Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress
Identifieur interne : 000106 ( Pmc/Corpus ); précédent : 000105; suivant : 000107Single-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.
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
Links to Exploration step
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Single-base-resolution methylomes of <italic>populus trichocarpa </italic>reveal the association between DNA methylation and drought stress</title><author><name sortKey="Liang, Dan" sort="Liang, Dan" uniqKey="Liang D" first="Dan" last="Liang">Dan Liang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Zhoujia" sort="Zhang, Zhoujia" uniqKey="Zhang Z" first="Zhoujia" last="Zhang">Zhoujia Zhang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Wu, Honglong" sort="Wu, Honglong" uniqKey="Wu H" first="Honglong" last="Wu">Honglong Wu</name><affiliation><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff></affiliation></author><author><name sortKey="Huang, Chunyu" sort="Huang, Chunyu" uniqKey="Huang C" first="Chunyu" last="Huang">Chunyu Huang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Shuai, Peng" sort="Shuai, Peng" uniqKey="Shuai P" first="Peng" last="Shuai">Peng Shuai</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></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><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name><affiliation><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></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></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Single-base-resolution methylomes of <italic>populus trichocarpa </italic>reveal the association between DNA methylation and drought stress</title><author><name sortKey="Liang, Dan" sort="Liang, Dan" uniqKey="Liang D" first="Dan" last="Liang">Dan Liang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Zhoujia" sort="Zhang, Zhoujia" uniqKey="Zhang Z" first="Zhoujia" last="Zhang">Zhoujia Zhang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Wu, Honglong" sort="Wu, Honglong" uniqKey="Wu H" first="Honglong" last="Wu">Honglong Wu</name><affiliation><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff></affiliation></author><author><name sortKey="Huang, Chunyu" sort="Huang, Chunyu" uniqKey="Huang C" first="Chunyu" last="Huang">Chunyu Huang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Shuai, Peng" sort="Shuai, Peng" uniqKey="Shuai P" first="Peng" last="Shuai">Peng Shuai</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></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><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Yunjie" sort="Wang, Yunjie" uniqKey="Wang Y" first="Yunjie" last="Wang">Yunjie Wang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Ling" sort="Yang, Ling" uniqKey="Yang L" first="Ling" last="Yang">Ling Yang</name><affiliation><nlm:aff id="I3">BGI-Tianjin, E3 building, Airport Business Park, Tianjin Airport Economic Area,Tianjin, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:aff id="I2">BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China</nlm:aff></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation><nlm:aff id="I1">College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China</nlm:aff></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 sortKey="Grigoriev, I" uniqKey="Grigoriev I">I Grigoriev</name></author><author><name sortKey="Hellsten, U" uniqKey="Hellsten U">U Hellsten</name></author><author><name sortKey="Putnam, N" uniqKey="Putnam N">N Putnam</name></author><author><name sortKey="Ralph, S" uniqKey="Ralph S">S Ralph</name></author><author><name sortKey="Rombauts, S" uniqKey="Rombauts S">S Rombauts</name></author><author><name sortKey="Salamov, A" uniqKey="Salamov A">A Salamov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuskan, Ga" uniqKey="Tuskan G">GA Tuskan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bogeat Triboulot, Mb" uniqKey="Bogeat Triboulot M">MB Bogeat-Triboulot</name></author><author><name sortKey="Brosche, M" uniqKey="Brosche M">M Brosche</name></author><author><name sortKey="Renaut, J" uniqKey="Renaut J">J Renaut</name></author><author><name sortKey="Jouve, L" uniqKey="Jouve L">L Jouve</name></author><author><name sortKey="Le Thiec, D" uniqKey="Le Thiec D">D Le Thiec</name></author><author><name sortKey="Fayyaz, P" uniqKey="Fayyaz P">P Fayyaz</name></author><author><name sortKey="Vinocur, B" uniqKey="Vinocur B">B Vinocur</name></author><author><name sortKey="Witters, E" uniqKey="Witters E">E Witters</name></author><author><name sortKey="Laukens, K" uniqKey="Laukens K">K Laukens</name></author><author><name sortKey="Teichmann, T" uniqKey="Teichmann T">T Teichmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, S" uniqKey="Tang S">S Tang</name></author><author><name sortKey="Liang, H" uniqKey="Liang H">H Liang</name></author><author><name sortKey="Yan, D" uniqKey="Yan D">D Yan</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name></author><author><name sortKey="Han, X" uniqKey="Han X">X Han</name></author><author><name sortKey="Carlson, J" uniqKey="Carlson J">J Carlson</name></author><author><name sortKey="Xia, X" uniqKey="Xia X">X Xia</name></author><author><name sortKey="Yin, W" uniqKey="Yin W">W Yin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shuai, P" uniqKey="Shuai P">P Shuai</name></author><author><name sortKey="Liang, D" uniqKey="Liang D">D Liang</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Yin, W" uniqKey="Yin W">W Yin</name></author><author><name sortKey="Xia, X" uniqKey="Xia X">X Xia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lister, R" uniqKey="Lister R">R Lister</name></author><author><name sortKey="O Malley, Rc" uniqKey="O Malley R">RC O'Malley</name></author><author><name sortKey="Tonti Filippini, J" uniqKey="Tonti Filippini J">J Tonti-Filippini</name></author><author><name sortKey="Gregory, Bd" uniqKey="Gregory B">BD Gregory</name></author><author><name sortKey="Berry, Cc" uniqKey="Berry C">CC Berry</name></author><author><name sortKey="Millar, Ah" uniqKey="Millar A">AH Millar</name></author><author><name sortKey="Ecker, Jr" uniqKey="Ecker J">JR Ecker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Elling, Aa" uniqKey="Elling A">AA Elling</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Li, N" uniqKey="Li N">N Li</name></author><author><name sortKey="Peng, Z" uniqKey="Peng Z">Z Peng</name></author><author><name sortKey="He, G" uniqKey="He G">G He</name></author><author><name sortKey="Sun, H" uniqKey="Sun H">H Sun</name></author><author><name sortKey="Qi, Y" uniqKey="Qi Y">Y Qi</name></author><author><name sortKey="Liu, Xs" uniqKey="Liu X">XS Liu</name></author><author><name sortKey="Deng, Xw" uniqKey="Deng X">XW Deng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lister, R" uniqKey="Lister R">R Lister</name></author><author><name sortKey="Pelizzola, M" uniqKey="Pelizzola M">M Pelizzola</name></author><author><name sortKey="Dowen, Rh" uniqKey="Dowen R">RH Dowen</name></author><author><name sortKey="Hawkins, Rd" uniqKey="Hawkins R">RD Hawkins</name></author><author><name sortKey="Hon, G" uniqKey="Hon G">G Hon</name></author><author><name sortKey="Tonti Filippini, J" uniqKey="Tonti Filippini J">J Tonti-Filippini</name></author><author><name sortKey="Nery, Jr" uniqKey="Nery J">JR Nery</name></author><author><name sortKey="Lee, L" uniqKey="Lee L">L Lee</name></author><author><name sortKey="Ye, Z" uniqKey="Ye Z">Z Ye</name></author><author><name sortKey="Ngo, Qm" uniqKey="Ngo Q">QM Ngo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xiang, H" uniqKey="Xiang H">H Xiang</name></author><author><name sortKey="Zhu, J" uniqKey="Zhu J">J Zhu</name></author><author><name sortKey="Chen, Q" uniqKey="Chen Q">Q Chen</name></author><author><name sortKey="Dai, F" uniqKey="Dai F">F Dai</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name></author><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Dong, Y" uniqKey="Dong Y">Y Dong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cao, X" uniqKey="Cao X">X Cao</name></author><author><name sortKey="Jacobsen, Se" uniqKey="Jacobsen S">SE Jacobsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Razin, A" uniqKey="Razin A">A Razin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Curradi, M" uniqKey="Curradi M">M Curradi</name></author><author><name sortKey="Izzo, A" uniqKey="Izzo A">A Izzo</name></author><author><name sortKey="Badaracco, G" uniqKey="Badaracco G">G Badaracco</name></author><author><name sortKey="Landsberger, N" uniqKey="Landsberger N">N Landsberger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Uthup, Tk" uniqKey="Uthup T">TK Uthup</name></author><author><name sortKey="Ravindran, M" uniqKey="Ravindran M">M Ravindran</name></author><author><name sortKey="Bini, K" uniqKey="Bini K">K Bini</name></author><author><name sortKey="Thakurdas, S" uniqKey="Thakurdas