Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress
Identifieur interne : 000070 ( Pmc/Checkpoint ); précédent : 000069; suivant : 000071Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress
Auteurs : Dan Liang [République populaire de Chine] ; Zhoujia Zhang [République populaire de Chine] ; Honglong Wu [République populaire de Chine] ; Chunyu Huang [République populaire de Chine] ; Peng Shuai [République populaire de Chine] ; Chu-Yu Ye [République populaire de Chine] ; Sha Tang [République populaire de Chine] ; Yunjie Wang [République populaire de Chine] ; Ling Yang [République populaire de Chine] ; Jun Wang [République populaire de Chine] ; Weilun Yin [République populaire de Chine] ; Xinli Xia [République populaire de Chine]Source :
- BMC Genetics [ 1471-2156 ] ; 2014.
Abstract
DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.
In this study, we examined single-base resolution methylomes of
These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in
Url:
DOI: 10.1186/1471-2156-15-S1-S9
PubMed: 25080211
PubMed Central: 4118614
Affiliations:
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first="Sha" last="Tang">Sha Tang</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name><affiliation wicri:level="1"><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name><affiliation wicri:level="3"><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="1"><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25080211</idno><idno type="pmc">4118614</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118614</idno><idno type="RBID">PMC:4118614</idno><idno type="doi">10.1186/1471-2156-15-S1-S9</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000106</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000106</idno><idno type="wicri:Area/Pmc/Curation">000106</idno><idno type="wicri:explorRef" 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100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Zhoujia" sort="Zhang, Zhoujia" uniqKey="Zhang Z" first="Zhoujia" last="Zhang">Zhoujia Zhang</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wu, Honglong" sort="Wu, Honglong" uniqKey="Wu H" first="Honglong" last="Wu">Honglong Wu</name><affiliation wicri:level="3"><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Huang, Chunyu" sort="Huang, Chunyu" uniqKey="Huang C" first="Chunyu" last="Huang">Chunyu Huang</name><affiliation wicri:level="1"><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Shuai, Peng" sort="Shuai, Peng" uniqKey="Shuai P" first="Peng" last="Shuai">Peng Shuai</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Ye, Chu Yu" sort="Ye, Chu Yu" uniqKey="Ye C" first="Chu-Yu" last="Ye">Chu-Yu Ye</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name><affiliation wicri:level="1"><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name><affiliation wicri:level="3"><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="1"><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation wicri:level="1"><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Genetics</title><idno type="eISSN">1471-2156</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.</p></sec><sec><title>Results</title><p>In this study, we examined single-base resolution methylomes of <italic>Populus </italic>under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in <italic>Populus</italic>. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all <italic>cis</italic>-splicing genes were non-methylated, suggesting that DNA methylation may not associate with <italic>cis</italic>-splicing. However, our results showed that 80% of <italic>trans</italic>-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in <italic>Populus </italic>drought stress responses through the changes of DNA methylation.</p></sec><sec><title>Conclusions</title><p>These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in <italic>Populus</italic>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jansson, S" uniqKey="Jansson S">S Jansson</name></author><author><name sortKey="Douglas, Cj" uniqKey="Douglas C">CJ Douglas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuskan, Ga" uniqKey="Tuskan G">GA Tuskan</name></author><author><name sortKey="Difazio, S" uniqKey="Difazio S">S Difazio</name></author><author><name sortKey="Jansson, S" uniqKey="Jansson S">S Jansson</name></author><author><name sortKey="Bohlmann, J" uniqKey="Bohlmann J">J Bohlmann</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genet</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genet</journal-id><journal-title-group><journal-title>BMC Genetics</journal-title></journal-title-group><issn pub-type="epub">1471-2156</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25080211</article-id><article-id pub-id-type="pmc">4118614</article-id><article-id pub-id-type="publisher-id">1471-2156-15-S1-S9</article-id><article-id pub-id-type="doi">10.1186/1471-2156-15-S1-S9</article-id><article-categories><subj-group subj-group-type="heading"><subject>Proceedings</subject></subj-group></article-categories><title-group><article-title>Single-base-resolution methylomes of <italic>populus trichocarpa </italic>reveal the association between DNA methylation and drought stress</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes" id="A1"><name><surname>Liang</surname><given-names>Dan</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>woshimao_10@163.com</email></contrib><contrib