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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations<xref ref-type="author-notes" rid="fn1"><sup>[C]</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref></title><author><name sortKey="Eichten, Steven R" sort="Eichten, Steven R" uniqKey="Eichten S" first="Steven R." last="Eichten">Steven R. Eichten</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Briskine, Roman" sort="Briskine, Roman" uniqKey="Briskine R" first="Roman" last="Briskine">Roman Briskine</name><affiliation><nlm:aff id="aff2">Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455</nlm:aff></affiliation></author><author><name sortKey="Song, Jawon" sort="Song, Jawon" uniqKey="Song J" first="Jawon" last="Song">Jawon Song</name><affiliation><nlm:aff id="aff3">Texas Advanced Computing Center, University of Texas, Austin Texas 78758</nlm:aff></affiliation></author><author><name sortKey="Li, Qing" sort="Li, Qing" uniqKey="Li Q" first="Qing" last="Li">Qing Li</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Swanson Wagner, Ruth" sort="Swanson Wagner, Ruth" uniqKey="Swanson Wagner R" first="Ruth" last="Swanson-Wagner">Ruth Swanson-Wagner</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Hermanson, Peter J" sort="Hermanson, Peter J" uniqKey="Hermanson P" first="Peter J." last="Hermanson">Peter J. Hermanson</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Waters, Amanda J" sort="Waters, Amanda J" uniqKey="Waters A" first="Amanda J." last="Waters">Amanda J. Waters</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Starr, Evan" sort="Starr, Evan" uniqKey="Starr E" first="Evan" last="Starr">Evan Starr</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="West, Patrick T" sort="West, Patrick T" uniqKey="West P" first="Patrick T." last="West">Patrick T. West</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Myers, Chad L" sort="Myers, Chad L" uniqKey="Myers C" first="Chad L." last="Myers">Chad L. Myers</name><affiliation><nlm:aff id="aff2">Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455</nlm:aff></affiliation></author><author><name sortKey="Vaughn, Matthew W" sort="Vaughn, Matthew W" uniqKey="Vaughn M" first="Matthew W." last="Vaughn">Matthew W. Vaughn</name><affiliation><nlm:aff id="aff3">Texas Advanced Computing Center, University of Texas, Austin Texas 78758</nlm:aff></affiliation></author><author><name sortKey="Springer, Nathan M" sort="Springer, Nathan M" uniqKey="Springer N" first="Nathan M." last="Springer">Nathan M. Springer</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23922207</idno><idno type="pmc">3784580</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784580</idno><idno type="RBID">PMC:3784580</idno><idno type="doi">10.1105/tpc.113.114793</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000380</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations<xref ref-type="author-notes" rid="fn1"><sup>[C]</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref></title><author><name sortKey="Eichten, Steven R" sort="Eichten, Steven R" uniqKey="Eichten S" first="Steven R." last="Eichten">Steven R. Eichten</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Briskine, Roman" sort="Briskine, Roman" uniqKey="Briskine R" first="Roman" last="Briskine">Roman Briskine</name><affiliation><nlm:aff id="aff2">Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455</nlm:aff></affiliation></author><author><name sortKey="Song, Jawon" sort="Song, Jawon" uniqKey="Song J" first="Jawon" last="Song">Jawon Song</name><affiliation><nlm:aff id="aff3">Texas Advanced Computing Center, University of Texas, Austin Texas 78758</nlm:aff></affiliation></author><author><name sortKey="Li, Qing" sort="Li, Qing" uniqKey="Li Q" first="Qing" last="Li">Qing Li</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Swanson Wagner, Ruth" sort="Swanson Wagner, Ruth" uniqKey="Swanson Wagner R" first="Ruth" last="Swanson-Wagner">Ruth Swanson-Wagner</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Hermanson, Peter J" sort="Hermanson, Peter J" uniqKey="Hermanson P" first="Peter J." last="Hermanson">Peter J. Hermanson</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Waters, Amanda J" sort="Waters, Amanda J" uniqKey="Waters A" first="Amanda J." last="Waters">Amanda J. Waters</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Starr, Evan" sort="Starr, Evan" uniqKey="Starr E" first="Evan" last="Starr">Evan Starr</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="West, Patrick T" sort="West, Patrick T" uniqKey="West P" first="Patrick T." last="West">Patrick T. West</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author><author><name sortKey="Myers, Chad L" sort="Myers, Chad L" uniqKey="Myers C" first="Chad L." last="Myers">Chad L. Myers</name><affiliation><nlm:aff id="aff2">Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455</nlm:aff></affiliation></author><author><name sortKey="Vaughn, Matthew W" sort="Vaughn, Matthew W" uniqKey="Vaughn M" first="Matthew W." last="Vaughn">Matthew W. Vaughn</name><affiliation><nlm:aff id="aff3">Texas Advanced Computing Center, University of Texas, Austin Texas 78758</nlm:aff></affiliation></author><author><name sortKey="Springer, Nathan M" sort="Springer, Nathan M" uniqKey="Springer N" first="Nathan M." last="Springer">Nathan M. Springer</name><affiliation><nlm:aff id="aff1">Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</nlm:aff></affiliation></author></analytic><series><title level="j">The Plant Cell</title><idno type="ISSN">1040-4651</idno><idno type="eISSN">1532-298X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>This study examines the DNA methylation patterns of a diverse set of maize lines to show that many methylation variants are associated with local genetic variation, some of which may be due to specific transposon insertion variation. These results provide insight into how DNA methylation varies within a crop and highlight the complex nature of genetic and epigenetic influences on DNA methylation.