S">S Thakurdas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Labra, M" uniqKey="Labra M">M Labra</name></author><author><name sortKey="Ghiani, A" uniqKey="Ghiani A">A Ghiani</name></author><author><name sortKey="Citterio, S" uniqKey="Citterio S">S Citterio</name></author><author><name sortKey="Sgorbati, S" uniqKey="Sgorbati S">S Sgorbati</name></author><author><name sortKey="Sala, F" uniqKey="Sala F">F Sala</name></author><author><name sortKey="Vannini, C" uniqKey="Vannini C">C Vannini</name></author><author><name sortKey="Ruffini Castiglione, M" uniqKey="Ruffini Castiglione M">M Ruffini-Castiglione</name></author><author><name sortKey="Bracale, M" uniqKey="Bracale M">M Bracale</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Colaneri, Ac" uniqKey="Colaneri A">AC Colaneri</name></author><author><name sortKey="Jones, Am" uniqKey="Jones A">AM Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, W S" uniqKey="Wang W">W-S Wang</name></author><author><name sortKey="Pan, Y J" uniqKey="Pan Y">Y-J Pan</name></author><author><name sortKey="Zhao, X Q" uniqKey="Zhao X">X-Q Zhao</name></author><author><name sortKey="Dwivedi, D" uniqKey="Dwivedi D">D Dwivedi</name></author><author><name sortKey="Zhu, L H" uniqKey="Zhu L">L-H Zhu</name></author><author><name sortKey="Ali, J" uniqKey="Ali J">J Ali</name></author><author><name sortKey="Fu, B Y" uniqKey="Fu B">B-Y Fu</name></author><author><name sortKey="Li, Z K" uniqKey="Li Z">Z-K Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, Y" uniqKey="Yu Y">Y Yu</name></author><author><name sortKey="Yang, X" uniqKey="Yang X">X Yang</name></author><author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name></author><author><name sortKey="Shi, F" uniqKey="Shi F">F Shi</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Wang, D" uniqKey="Wang D">D Wang</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rico, L" uniqKey="Rico L">L Rico</name></author><author><name sortKey="Ogaya, R" uniqKey="Ogaya R">R Ogaya</name></author><author><name sortKey="Barbeta, A" uniqKey="Barbeta A">A Barbeta</name></author><author><name sortKey="Pe Uelas, J" uniqKey="Pe Uelas J">J Peñuelas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Griffiths, H" uniqKey="Griffiths H">H Griffiths</name></author><author><name sortKey="Parry, Ma" uniqKey="Parry M">MA Parry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Yang, F" uniqKey="Yang F">F Yang</name></author><author><name sortKey="Xiao, X" uniqKey="Xiao X">X Xiao</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author><author><name sortKey="Korpelainen, H" uniqKey="Korpelainen H">H Korpelainen</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Regier, N" uniqKey="Regier N">N Regier</name></author><author><name sortKey="Streb, S" uniqKey="Streb S">S Streb</name></author><author><name sortKey="Cocozza, C" uniqKey="Cocozza C">C Cocozza</name></author><author><name sortKey="Schaub, M" uniqKey="Schaub M">M Schaub</name></author><author><name sortKey="Cherubini, P" uniqKey="Cherubini P">P Cherubini</name></author><author><name sortKey="Zeeman, Sc" uniqKey="Zeeman S">SC Zeeman</name></author><author><name sortKey="Frey, B" uniqKey="Frey B">B Frey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hayatsu, H" uniqKey="Hayatsu H">H Hayatsu</name></author><author><name sortKey="Tsuji, K" uniqKey="Tsuji K">K Tsuji</name></author><author><name sortKey="Negishi, K" uniqKey="Negishi K">K Negishi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Gj" uniqKey="Zhang G">GJ Zhang</name></author><author><name sortKey="Guo, Gw" uniqKey="Guo G">GW Guo</name></author><author><name sortKey="Hu, Xd" uniqKey="Hu X">XD Hu</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Li, Qy" uniqKey="Li Q">QY Li</name></author><author><name sortKey="Li, Rq" uniqKey="Li R">RQ Li</name></author><author><name sortKey="Zhuang, Rh" uniqKey="Zhuang R">RH Zhuang</name></author><author><name sortKey="Lu, Zk" uniqKey="Lu Z">ZK Lu</name></author><author><name sortKey="He, Zq" uniqKey="He Z">ZQ He</name></author><author><name sortKey="Fang, Xd" uniqKey="Fang X">XD Fang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Du, Z" uniqKey="Du Z">Z Du</name></author><author><name sortKey="Zhou, X" uniqKey="Zhou X">X Zhou</name></author><author><name sortKey="Ling, Y" uniqKey="Ling Y">Y Ling</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Su, Z" uniqKey="Su Z">Z Su</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Horiuchi, T" uniqKey="Horiuchi T">T Horiuchi</name></author><author><name sortKey="Aigaki, T" uniqKey="Aigaki T">T Aigaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Akiva, P" uniqKey="Akiva P">P Akiva</name></author><author><name sortKey="Toporik, A" uniqKey="Toporik A">A Toporik</name></author><author><name sortKey="Edelheit, S" uniqKey="Edelheit S">S Edelheit</name></author><author><name sortKey="Peretz, Y" uniqKey="Peretz Y">Y Peretz</name></author><author><name sortKey="Diber, A" uniqKey="Diber A">A Diber</name></author><author><name sortKey="Shemesh, R" uniqKey="Shemesh R">R Shemesh</name></author><author><name sortKey="Novik, A" uniqKey="Novik A">A Novik</name></author><author><name sortKey="Sorek, R" uniqKey="Sorek R">R Sorek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Filichkin, Sa" uniqKey="Filichkin S">SA Filichkin</name></author><author><name sortKey="Priest, Hd" uniqKey="Priest H">HD Priest</name></author><author><name sortKey="Givan, Sa" uniqKey="Givan S">SA Givan</name></author><author><name sortKey="Shen, R" uniqKey="Shen R">R Shen</name></author><author><name sortKey="Bryant, Dw" uniqKey="Bryant D">DW Bryant</name></author><author><name sortKey="Fox, Se" uniqKey="Fox S">SE Fox</name></author><author><name sortKey="Wong, Wk" uniqKey="Wong W">WK Wong</name></author><author><name sortKey="Mockler, Tc" uniqKey="Mockler T">TC Mockler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mazzucotelli, E" uniqKey="Mazzucotelli E">E Mazzucotelli</name></author><author><name sortKey="Mastrangelo, Aa" uniqKey="Mastrangelo A">AA Mastrangelo</name></author><author><name sortKey="Crosatti, C" uniqKey="Crosatti C">C Crosatti</name></author><author><name sortKey="Guerra, D" uniqKey="Guerra D">D Guerra</name></author><author><name sortKey="Stanca, Am" uniqKey="Stanca A">AM Stanca</name></author><author><name sortKey="Cattivelli, L" uniqKey="Cattivelli L">L Cattivelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palusa, Sg" uniqKey="Palusa S">SG Palusa</name></author><author><name sortKey="Ali, Gs" uniqKey="Ali G">GS Ali</name></author><author><name sortKey="Reddy, Asn" uniqKey="Reddy A">ASN Reddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="He, K" uniqKey="He K">K He</name></author><author><name sortKey="Ma, Y" uniqKey="Ma Y">Y Ma</name></author><author><name sortKey="Su, N" uniqKey="Su N">N Su</name></author><author><name sortKey="He, H" uniqKey="He H">H He</name></author><author><name sortKey="Stolc, V" uniqKey="Stolc V">V Stolc</name></author><author><name sortKey="Tongprasit, W" uniqKey="Tongprasit W">W Tongprasit</name></author><author><name sortKey="Jin, W" uniqKey="Jin W">W Jin</name></author><author><name sortKey="Jiang, J" uniqKey="Jiang J">J Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zemach, A" uniqKey="Zemach A">A Zemach</name></author><author><name sortKey="Mcdaniel, Ie" uniqKey="Mcdaniel I">IE McDaniel</name></author><author><name sortKey="Silva, P" uniqKey="Silva P">P Silva</name></author><author><name sortKey="Zilberman, D" uniqKey="Zilberman D">D Zilberman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P Perez-Rodriguez</name></author><author><name sortKey="Riano Pachon, Dm" uniqKey="Riano Pachon D">DM Riano-Pachon</name></author><author><name sortKey="Correa, Lg" uniqKey="Correa L">LG Correa</name></author><author><name sortKey="Rensing, Sa" uniqKey="Rensing S">SA Rensing</name></author><author><name sortKey="Kersten, B" uniqKey="Kersten B">B Kersten</name></author><author><name sortKey="Mueller Roeber, B" uniqKey="Mueller Roeber B">B Mueller-Roeber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thornburg, Bg" uniqKey="Thornburg B">BG Thornburg</name></author><author><name sortKey="Gotea, V" uniqKey="Gotea V">V Gotea</name></author><author><name sortKey="Makalowski, W" uniqKey="Makalowski W">W Makalowski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vining, Kj" uniqKey="Vining K">KJ Vining</name></author><author><name sortKey="Pomraning, Kr" uniqKey="Pomraning K">KR Pomraning</name></author><author><name sortKey="Wilhelm, Lj" uniqKey="Wilhelm L">LJ Wilhelm</name></author><author><name sortKey="Priest, Hd" uniqKey="Priest H">HD Priest</name></author><author><name sortKey="Pellegrini, M" uniqKey="Pellegrini M">M Pellegrini</name></author><author><name sortKey="Mockler, Tc" uniqKey="Mockler T">TC Mockler</name></author><author><name sortKey="Freitag, M" uniqKey="Freitag M">M