contrib-type="author" equal-contrib="yes" id="A2"><name><surname>Zhang</surname><given-names>Zhoujia</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>gddmwx@163.com</email></contrib><contrib contrib-type="author" equal-contrib="yes" id="A3"><name><surname>Wu</surname><given-names>Honglong</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>wuhonglong@genomics.cn</email></contrib><contrib contrib-type="author" equal-contrib="yes" id="A4"><name><surname>Huang</surname><given-names>Chunyu</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>huangchunyu@bgitechsolutions.com</email></contrib><contrib contrib-type="author" equal-contrib="yes" id="A5"><name><surname>Shuai</surname><given-names>Peng</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>shuaipong@163.com</email></contrib><contrib contrib-type="author" id="A6"><name><surname>Ye</surname><given-names>Chu-Yu</given-names></name><xref ref-type="aff" rid="I1">1</xref><email></email></contrib><contrib contrib-type="author" id="A7"><name><surname>Tang</surname><given-names>Sha</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>shah1986@bjfu.edu.cn</email></contrib><contrib contrib-type="author" id="A8"><name><surname>Wang</surname><given-names>Yunjie</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>wangyunjie@bgitechsolutions.com</email></contrib><contrib contrib-type="author" id="A9"><name><surname>Yang</surname><given-names>Ling</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>yangling@genomics.org.cn</email></contrib><contrib contrib-type="author" id="A10"><name><surname>Wang</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>wangj@genomics.cn</email></contrib><contrib contrib-type="author" corresp="yes" id="A11"><name><surname>Yin</surname><given-names>Weilun</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>xiaxl@bjfu.edu.cn</email></contrib><contrib contrib-type="author" corresp="yes" id="A12"><name><surname>Xia</surname><given-names>Xinli</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>yinwl@bjfu.edu.cn</email></contrib></contrib-group><aff id="I1"><label>1</label>College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</aff><aff id="I2"><label>2</label>BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</aff><aff id="I3"><label>3</label>BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</aff><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>20</day><month>6</month><year>2014</year></pub-date><volume>15</volume><issue>Suppl 1</issue><supplement><named-content content-type="supplement-title">Selected articles from the International Symposium on Quantitative Genetics and Genomics of Woody Plants</named-content><named-content content-type="supplement-editor">Rongling Wu and Zuoheng Wang</named-content></supplement><fpage>S9</fpage><lpage>S9</lpage><permissions><copyright-statement>Copyright © 2014 Liang et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Liang et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><self-uri xlink:href="http://www.biomedcentral.com/1471-2156/15/S1/S9"></self-uri><abstract><sec><title>Background</title><p>DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.</p></sec><sec><title>Results</title><p>In this study, we examined single-base resolution methylomes of <italic>Populus </italic>under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in <italic>Populus</italic>. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all <italic>cis</italic>-splicing genes were non-methylated, suggesting that DNA methylation may not associate with <italic>cis</italic>-splicing. However, our results showed that 80% of <italic>trans</italic>-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in <italic>Populus </italic>drought stress responses through the changes of DNA methylation.</p></sec><sec><title>Conclusions</title><p>These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in <italic>Populus</italic>.</p></sec></abstract><kwd-group><kwd>Methylation</kwd><kwd>populus trichocarpa</kwd><kwd>drought tolerance</kwd><kwd>alternative splicing</kwd></kwd-group><conference><conf-date>16-18 August 2013</conf-date><conf-name>International Symposium on Quantitative Genetics and Genomics of Woody Plants</conf-name><conf-loc>Nantong, China</conf-loc></conference></article-meta></front></pmc><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li><li>Tianjin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Liang, Dan" sort="Liang, Dan" uniqKey="Liang D" first="Dan" last="Liang">Dan Liang</name></noRegion><name sortKey="Huang, Chunyu" sort="Huang, Chunyu" uniqKey="Huang C" first="Chunyu" last="Huang">Chunyu Huang</name><name sortKey="Shuai, Peng" sort="Shuai, Peng" uniqKey="Shuai P" first="Peng" last="Shuai">Peng Shuai</name><name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name><name sortKey="Wu, Honglong" sort="Wu, Honglong" uniqKey="Wu H" first="Honglong" last="Wu">Honglong Wu</name><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name><name sortKey="Ye, Chu Yu" sort="Ye, Chu Yu" uniqKey="Ye C" first="Chu-Yu" last="Ye">Chu-Yu Ye</name><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><name sortKey="Zhang, Zhoujia" sort="Zhang, Zhoujia" uniqKey="Zhang Z" first="Zhoujia" last="Zhang">Zhoujia Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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