="url">http://english.cas.cn/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>République populaire de Chine</country></affiliation></author><author><name sortKey="Remigereau, Marie Stanislas" sort="Remigereau, Marie Stanislas" uniqKey="Remigereau M" first="Marie-Stanislas" last="Remigereau">Marie-Stanislas Remigereau</name></author><author><name sortKey="Osborne, Edward J" sort="Osborne, Edward J" uniqKey="Osborne E" first="Edward J" last="Osborne">Edward J. 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Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Microbiology and Genetics</orgName><desc><address><addrLine>Dr. Bohr-Gasse 9, A-1030, Vienna</addrLine><country key="AT"></country></address></desc><listRelation><relation active="#struct-300742" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-300742" type="direct"><org type="institution" xml:id="struct-300742" status="VALID"><orgName>Universität Wien</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>Autriche</country></affiliation></author><author><name sortKey="Song, Qiang" sort="Song, Qiang" uniqKey="Song Q" first="Qiang" last="Song">Qiang Song</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-100835" status="INCOMING"><orgName>Department of Physics</orgName><desc><address><country key="CA"></country></address></desc><listRelation><relation active="#struct-366034" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-366034" type="direct"><org type="institution" xml:id="struct-366034" status="VALID"><orgName>University of British Columbia</orgName><desc><address><country key="CA"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>Canada</country></affiliation></author><author><name sortKey="Long, Quan" sort="Long, Quan" uniqKey="Long Q" first="Quan" last="Long">Quan Long</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-133218" status="OLD"><orgName>Centre de Recherche en Informatique de Nancy</orgName><orgName type="acronym">CRIN</orgName><desc><address><addrLine>CRIN RFIA Campus Scientifique B.P. 239 54506 Vandoeuvre-Les-Nancy</addrLine><country key="FR"></country></address></desc><listRelation><relation active="#struct-441569" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-441569" type="direct"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country></affiliation></author><author><name sortKey="R Tsch, Gunnar" sort="R Tsch, Gunnar" uniqKey="R Tsch G" first="Gunnar" last="R Tsch">Gunnar R Tsch</name></author><author><name sortKey="Stegle, Oliver" sort="Stegle, Oliver" uniqKey="Stegle O" first="Oliver" last="Stegle">Oliver Stegle</name></author><author><name sortKey="Clark, Richard M" sort="Clark, Richard M" uniqKey="Clark R" first="Richard M" last="Clark">Richard M. Clark</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-188337" status="INCOMING"><orgName>US Geological Survey</orgName><orgName type="acronym">USGS</orgName><desc><address><addrLine>Box 25046, MS 974, Denver, CO 80225, USA</addrLine><country key="US"></country></address></desc><listRelation><relation active="#struct-317067" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-317067" type="direct"><org type="institution" xml:id="struct-317067" status="INCOMING"><orgName>Denver Federal Center</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>États-Unis</country></affiliation></author><author><name sortKey="Nordborg, Magnus" sort="Nordborg, Magnus" uniqKey="Nordborg M" first="Magnus" last="Nordborg">Magnus Nordborg</name></author></analytic></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.</div></front></TEI><affiliations><list><country><li>Autriche</li><li>Canada</li><li>France</li><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Pays de la Loire</li></region><settlement><li>Nantes</li></settlement><orgName><li>Université de Nantes</li></orgName></list><tree><noCountry><name sortKey="Drewe, Philipp" sort="Drewe, Philipp" uniqKey="Drewe P" first="Philipp" last="Drewe">Philipp Drewe</name><name sortKey="Dubin, Manu J" sort="Dubin, Manu J" uniqKey="Dubin M" first="Manu J" last="Dubin">Manu J. Dubin</name><name sortKey="Irez, Selen" sort="Irez, Selen" uniqKey="Irez S" first="Selen" last="Irez">Selen Irez</name><name sortKey="Jagoda, Joanna" sort="Jagoda, Joanna" uniqKey="Jagoda J" first="Joanna" last="Jagoda">Joanna Jagoda</name><name sortKey="Kahles, Andre" sort="Kahles, Andre" uniqKey="Kahles A" first="André" last="Kahles">André Kahles</name><name sortKey="Nordborg, Magnus" sort="Nordborg, Magnus" uniqKey="Nordborg M" first="Magnus" last="Nordborg">Magnus Nordborg</name><name sortKey="Osborne, Edward J" sort="Osborne, Edward J" uniqKey="Osborne E" first="Edward J" last="Osborne">Edward J. Osborne</name><name sortKey="Paolo Casale, Francesco" sort="Paolo Casale, Francesco" uniqKey="Paolo Casale F" first="Francesco" last="Paolo Casale">Francesco Paolo Casale</name><name sortKey="R Tsch, Gunnar" sort="R Tsch, Gunnar" uniqKey="R Tsch G" first="Gunnar" last="R Tsch">Gunnar R Tsch</name><name sortKey="Remigereau, Marie Stanislas" sort="Remigereau, Marie Stanislas" uniqKey="Remigereau M" first="Marie-Stanislas" last="Remigereau">Marie-Stanislas Remigereau</name><name sortKey="Stegle, Oliver" sort="Stegle, Oliver" uniqKey="Stegle O" first="Oliver" last="Stegle">Oliver Stegle</name><name sortKey="Vilhjalmsson, Bjarni" sort="Vilhjalmsson, Bjarni" uniqKey="Vilhjalmsson B" first="Bjarni" last="Vilhjálmsson">Bjarni Vilhjálmsson</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Zhang, Pei" sort="Zhang, Pei" uniqKey="Zhang P" first="Pei" last="Zhang">Pei Zhang</name></noRegion><name sortKey="Meng, Dazhe" sort="Meng, Dazhe" uniqKey="Meng D" first="Dazhe" last="Meng">Dazhe Meng</name></country><country name="France"><region name="Pays de la Loire"><name sortKey="Jean, Geraldine" sort="Jean, Geraldine" uniqKey="Jean G" first="Géraldine" last="Jean">Géraldine Jean</name></region><name sortKey="Long, Quan" sort="Long, Quan" uniqKey="Long Q" first="Quan" last="Long">Quan Long</name></country><country name="Autriche"><noRegion><name sortKey="Voronin, Viktor" sort="Voronin, Viktor" uniqKey="Voronin V" first="Viktor" last="Voronin">Viktor Voronin</name></noRegion></country><country name="Canada"><noRegion><name sortKey="Song, Qiang" sort="Song, Qiang" uniqKey="Song Q" first="Qiang" last="Song">Qiang Song</name></noRegion></country><country name="États-Unis"><noRegion><name sortKey="Clark, Richard M" sort="Clark, Richard M" uniqKey="Clark R" first="Richard M" last="Clark">Richard M. Clark</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
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