Freitag</name></author><author><name sortKey="Strauss, Sh" uniqKey="Strauss S">SH Strauss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, Xy" uniqKey="Li X">XY Li</name></author><author><name sortKey="Wang, Xf" uniqKey="Wang X">XF Wang</name></author><author><name sortKey="He, K" uniqKey="He K">K He</name></author><author><name sortKey="Ma, Yq" uniqKey="Ma Y">YQ Ma</name></author><author><name sortKey="Su, N" uniqKey="Su N">N Su</name></author><author><name sortKey="He, H" uniqKey="He H">H He</name></author><author><name sortKey="Stolc, V" uniqKey="Stolc V">V Stolc</name></author><author><name sortKey="Tongprasit, W" uniqKey="Tongprasit W">W Tongprasit</name></author><author><name sortKey="Jin, Ww" uniqKey="Jin W">WW Jin</name></author><author><name sortKey="Jiang, Jm" uniqKey="Jiang J">JM Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shukla, S" uniqKey="Shukla S">S Shukla</name></author><author><name sortKey="Kavak, E" uniqKey="Kavak E">E Kavak</name></author><author><name sortKey="Gregory, M" uniqKey="Gregory M">M Gregory</name></author><author><name sortKey="Imashimizu, M" uniqKey="Imashimizu M">M Imashimizu</name></author><author><name sortKey="Shutinoski, B" uniqKey="Shutinoski B">B Shutinoski</name></author><author><name sortKey="Kashlev, M" uniqKey="Kashlev M">M Kashlev</name></author><author><name sortKey="Oberdoerffer, P" uniqKey="Oberdoerffer P">P Oberdoerffer</name></author><author><name sortKey="Sandberg, R" uniqKey="Sandberg R">R Sandberg</name></author><author><name sortKey="Oberdoerffer, S" uniqKey="Oberdoerffer S">S Oberdoerffer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chodavarapu, Rk" uniqKey="Chodavarapu R">RK Chodavarapu</name></author><author><name sortKey="Feng, Sh" uniqKey="Feng S">SH Feng</name></author><author><name sortKey="Bernatavichute, Yv" uniqKey="Bernatavichute Y">YV Bernatavichute</name></author><author><name sortKey="Chen, Py" uniqKey="Chen P">PY Chen</name></author><author><name sortKey="Stroud, H" uniqKey="Stroud H">H Stroud</name></author><author><name sortKey="Yu, Yc" uniqKey="Yu Y">YC Yu</name></author><author><name sortKey="Hetzel, Ja" uniqKey="Hetzel J">JA Hetzel</name></author><author><name sortKey="Kuo, F" uniqKey="Kuo F">F Kuo</name></author><author><name sortKey="Kim, J" uniqKey="Kim J">J Kim</name></author><author><name sortKey="Cokus, Sj" uniqKey="Cokus S">SJ Cokus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Yazaki, J" uniqKey="Yazaki J">J Yazaki</name></author><author><name sortKey="Sundaresan, A" uniqKey="Sundaresan A">A Sundaresan</name></author><author><name sortKey="Cokus, S" uniqKey="Cokus S">S Cokus</name></author><author><name sortKey="Chan, Sw" uniqKey="Chan S">SW Chan</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H Chen</name></author><author><name sortKey="Henderson, Ir" uniqKey="Henderson I">IR Henderson</name></author><author><name sortKey="Shinn, P" uniqKey="Shinn P">P Shinn</name></author><author><name sortKey="Pellegrini, M" uniqKey="Pellegrini M">M Pellegrini</name></author><author><name sortKey="Jacobsen, Se" uniqKey="Jacobsen S">SE Jacobsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Zhu, J" uniqKey="Zhu J">J Zhu</name></author><author><name sortKey="Hu, F" uniqKey="Hu F">F Hu</name></author><author><name sortKey="Ge, S" uniqKey="Ge S">S Ge</name></author><author><name sortKey="Ye, M" uniqKey="Ye M">M Ye</name></author><author><name sortKey="Xiang, H" uniqKey="Xiang H">H Xiang</name></author><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name></author><author><name sortKey="Zheng, X" uniqKey="Zheng X">X Zheng</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kapitonov, Vv" uniqKey="Kapitonov V">VV Kapitonov</name></author><author><name sortKey="Jurka, J" uniqKey="Jurka J">J Jurka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwartz, D" uniqKey="Schwartz D">D Schwartz</name></author><author><name sortKey="Dennis, E" uniqKey="Dennis E">E Dennis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Banks, Ja" uniqKey="Banks J">JA Banks</name></author><author><name sortKey="Masson, P" uniqKey="Masson P">P Masson</name></author><author><name sortKey="Fedoroff, N" uniqKey="Fedoroff N">N Fedoroff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martienssen, Ra" uniqKey="Martienssen R">RA Martienssen</name></author><author><name sortKey="Colot, V" uniqKey="Colot V">V Colot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kato, M" uniqKey="Kato M">M Kato</name></author><author><name sortKey="Miura, A" uniqKey="Miura A">A Miura</name></author><author><name sortKey="Bender, J" uniqKey="Bender J">J Bender</name></author><author><name sortKey="Jacobsen, Se" uniqKey="Jacobsen S">SE Jacobsen</name></author><author><name sortKey="Kakutani, T" uniqKey="Kakutani T">T Kakutani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bourque, G" uniqKey="Bourque G">G Bourque</name></author><author><name sortKey="Leong, B" uniqKey="Leong B">B Leong</name></author><author><name sortKey="Vega, Vb" uniqKey="Vega V">VB Vega</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author><author><name sortKey="Lee, Yl" uniqKey="Lee Y">YL Lee</name></author><author><name sortKey="Srinivasan, Kg" uniqKey="Srinivasan K">KG Srinivasan</name></author><author><name sortKey="Chew, Jl" uniqKey="Chew J">JL Chew</name></author><author><name sortKey="Ruan, Y" uniqKey="Ruan Y">Y Ruan</name></author><author><name sortKey="Wei, Cl" uniqKey="Wei C">CL Wei</name></author><author><name sortKey="Ng, Hh" uniqKey="Ng H">HH Ng</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="abstract" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<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><body><sec><title>Background</title><p><italic>Populus </italic>(<italic>Populus </italic>sp.) is an ideal model system for investigating molecular mechanisms of trees in response to environmental stresses, due to its advantages including rapid growth, high yield, easy propagation, importance in the economy and available genomic resources [<xref ref-type="bibr" rid="B1">1</xref>,<xref ref-type="bibr" rid="B2">2</xref>]. Drought is a major abiotic stress that limits the survival and growth of young poplar plants [<xref ref-type="bibr" rid="B3">3</xref>]. Therefore, many studies have focused on understanding drought responsive mechanisms in <italic>Populus </italic>[<xref ref-type="bibr" rid="B4">4</xref>-<xref ref-type="bibr" rid="B6">6</xref>].</p><p>DNA methylation is an important biological form of epigenetic modification. Currently, methylation analysis is widely used to explore various mechanisms underlying biological survival in plants [<xref ref-type="bibr" rid="B7">7</xref>,<xref ref-type="bibr" rid="B8">8</xref>], humans [<xref ref-type="bibr" rid="B9">9</xref>], and insects [<xref ref-type="bibr" rid="B10">10</xref>]. Plant genomes show extensive cytosine methylation at CG, CNG (N represents any nucleotide), and CHH (H represents A, C or T) sites [<xref ref-type="bibr" rid="B11">11</xref>]. Previous studies indicated that the effect of DNA methylation in plants refers to DNA methylation preventing DNA transcription by combining with the genomic sequence of transcription factors, and another refers to specific proteins (known as methyl-CpG binding proteins) binding with methylated DNA and acting as competitors of transcription factors. Complexes of proteins affect chromosome histone acetylation, leading to transcriptional inhibition [<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>]. Methylation induced by biotic stress is generally associated with the silencing of parasitic DNA and expression of resistant genes, while abiotic stress-induced methylation is supposed to be linked with the transcription factors which participate in numerous biochemical pathways involved in acclimatization and stress response in plants [<xref ref-type="bibr" rid="B14">14</xref>].</p><p>Numerous studies have shown that DNA methylation levels could be affected by plant stress in <italic>Arabidopsis</italic>, rice, pea and other plants [<xref ref-type="bibr" rid="B15">15</xref>-<xref ref-type="bibr" rid="B18">18</xref>], but few about trees. Uthup et al. have reported the identification of DNA methylation patterns and their putative relationship with abiotic stress in the tree crop <italic>Hevea brasiliensis </italic>[<xref ref-type="bibr" rid="B14">14</xref>]. The percentage of hypermethylated loci increased, and that of fully methylated loci clearly decreased in <italic>Quercus ilex </italic>trees exposed to drought [<xref ref-type="bibr" rid="B19">19</xref>]. However, no studies performed methylation analysis of <italic>Populus </italic>at the genomic level under drought stress by using high-throughput bisulfite sequencing. To improve our understanding of the resistance mechanisms at the molecular level in <italic>Populus</italic>, we investigated DNA methylomes of <italic>Populus </italic><italic>trichocarpa </italic>under normal and drought conditions, focusing on epigenetic regulation of stress responses.