Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress.
Identifieur interne : 002051 ( Main/Exploration ); précédent : 002050; suivant : 002052Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress.
Auteurs : Dan Liang ; Zhoujia Zhang ; Honglong Wu ; Chunyu Huang ; Peng Shuai ; Chu-Yu Ye ; Sha Tang ; Yunjie Wang ; Ling Yang ; Jun Wang ; Weilun Yin ; Xinli XiaSource :
- BMC genetics [ 1471-2156 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant, Transcription Factors.
- genetics : Populus, Stress, Physiological.
- DNA Methylation, Droughts, Epigenesis, Genetic, RNA Splicing, Transcriptome.
Abstract
BACKGROUND
DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.
RESULTS
In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2 kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000 bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-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 Populus drought stress responses through the changes of DNA methylation.
CONCLUSIONS
These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.
DOI: 10.1186/1471-2156-15-S1-S9
PubMed: 25080211
PubMed Central: PMC4118614
Affiliations:
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Le document en format XML
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sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25080211</idno><idno type="pmid">25080211</idno><idno type="doi">10.1186/1471-2156-15-S1-S9</idno><idno type="pmc">PMC4118614</idno><idno type="wicri:Area/Main/Corpus">002059</idno><idno 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Huang</name></author><author><name sortKey="Shuai, Peng" sort="Shuai, Peng" uniqKey="Shuai P" first="Peng" last="Shuai">Peng Shuai</name></author><author><name sortKey="Ye, Chu Yu" sort="Ye, Chu Yu" uniqKey="Ye C" first="Chu-Yu" last="Ye">Chu-Yu Ye</name></author><author><name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name></author></analytic><series><title level="j">BMC genetics</title><idno type="eISSN">1471-2156</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA Methylation (MeSH)</term><term>DNA, Plant (genetics)</term><term>Droughts (MeSH)</term><term>Epigenesis, Genetic (MeSH)</term><term>Populus (genetics)</term><term>RNA Splicing (MeSH)</term><term>Stress, Physiological (genetics)</term><term>Transcription Factors (genetics)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Facteurs de transcription (génétique)</term><term>Méthylation de l'ADN (MeSH)</term><term>Populus (génétique)</term><term>Stress physiologique (génétique)</term><term>Sécheresses (MeSH)</term><term>Transcriptome (MeSH)</term><term>Épigenèse génétique (MeSH)</term><term>Épissage des ARN (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term><term>Stress, Physiological</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Facteurs de transcription</term><term>Populus</term><term>Stress physiologique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Methylation</term><term>Droughts</term><term>Epigenesis, Genetic</term><term>RNA Splicing</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Méthylation de l'ADN</term><term>Sécheresses</term><term>Transcriptome</term><term>Épigenèse génétique</term><term>Épissage des ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2 kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000 bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-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 Populus drought stress responses through the changes of DNA methylation.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25080211</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>16</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1471-2156</ISSN><JournalIssue CitedMedium="Internet"><Volume>15 Suppl 1</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>BMC genetics</Title><ISOAbbreviation>BMC Genet</ISOAbbreviation></Journal><ArticleTitle>Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress.</ArticleTitle><Pagination><MedlinePgn>S9</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2156-15-S1-S9</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2 kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000 bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-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 Populus drought stress responses through the changes of DNA methylation.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Dan</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhoujia</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Honglong</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Chunyu</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Shuai</LastName><ForeName>Peng</ForeName><Initials>P</Initials></Author><Author 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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></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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