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Cell</journal-id><journal-id journal-id-type="iso-abbrev">Plant Cell</journal-id><journal-id journal-id-type="hwp">plantcell</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>The Plant Cell</journal-title></journal-title-group><issn pub-type="ppub">1040-4651</issn><issn pub-type="epub">1532-298X</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23922207</article-id><article-id pub-id-type="pmc">3784580</article-id><article-id pub-id-type="publisher-id">114793</article-id><article-id pub-id-type="doi">10.1105/tpc.113.114793</article-id><article-categories><subj-group subj-group-type="heading"><subject>Large-Scale Biology Articles</subject></subj-group></article-categories><title-group><article-title>Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations<xref ref-type="author-notes" rid="fn1"><sup>[C]</sup></xref><xref ref-type="author-notes" rid="fn2"><sup>[W]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Eichten</surname><given-names>Steven R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-2268-395X</contrib-id></contrib><contrib contrib-type="author"><name><surname>Briskine</surname><given-names>Roman</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Song</surname><given-names>Jawon</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Qing</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Swanson-Wagner</surname><given-names>Ruth</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hermanson</surname><given-names>Peter J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Waters</surname><given-names>Amanda J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Starr</surname><given-names>Evan</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>West</surname><given-names>Patrick T.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tiffin</surname><given-names>Peter</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Myers</surname><given-names>Chad L.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Vaughn</surname><given-names>Matthew W.</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Springer</surname><given-names>Nathan M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-7301-4759</contrib-id></contrib><aff id="aff1"><label>a</label>Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108</aff><aff id="aff2"><label>b</label>Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455</aff><aff id="aff3"><label>c</label>Texas Advanced Computing Center, University of Texas, Austin Texas 78758</aff></contrib-group><author-notes><corresp id="cor1"><label>1</label>Address correspondence to <email>springer@umn.edu</email>.</corresp><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org">www.plantcell.org</ext-link>) is: Nathan M. Springer (<email>springer@umn.edu</email>).</p></fn><fn id="fn1"><label>[C]</label><p>Some figures in this article are displayed in color online but in black and white in the print edition.</p></fn><fn id="fn2"><label>[W]</label><p>Online version contains Web-only data.</p></fn><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org/cgi/doi/10.1105/tpc.113.114793">www.plantcell.org/cgi/doi/10.1105/tpc.113.114793</ext-link></p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>8</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>6</day><month>8</month><year>2013</year></pub-date><volume>25</volume><issue>8</issue><fpage>2783</fpage><lpage>2797</lpage><history><date date-type="received"><day>12</day><month>6</month><year>2013</year></date><date date-type="rev-recd"><day>12</day><month>7</month><year>2013</year></date><date date-type="accepted"><day>15</day><month>7</month><year>2013</year></date></history><permissions><copyright-statement>© 2013 American Society of Plant Biologists. All rights reserved.</copyright-statement><copyright-year>2013</copyright-year></permissions><self-uri xlink:role="icon" xlink:type="simple" xlink:href="PC_114793_ic1.gif"></self-uri><abstract abstract-type="precis"><p>This study examines the DNA methylation patterns of a diverse set of maize lines to show that many methylation variants are associated with local genetic variation, some of which may be due to specific transposon insertion variation. These results provide insight into how DNA methylation varies within a crop and highlight the complex nature of genetic and epigenetic influences on DNA methylation.</p></abstract><abstract><p>DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, genetic changes such as transposon insertions can also lead to changes in DNA methylation. Genome-wide profiles of DNA methylation for 20 maize (<italic>Zea mays</italic>) inbred lines were used to discover differentially methylated regions (<xref ref-type="def" rid="def2">DMRs</xref>). The methylation level for each of these <xref ref-type="def" rid="def2">DMRs</xref> was also assayed in 31 additional maize or teosinte genotypes, resulting in the discovery of 1966 common <xref ref-type="def" rid="def2">DMRs</xref> and 1754 rare <xref ref-type="def" rid="def2">DMRs</xref>. Analysis of recombinant inbred lines provides evidence that the majority of <xref ref-type="def" rid="def2">DMRs</xref> are heritable. A local association scan found that nearly half of the <xref ref-type="def" rid="def2">DMRs</xref> with common variation are significantly associated with single nucleotide polymorphisms found within or near the <xref ref-type="def" rid="def2">DMR</xref>. Many of the <xref ref-type="def" rid="def2">DMRs</xref> that are significantly associated with local genetic variation are found near transposable elements that may contribute to the variation in DNA methylation. Analysis of gene expression in the same samples used for DNA methylation profiling identified over 300 genes with expression patterns that are significantly associated with DNA methylation variation. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic changes that are often stably inherited and can influence the expression of nearby genes.</p></abstract><counts><page-count count="15"></page-count></counts></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">SNP</term><def id="def1"><p>single nucleotide polymorphism</p></def></def-item><def-item><term id="term2">DMR</term><def id="def2"><p>differentially methylated region</p></def></def-item><def-item><term id="term3">RIL</term><def id="def3"><p>recombinant inbred line</p></def></def-item><def-item><term id="term4">LD</term><def id="def4"><p>linkage disequilibrium</p></def></def-item><def-item><term id="term5">meDIP</term><def id="def5"><p>methylated DNA immunoprecipitation</p></def></def-item><def-item><term id="term6">NAM</term><def id="def6"><p>nested association mapping</p></def></def-item><def-item><term id="term7">qPCR</term><def id="def7"><p>quantitative PCR</p></def></def-item><def-item><term id="term8">NCBI</term><def id="def8"><p>National Center for Biotechnology Information</p></def></def-item></def-list></glossary></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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