</p></sec><sec sec-type="results"><title>Results</title><sec><title>Bisulfite sequencing of the <italic>Populus trichocarpa </italic>genome</title><p>To generate the single-base resolution methylome of <italic>P. trichocarpa </italic>under normal (i.e., well water; WW) and drought stress (i.e., water stress; WS) conditions, we applied the Illumina Hiseq 2000 platform for bisulfite sequencing of DNA extracted from leaves. Reads that aligned to the unmethylated lambda DNA, which were added to the total DNA before applying the bisulfite treatment, were used to calculate the conversion rate. The conversion rates of WW and WS were 99.40% and 99.45%, respectively. Two sets of raw data were obtained from sequencing, with the output of 16.86 giga base pair (Gb) in WW sample and 16.63 Gb in WS. We subsequently used a series of filter criteria to ensure the data quality, including trimming low-quality reads(reads that contain more than 50% unknown bases) and retaining unique-aligned reads. Finally, 72.96% of the reads in WW and 76.69% of the reads in WS were used for further analysis. These data were estimated to cover the whole genome with 28.45- and 29.93-fold sequencing depths (Additional file <xref ref-type="supplementary-material" rid="S1">1</xref>). To avoid the effects of individual SNPs, the online original reference (<ext-link ext-link-type="uri" xlink:href="http://genome.jgi-psf.org/poplar/poplar.home.html">http://genome.jgi-psf.org/poplar/poplar.home.html</ext-link>) was modified by the resequence data.</p></sec><sec><title>DNA methylation in <italic>Populus trichocarpa</italic></title><p>Our results showed that methylated cytosines (mCs) accounting for 10.04% of all cytosines in the whole genome under drought stress were significantly more than those (7.75 %) in WW (Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>). Distribution of cytosine methylation levels showed that more proportions of mCG and mCHG have higher methylation levels as compared with mCHH (Figure <xref ref-type="fig" rid="F1">1-a</xref>). CG sites were much higher methylated in gene region than other sites (Figure <xref ref-type="fig" rid="F1">1-b</xref>). Additionally, our results showed that methylated sites were concentrated in the non-CG sites in the <italic>Populus </italic>genome, especially in mCHH (Figure <xref ref-type="fig" rid="F1">1-c</xref>), and the basic group of HH or mCHH tended to contain twofold more A or T (Additional file <xref ref-type="supplementary-material" rid="S3">3</xref>). Since the chromosome structure of the <italic>P. trichocarpa </italic>genome is imperfect, we concatenated the remaining fragments as the 20<sup>th </sup>scaffold in addition to the existing 19 scaffolds and then analyzed the distribution of the mCs across chromosomes, which shows that there was a high methylated cytosine density in centromere regions that consisted of more repetitive sequences (Additional file <xref ref-type="supplementary-material" rid="S4">4</xref>).</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>The global pattern of <italic>Populus </italic>DNA methylomes</bold>. (a) The percentage of methylated cytosines distribution in each sequence context (H=A, T, C). The <italic>y </italic>axis indicates the percentage methylated cytosines according to each methylation level which show on <italic>x </italic>axis.(methylation level = # of mC / # of C * 100%) (b) Distribution of CG, CHG and CHH methylation levels in each sequence context of gene related region, including upstream, first exon, first intron, internal exon, internal intron, last exon and downstream.. The <italic>x </italic>axis shows seven elements, the <italic>y </italic>axis represents average methylation levels of cytosines. The red dots represent average methylation levels of bins, the curve shows the average value of 5 bins with 1-bin step, and the green dotted line indicate TSSs (transcription start sites) (c) The percentage and absolute number of methylated cytosines that identified in WW(left) and WS(right) in each sequence context.</p></caption><graphic xlink:href="1471-2156-15-S1-S9-1"></graphic></fig><p>The following analysis was to investigate the methylation profiles of coding sequences (CDSs), introns, untranslated regions (UTRs), small RNAs, repetitive DNAs under relative and <italic>absolute </italic>methylation standards [<xref ref-type="bibr" rid="B10">10</xref>]. We found that methylation levels in coding regions were higher than that in 5'- and 3'-UTRs. The methylation levels of repetitive regions were significantly higher than those of gene body regions (p < 7.71E-07, Wilcoxon RankSum test). Furthermore, the methylation levels <italic>of </italic>2000bp upstream of the transcriptional start site (<italic>up2K)</italic>, 2000bp downstream of the transcriptional termination site (down2K), and repetitive sequences were significantly higher after drought treatment (p < 0.001625, Wilcoxon RankSum test) <italic>(</italic>Figure. <italic>2)</italic>.</p><p>Gene Ontology analysis demonstrated biological processes related to biological regulation were enriched in both newly methylated and demethylated genes after drought stress as compared with the whole <italic>Populus </italic>genome, indicating that methylation or demethylation of these biological regulation related genes may play important roles in drought stress response of <italic>Populus </italic>(Additional file <xref ref-type="supplementary-material" rid="S5">5</xref>-a,b).</p></sec><sec><title>Prediction and validation of splicing events in <bold><italic>P. trichocarpa</italic></bold></title><p>We used transcriptome sequencing technology to further investigate the expression profiles of two samples (i.e., WW and WS). A total of 130,884,860 and 138,441,434 raw reads were generated, and 86,385,459 (66.00%) and 90,236,283 (65.18%) unique alignment reads were retained in WW and WS, respectively (Additional file <xref ref-type="supplementary-material" rid="S6">6</xref>). We analyzed two splicing forms of the genes, i.e., the <italic>trans</italic>-splicing and <italic>cis</italic>-splicing models. <italic>Cis</italic>-splicing occurs within a single transcript, which can produce multiple mRNA transcripts. <italic>Trans</italic>-splicing occurs at the bonding point, which is formed by two different genes [<xref ref-type="bibr" rid="B26">26</xref>]. Recently, alternative splicing and gene fusion were discovered by high-throughput sequencing in more species, such as human [<xref ref-type="bibr" rid="B27">27</xref>], rice [<xref ref-type="bibr" rid="B24">24</xref>] and <italic>Arabidopsis</italic>[<xref ref-type="bibr" rid="B28">28</xref>]. However, no information on alternative splicing in Populus was available. We found four alternative splicing types in <italic>P. trichocarpa</italic>: A) Exon skipping, B) intron retention, C) alternative 5 'splice sites, and D) alternative 3' splice sites, according to the classification of alternative splicing types in rice [<xref ref-type="bibr" rid="B24">24</xref>] and 11791 and 13251 alternative splicing genes in WW and WS, respectively. At least 20% of intron-containing genes in P. <italic>trichocarpa </italic>were spliced, which is lower than that (42%) in <italic>Arabidopsis </italic>[<xref ref-type="bibr" rid="B28">28</xref>]. More genes in WS were alternatively spliced in four alternative splicing types <italic>(</italic>Figure. <italic>3)</italic>, especially the alternative 3' splice sites were <italic>more </italic>increased, suggesting that alternative splicing can be regulated and associated with environmental stress as previous reports [<xref ref-type="bibr" rid="B29">29</xref>,<xref ref-type="bibr" rid="B30">30</xref>] and methylation may play more acting on alternative 3' splice sites after drought treatment in <italic>Populus</italic>. Particularly, in terms of the methylation level of 20 bp sequences containing alternative splicing sites, more than 80% of all alternative splicing sites in two samples were non-methylated, while none of the genes were methylated (Additional file <xref ref-type="supplementary-material" rid="S7">7</xref>-a). Interestingly, we found that 80% of the fusion genes were methylated and the splicing events were decreased after the drought treatment (Table <xref ref-type="table" rid="T1">1</xref>). To verify the accuracy of the fusion gene, that identified 227 and 161 in WW and WS, we randomly selected 10 genes in the two groups of fusion materials to test by RT-PCR, six of which were verified (Additional file <xref ref-type="supplementary-material" rid="S7">7</xref>-b). The probability (6/10) was slightly lower than expected based on the accuracies in human and rice [<xref ref-type="bibr" rid="B24">24</xref>,<xref ref-type="bibr" rid="B27">27</xref>].</p><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Numbers of methylated and unmethylated gene fusions.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center">Sample</th><th align="center">Methylated genes in the genome</th><th align="center">Unmethylated genes in the genome</th><th align="center">Fusion genes both methylated</th><th align="center">Fusion genes both unmethylated</th><th align="center">Fusion genes one methylated</th></tr></thead><tbody><tr><td align="center">WW</td><td align="center">23983</td><td align="center">8071</td><td align="center">194</td><td align="center">4</td><td align="center">29</td></tr><tr><td align="center">WS</td><td align="center">22498</td><td align="center">8895</td><td align="center">130</td><td align="center">11</td><td align="center">20</td></tr></tbody></table></table-wrap></sec><sec><title>Effects of DNA methylation on gene expression in P. trichocarpa</title><p>To compare the effects of Populus DNA methylation on gene expression in two samples (i.e., WW and WS), we used transcriptome sequencing to determine the expression levels of methylated and unmethylated genes. Generally speaking, the expression levels of examined 17714 expressed genes were positively correlated with their methylation levels. We found that 7392 genes exhibited rising trends in methylation and expression levels after drought treatment. Methylation and expression levels were both reduced in 10322 genes under drought stress.</p><p>To further analyze the relationship between gene expression and methylation levels, we divided these genes into four categories based on expression levels: High expression, medium expression, low expression, and silent genes, from the bottom one-third to the top one-third (Figure. 4-a). We found that silent genes had significantly higher methylation levels than expressed genes, indicating that gene silence may be caused by high methylation level (<italic>p </italic>= 6.8E-08, Wilcoxon Rank Sum test). For expressed genes, methylation levels in gene body and upstream region were positively correlated with gene expression (Additional file <xref ref-type="supplementary-material" rid="S8">8</xref>). Nonetheless, gene expression levels had negative correlations with methylation at transcription start sites (TSSs), transcriptional termination regions (TTRs) and downstream regions.</p><p>Gene-body methylation genes had significantly higher expression levels than body-unmethylated genes (<italic>p </italic>= 6.01E-07, Wilcoxon rank sum test) indicating a positive correlation between gene expression and gene-body methylation (Figure. 4-c). Interestingly, the results showed that upstream2k-methylated genes have significantly higher expression level than upstream 2k-unmethylated genes (<italic>p </italic>= 7.41E-05, Wilcoxon rank sum test) [<xref ref-type="bibr" rid="B31">31</xref>] (Figure. 4-d). However, further analysis was performed on the 100bp upstream of the transcriptional start site (TSS), and found that genes methylated in this region had significantly higher expression level than unmethylated genes (<italic>p </italic>= 8.6E-06, Wilcoxon rank sum test), indicating that methylation of this region induced gene expression (Figure.4-e). Coincident with the situation of 100 bp upstream of the TSS, downstream2k-unmethylated genes have higher expression level than downstream2k-methylated genes (Figure. 4-f).</p><p>As regards changes after drought treatment, the methylation levels of the silent genes increased significantly (<italic>p </italic>= 6.796E-08, Wilcoxon rank sum test) (Figure.4-a,b). The expression level of upstream2k-unmethylated genes was reduced, while it increased for genes methylated in 100bp upstream of TSS. Downstream2k-unmethylated genes have higher expression level after treatment. Gene-body methylated and unmethylated genes have no significant change.</p></sec><sec><title>Differentially expressed and methylated transcription factors</title><p>Due to critical roles of transcription factors (TFs) in responses to external stimuli by influencing the expression of downstream targets, we identified differentially expressed and methylated TFs in <italic>P. trichocarpa </italic>according to two TF databases (i.e., DPTF (<ext-link ext-link-type="uri" xlink:href="http://dptf.cbi.pku.edu.cn/index.php">http://dptf.cbi.pku.edu.cn/index.php</ext-link>) [<xref ref-type="bibr" rid="B32">32</xref>] and PlnTFDB (<ext-link ext-link-type="uri" xlink:href="http://plntfdb.bio.uni-potsdam.de/v3.0/">http://plntfdb.bio.uni-potsdam.de/v3.0/</ext-link>) [<xref ref-type="bibr" rid="B33">33</xref>]. A total of 1156 TFs showed reduced methylation and expression levels after drought treatment. These TFs were distributed in 79 families, including MYB, AP2, WRKY, NAC, and bHLH. We also found that 690 TFs showed increased methylation and expression levels after drought treatment. Most of them belong to C3H, PHD, MYB, ARF, and bZIP families (Additional file <xref ref-type="supplementary-material" rid="S9">9</xref>).</p><p>Transposable elements (TEs) can influence gene regulation on a genomic scale by carrying potential transcription-regulating signals. To further analyze the mechanism underlying the TF response to drought stress by hypermethylation of transposons, we found 389 and 334 TFs were located by TEs in promoters and in gene bodies using the described method by Thornburg [<xref ref-type="bibr" rid="B34">34</xref>], respectively. The methylation levels of 138 TEs in promoters were elevated by drought treatment, while those of 251 TEs were reduced. The methylation levels of 163 TEs in gene body regions were elevated under drought treatment, while those of 171 TEs were reduced. These two kind of transcription factors were divided into 64 and 60 families (Additional file <xref ref-type="supplementary-material" rid="S10">10</xref>, <xref ref-type="supplementary-material" rid="S11">11</xref>), respectively, which were concentrated in both the major transcription factor families and some related to stress signal transduction, such as C2C2 and EIL proteins.</p></sec></sec><sec><title>Disscussion</title><p>Although the relationship between DNA methylation and gene expression has been explored in <italic>Populus </italic>and other plants [<xref ref-type="bibr" rid="B35">35</xref>,<xref ref-type="bibr" rid="B36">36</xref>], the resolution of genome-wide methylated cytosines requires more elaborate and comprehensive methylomic studies to characterize the functional effects of <italic>Populus </italic>DNA methylation. We obtained the single-base resolution methylomes of <italic>Populus</italic>, which was used to investigate the changes of DNA methylation under drought treatment via the high-throughput sequencing, and found the genome-wide methylation level in <italic>P. trichocarpa </italic>was slightly higher than that in <italic>Arabidopsis </italic>[<xref ref-type="bibr" rid="B24">24</xref>] but lower than humans [<xref ref-type="bibr" rid="B9">9</xref>]. Moreover, having found plausible patterns with our comprehensive dataset, our results have a number of implications, which will have a promising application in the future research on <italic>Populus </italic>and may give some cue on other plants' studies.</p><sec><title>The relationship of methylation and splicing events in <bold><italic>P. trichocarpa</italic></bold></title><p>The role of DNA methylation in alternative splicing is supported by Shukla et al. [<xref ref-type="bibr" rid="B37">37</xref>] in CD45 cells, as well as by Chodavarapu et al. in <italic>Arabidopsis thaliana</italic>, showing that DNA methylation is highly enriched in exons and may have an important role in alternative splicing [<xref ref-type="bibr" rid="B38">38</xref>]. We did not find any methylated sites in more than 80% of alternative splicing genes. In contrast with the previous results, DNA methylation is not enriched in exons and the methylation levels in exons were not significant higher than the other regions <italic>in Populus</italic>. Therefore, our results can't speculate that DNA methylation may play an important role in alternative splicing in <italic>Populus </italic>genome. By contrast, our results showed that all fusion genes were methylated, that inferred that this phenomenon might be associated with the mechanisms of two different splicing forms. Methylation may not affect the enzymatic reaction that results in alternative splicing, but can affect chromosomal rearrangements, RNA editing and other structural variations what might cause the occurrence of gene fusion.</p><p>Drought treatment has different effects on two different splicing forms, the number of genes with alternative splicing events was increased, while fusion genes were reduced after the drought treatment. Since the effects of drought on the complex network of signaling pathway <italic>in Populus</italic>, we can not point out the direct cause, but it can be speculated that it may be related to the formation or activity of cleavage enzyme, which main activates at 3 ' and 5 ' two positions.</p></sec><sec><title>DNA methylation and gene expression</title><p>The way of the expression of genes affected by DNA methylation in plant is combining with specific protein, which competes with transcription factors. The complex causes the changes in chromosome histone acetylation, leading to the inhibition of transcription, that point was more prominent in poplar. In <italic>Populus</italic>, about 60% of silent genes were affected by methylation. After the drought treatment, the probability was increased, indicating that the influence of gene expression by methylation increased with the external environmental stimuli.</p><p>For expressed genes, methylation in 100 bp upstream of the TSS represses gene expression, which is consistent with the findings from <italic>A. thaliana</italic>[<xref ref-type="bibr" rid="B39">39</xref>], human [<xref ref-type="bibr" rid="B9">9</xref>] and rice [<xref ref-type="bibr" rid="B40">40</xref>], confirming that neighbouring upstream of TSS methylation is a general mechanism suppressing gene expression in eukaryotes. However, we found that methylation level in 100-2000 bp upstream was positively correlated with gene expression. It is interesting that the expression of genes methylated in 100bp upstream of TSS were affected after the drought treatment, which indicated that drought treatment reduced the chances of combining with specific protein and increased levels of gene expression. In the TTR (transcriptional termination regions) and the downstream region, methylation and expression were negatively correlated, indicating that they had significant effect on gene expression through interfering with transcriptional termination site.</p><p>Drought is one of the major environmental factors that affected gene expression by complex signaling networks, including cytosine methylation, histone acetylation and H3K9 methylation [<xref ref-type="bibr" rid="B17">17</xref>]. In <italic>Populus</italic>, the expression of gene was affected by drought on genetic elements in upstream and downstream. Combined with changes in methylation levels, 100 bp upstream of the TSS was focused. To further understand the relationship between methylation and drought, we need to make sure the genetic elements in different locations of upstream.</p></sec><sec><title>Methylated transcription factors with TE in drought tolerance</title><p>Transcription factors involved in signal transduction related to various stresses, such as drought. Diverse biological activities were regulated directly or indirectly by these transcription factors. The demethylation of transcription factors under drought stress may reduce the stability of the gene, thereby affecting its expression. (For example, BZIP, WRKY, AP2 / EREBP and MYB, four major transcription factor families, play an important role in plant stress resistance, and many TFs of expression changed by methylation in our results also belong to them.).</p><p>The use of transposable elements (TEs) for reverse transcription, DNA cutting and ligation or DNA binding are well-documented [<xref ref-type="bibr" rid="B41">41</xref>]. Changes in transposition activity correlated with methylation were first described in maize [<xref ref-type="bibr" rid="B42">42</xref>,<xref ref-type="bibr" rid="B43">43</xref>]. Subsequently, in both plants and animals [<xref ref-type="bibr" rid="B44">44</xref>], the role of DNA methylation in transposons was directly tested by loss of DNA methylation (which is sufficient for the mobilization of transposons) [<xref ref-type="bibr" rid="B45">45</xref>]. TEs can influence gene regulation on a genomic scale by carrying potential transcription-regulating signals. When inserted in promoter regions, they can alter gene expression patterns by introducing new transcription factor binding sites [<xref ref-type="bibr" rid="B46">46</xref>]. Our data indicated that transcription factors that affect gene expression after drought treatment were affected by methylated transposons in <italic>Populus</italic>. We found methylated transposons in C2C2, WRKY MYB and other families that involved in signal transduction pathway of drought. When the environment changes, transposition frequency in plants increased. TEs were inserted into positive transcription factors and promoted expression, consequently increasing the expression of resistance genes. Insertion in some locations could inhibit the expression of positive transcription factors and decrease the resistance of a gene (such as by insertion of a negative transcription factor), which may have the opposite effect. Analysis of methylated transposons in transcription factors may increase our understanding of the specific mechanisms by which transcription factors regulate the stress response in plants.</p></sec></sec><sec sec-type="conclusions"><title>Conclusions</title><p>In this study, genome-wide DNA methylation sequencing of poplar leaves with WW and WS treatments were established using high-throughput technology. It confirmed that <italic>cis</italic>-splicing sites are unmethylated, while <italic>trans</italic>-splicing sites are methylated in poplar, to our knowledge this is the first report of an association between methylation and variable splicing. It further demonstrated that DNA methylation in the regulation of stress-responsive genes by identifying methylated transposable elements (TEs) in promoters and the gene body of transcription factors. Finally, the mechanism that the DNA methylation played on the gene expression, alternative splicing, and other phenomenon was still unclear based on current technology and experiment condition, otherwise our study pave the way for future discovering of methylation-associated mechanism in large-scale integrative multi-omics datasets.</p></sec><sec sec-type="methods"><title>Methods</title><sec><title>Plant materials</title><p><italic>Populus trichocarpa </italic>(Torr. & Gray) seedlings were planted separately into 10-L plastic pots filled with a mixture of clay, silt and sand (2:2:2, v/v). They were grown under well-watered (WW) conditions in a greenhouse at Beijing Forestry University for 2 months. The plants were supplemented with light for 15 h d<sup>-1</sup>, and temperature and humidity were kept constant. According to previous reports [<xref ref-type="bibr" rid="B20">20</xref>-<xref ref-type="bibr" rid="B22">22</xref>], the plantlets were divided into two groups, which were subjected to the following watering regimes: well-watered (WW) treatment (maintaining 100% of field capacity) and water-stress (WS) treatment (maintaining 25% of field capacity). Volumetric soil water content was kept at 24% in the WW treatment, while in the WS treatment the volumetric soil water content was kept at approximately 10%. Net photosynthetic rate, transpiration rate and leaf water potential (WP) were measured using the PsyPro WP data logger (Wescor) and Li-6400 Photosynthesis System (Li-Cor). After 5 weeks, plants of similar height (~75 cm) were selected for the experiment. Five replicates (four plantlets per replicate) were used to minimize random errors. Mature leaves from the same position (8-10th counting from the apex) of different individual plants were collected and frozen immediately in liquid nitrogen for DNA extraction.</p></sec><sec><title>BS-Seq libraries construction and sequencing</title><p>Total DNA was extracted from the leaves collected from our experiment. Total DNA was prepared by proteinase K/phenol extraction following the manufacturer's instructions. The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of ~250 bp, followed by the blunt ending, dA addition to 3'-end, and adaptor addition following the manufacturer's protocol. The bisulfite conversion of the adaptor-added DNA was performed as described previously [<xref ref-type="bibr" rid="B23">23</xref>]. Ultra-high-throughput pair-end sequencing was performed using the Hiseq 2000 according to the manufacturer's instructions. Raw data were processed using Illumina base-calling pipeline.</p></sec><sec><title>Mapping and processing of BS-Seq reads</title><p>Integrated with the <italic>Populus </italic>reference (v2.0) and resequencing data, we constructed a consensus sequence as a reference to align the methylation data. Because the strand-specific of methylation, two artificial genomes were construct, the T genome that whose cytosines had been converted to thymines and the A genome whose guanines had been converted to adenosines. After removing the low quality reads, all cytosines of reads1 were converted to thymines and all guanines of reads2 were converted to adenosines, and then all these reads were aligned to the T genome and A genome using SOAPaligner (v2.01) software with parameters -m 175 -x 325 -v(default 2), respectively. To increase the accuracy of methylation related analysis, reads that aligned to more than one positions were discarded.</p><p>All the unmethylated cytosine can be converted from cytosine to thymine during the process of bisulfite conversion, but the methylated cytosine will be the same. To remove the methylcytosines from the background noise which cause by the non-conversion of bisulfite, we use the conversion rate of lambda DNA input as a negative control was calculated following the formula: p = 1 - (# of methylated cytosines) / (# of cytosines). Using this value as a measure of the false mC discovery rate, mC was identified at each base position according to the binomial probability distribution, following the correction algorithm of Lister et al. [<xref ref-type="bibr" rid="B9">9</xref>].</p></sec><sec><title>Transcriptome sequencing</title><p>For the synthesis of cDNA and Solexa sequencing, we prepared 45 μg of total RNA for treated and control sample at concentrations of approximately 1500 ng/μl. We then enriched the poly (A) mRNA using beads with Oligo (dT) and interrupted mRNA into short fragments with fragmentation buffer. Using these short fragments as templates, we synthesized first-strand cDNA with hexamer-primers and reverse transcriptase (Invitrogen). The second-strand cDNA was synthesized using buffer, dNTPs, RNaseH (Invitrogen) and DNA polymerase I (New England BioLabs). The short fragments were then purified using a QiaQuick PCR extraction kit and re- solved with EB buffer to finish the end reparation, and was connected using sequencing adaptors. After resolution by agarose gel electrophoresis, we selected fragments suitable for PCR amplification. We then constructed two paired-end libraries which were sequenced using an Illumina HiSeq 2000.</p></sec><sec><title>Prediction of splicing events</title><p>The pair-end reads that aligned to two different genes were considered candidate fusion genes. To ensure the accuracy of detecting the fusion genes, PE reads that aligned to more than one location were discarded. Junction sequences were obtained by combining the exons of candidate genes. Junction reads and PE reads having only one end were compared to reference genes (5-bp overlap at least on the fusion point), and the candidate genes were supported by both PE reads and junction reads. The homologous candidate genes were detected and excluded, and the identification of alternative splicing sites was performed as described previously [<xref ref-type="bibr" rid="B24">24</xref>].</p><p>Collected potential splice sites by enumerating all possible pairs of donor sites (GT on the forward strand and AC on the reverse strand) and acceptor sites (AG on the forward strand and CT on the reverse strand) inside intron regions. Secondly, filtered all potential splice sites through the information of supported reads. At least two unique mapped reads convered on the junction site and having a minimum of five bases on both sides of the junction. Finally, categorized all these splice sites into seven types including exon skipping (ES), intron retention (IR), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), alternative first exons (AFE), and alternative last exons (ALE).</p></sec><sec><title>Gene ontology (GO) analysis</title><p>GO annotations of poplar genes were downloaded from (<ext-link ext-link-type="uri" xlink:href="http://bioinfo.cau.edu.cn/agriGO/download/item2term_46">http://bioinfo.cau.edu.cn/agriGO/download/item2term_46</ext-link>). GO comparative analyses between interested gene groups were performed using BGI WEGO (<ext-link ext-link-type="uri" xlink:href="http://wego.genomics.org.cn/cgi-bin/wego/index.pl">http://wego.genomics.org.cn/cgi-bin/wego/index.pl</ext-link>). GO enrichment analysis was performed using Blast2GO and agriGO (<ext-link ext-link-type="uri" xlink:href="http://bioinfo.cau.edu.cn/agriGO">http://bioinfo.cau.edu.cn/agriGO</ext-link>/) with Fisher's exact test [<xref ref-type="bibr" rid="B25">25</xref>].</p></sec></sec><sec><title>Competing interests</title><p>The authors declare that they have no competing interests.</p></sec><sec><title>Authors' contributions</title><p>DL PS designed and conducted the experiments, DL HL CH PS ZZ ST analyzed the data, DL HLPS WY XX drafted the manuscript, WY XX supervised the project. All authors have read and approved the final version of this manuscript.</p><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Relative methylation levels of the corresponding genomic region</bold>. The <italic>y </italic>axis shows the relative methylation level in each element of genomic region (<italic>x </italic>axis), which contains upstream, 5' UTR, CDS, Intron, 3' UTR, Downstream and repeative sequences.</p></caption><graphic xlink:href="1471-2156-15-S1-S9-2"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>The Histogram chart of alternative splicing events and genes identified in WW and WS</bold>. The green columns indicate the number of alternative splicing events and the red columns show the total number of gene in each events.</p></caption><graphic xlink:href="1471-2156-15-S1-S9-3"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><p><bold>The relationship between methylation level and gene expression</bold>. (a) The methylation level trend (<italic>y </italic>axis) of four different gene clusters (High, medium, low, and silent genes, from the bottom one-third to the top one-third and non-expressed according to Transcriptome Sequencing data) in gene-associated region(<italic>x </italic>axis) in WW. (b) The methylation level trend (<italic>y </italic>axis) of four different gene clusters in gene-associated region(<italic>x </italic>axis) in WS (c) Distribution of methylated and unmethylated gene expression levels in gene-body. The horizontal axis represents expression level, and the vertical axis represents the percentage of genes on a particular expression level. (d) Distribution of methylated and unmethylated gene expression levels in upstream2k. (e) Distribution of methylated and unmethylated gene expression levels in 100bp upstream of the TSS. (f) Distribution of methylated and unmethylated gene expression levels in downstream2k.</p></caption><graphic xlink:href="1471-2156-15-S1-S9-4"></graphic></fig></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="S1"><caption><title>Additional file 1</title><p>Description of the data for the <italic>Populus </italic>of two treatments</p></caption><media xlink:href="1471-2156-15-S1-S9-S1.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S2"><caption><title>Additional file 2</title><p>Three methylation patterns of <italic>Populus</italic></p></caption><media xlink:href="1471-2156-15-S1-S9-S2.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S3"><caption><title>Additional file 3</title><p><bold>Seqlogo of the sequences proximal to DNA methylation cytosines</bold>. One stack for each position in these two sequence contexts (CHG, CHH), The overall height of the stack indicates the sequence conservation at that position, while the height of bases within the stack indicates the relative frequency of each base at that position. (red = T, green = A, blue = C, yellow = G)</p></caption><media xlink:href="1471-2156-15-S1-S9-S3.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S4"><caption><title>Additional file 4</title><p>Density of methylcytosines identified in each chromosome in <italic>Populus</italic>. Red dots indicate the density of all methylcytosines in 10 kb windows. The top panel shows the Watson strand information and the bottom panel displays crick strand information.</p></caption><media xlink:href="1471-2156-15-S1-S9-S4.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S5"><caption><title>Additional file 5</title><p><bold>GO enrichment analysis newly methylated and demethylated genes</bold>.</p></caption><media xlink:href="1471-2156-15-S1-S9-S5.xlsx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S6"><caption><title>Additional file 6</title><p>Description of the data for the <italic>Populus </italic>of two treatments by Transcriptome Sequencing</p></caption><media xlink:href="1471-2156-15-S1-S9-S6.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S7"><caption><title>Additional file 7</title><p><bold>Results of two splicing forms</bold>. (a) Four kinds of alternative splicing types were compared to each other on methylation level; (b) the PCR result of the fusion genes verification.</p></caption><media xlink:href="1471-2156-15-S1-S9-S7.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S8"><caption><title>Additional file 8</title><p><bold>The correlation between gene methylation and gene expression</bold>. The upstream, gene body and downstream were split into 20 bins that lay on x-axis for investigating the spearman rank correlation(y-axis) between methylation and expression. Red line stands for WW and blue line stands for WS.</p></caption><media xlink:href="1471-2156-15-S1-S9-S8.docx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S9"><caption><title>Additional file 9</title><p>Category of co-regulated transcription factors</p></caption><media xlink:href="1471-2156-15-S1-S9-S9.xlsx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S10"><caption><title>Additional file 10</title><p>Category of transcription factors with methylated TE that located in promoter</p></caption><media xlink:href="1471-2156-15-S1-S9-S10.xlsx"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S11"><caption><title>Additional file 11</title><p>Category of transcription factors with methylated TE that located in gene</p></caption><media xlink:href="1471-2156-15-S1-S9-S11.xlsx"><caption><p>Click here for file</p></caption></media></supplementary-material></sec></body><back><sec><title>Declarations</title><p>Publication charges for this work were supported by the National Natural Science Foundation of China (31070597, 31270656), the fund from the Ministry of Science and Technology of China (2009CB119101), and the Scientific Research and Graduate Training Joint Programs from BMEC (Stress Tolerance and DNA Methylation in Populus).</p><p>This article has been published as part of <italic>BMC Genetics </italic>Volume 15 Supplement 1, 2014: Selected articles from the International Symposium on Quantitative Genetics and Genomics of Woody Plants. The full contents of the supplement are available online at <ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/bmcgenet/supplements/15/S1">http://www.biomedcentral.com/bmcgenet/supplements/15/S1</ext-link>.</p></sec><ref-list><ref id="B1"><mixed-citation publication-type="journal"><name><surname>Jansson</surname><given-names>S</given-names></name><name><surname>Douglas</surname><given-names>CJ</given-names></name><article-title>Populus: a model system for plant biology</article-title><source>Annu Rev Plant Biol</source><year>2007</year><volume>58</volume><fpage>435</fpage><lpage>458</lpage><pub-id pub-id-type="doi">10.1146/annurev.arplant.58.032806.103956</pub-id><pub-id pub-id-type="pmid">17280524</pub-id></mixed-citation></ref><ref id="B2"><mixed-citation publication-type="journal"><name><surname>Tuskan</surname><given-names>GA</given-names></name><name><surname>Difazio</surname><given-names>S</given-names></name><name><surname>Jansson</surname><given-names>S</given-names></name><name><surname>Bohlmann</surname><given-names>J</given-names></name><name><surname>Grigoriev</surname><given-names>I</given-names></name><name><surname>Hellsten</surname><given-names>U</given-names></name><name><surname>Putnam</surname><given-names>N</given-names></name><name><surname>Ralph</surname><given-names>S</given-names></name><name><surname>Rombauts</surname><given-names>S</given-names></name><name><surname>Salamov</surname><given-names>A</given-names></name><etal></etal><article-title>The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)</article-title><source>Science</source><year>2006</year><volume>313</volume><issue>5793</issue><fpage>1596</fpage><lpage>1604</lpage><pub-id pub-id-type="doi">10.1126/science.1128691</pub-id><pub-id pub-id-type="pmid">16973872</pub-id></mixed-citation></ref><ref id="B3"><mixed-citation publication-type="journal"><name><surname>Tuskan</surname><given-names>GA</given-names></name><article-title>Short-rotation woody crop supply systems in the United States: what do we know and what do we need to know?</article-title><source>Biomass and Bioenergy</source><year>1998</year><volume>14</volume><issue>4</issue><fpage>307</fpage><lpage>315</lpage><pub-id pub-id-type="doi">10.1016/S0961-9534(97)10065-4</pub-id></mixed-citation></ref><ref id="B4"><mixed-citation publication-type="journal"><name><surname>Bogeat-Triboulot</surname><given-names>MB</given-names></name><name><surname>Brosche</surname><given-names>M</given-names></name><name><surname>Renaut</surname><given-names>J</given-names></name><name><surname>Jouve</surname><given-names>L</given-names></name><name><surname>Le Thiec</surname><given-names>D</given-names></name><name><surname>Fayyaz</surname><given-names>P</given-names></name><name><surname>Vinocur</surname><given-names>B</given-names></name><name><surname>Witters</surname><given-names>E</given-names></name><name><surname>Laukens</surname><given-names>K</given-names></name><name><surname>Teichmann</surname><given-names>T</given-names></name><etal></etal><article-title>Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions</article-title><source>Plant physiology</source><year>2007</year><volume>143</volume><issue>2</issue><fpage>876</fpage><lpage>892</lpage><pub-id pub-id-type="pmid">17158588</pub-id></mixed-citation></ref><ref id="B5"><mixed-citation publication-type="other"><name><surname>Tang</surname><given-names>S</given-names></name><name><surname>Liang</surname><given-names>H</given-names></name><name><surname>Yan</surname><given-names>D</given-names></name><name><surname>Zhao</surname><given-names>Y</given-names></name><name><surname>Han</surname><given-names>X</given-names></name><name><surname>Carlson</surname><given-names>J</given-names></name><name><surname>Xia</surname><given-names>X</given-names></name><name><surname>Yin</surname><given-names>W</given-names></name><article-title>Populus euphratica: the transcriptomic response to drought stress</article-title><source>Plant Mol Biol</source><year>2013</year><fpage>1</fpage><lpage>19</lpage></mixed-citation></ref><ref id="B6"><mixed-citation publication-type="journal"><name><surname>Shuai</surname><given-names>P</given-names></name><name><surname>Liang</surname><given-names>D</given-names></name><name><surname>Zhang</surname><given-names>Z</given-names></name><name><surname>Yin</surname><given-names>W</given-names></name><name><surname>Xia</surname><given-names>X</given-names></name><article-title>Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis</article-title><source>Bmc Genomics</source><year>2013</year><volume>14</volume><issue>1</issue><fpage>233</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-14-233</pub-id><pub-id pub-id-type="pmid">23570526</pub-id></mixed-citation></ref><ref id="B7"><mixed-citation publication-type="journal"><name><surname>Lister</surname><given-names>R</given-names></name><name><surname>O'Malley</surname><given-names>RC</given-names></name><name><surname>Tonti-Filippini</surname><given-names>J</given-names></name><name><surname>Gregory</surname><given-names>BD</given-names></name><name><surname>Berry</surname><given-names>CC</given-names></name><name><surname>Millar</surname><given-names>AH</given-names></name><name><surname>Ecker</surname><given-names>JR</given-names></name><article-title>Highly integrated single-base resolution maps of the epigenome in Arabidopsis</article-title><source>Cell</source><year>2008</year><volume>133</volume><issue>3</issue><fpage>523</fpage><lpage>536</lpage><pub-id pub-id-type="doi">10.1016/j.cell.2008.03.029</pub-id><pub-id pub-id-type="pmid">18423832</pub-id></mixed-citation></ref><ref id="B8"><mixed-citation publication-type="journal"><name><surname>Wang</surname><given-names>X</given-names></name><name><surname>Elling</surname><given-names>AA</given-names></name><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Li</surname><given-names>N</given-names></name><name><surname>Peng</surname><given-names>Z</given-names></name><name><surname>He</surname><given-names>G</given-names></name><name><surname>Sun</surname><given-names>H</given-names></name><name><surname>Qi</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>XS</given-names></name><name><surname>Deng</surname><given-names>XW</given-names></name><article-title>Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize</article-title><source>The Plant Cell Online</source><year>2009</year><volume>21</volume><issue>4</issue><fpage>1053</fpage><lpage>1069</lpage><pub-id pub-id-type="doi">10.1105/tpc.109.065714</pub-id></mixed-citation></ref><ref id="B9"><mixed-citation publication-type="journal"><name><surname>Lister</surname><given-names>R</given-names></name><name><surname>Pelizzola</surname><given-names>M</given-names></name><name><surname>Dowen</surname><given-names>RH</given-names></name><name><surname>Hawkins</surname><given-names>RD</given-names></name><name><surname>Hon</surname><given-names>G</given-names></name><name><surname>Tonti-Filippini</surname><given-names>J</given-names></name><name><surname>Nery</surname><given-names>JR</given-names></name><name><surname>Lee</surname><given-names>L</given-names></name><name><surname>Ye</surname><given-names>Z</given-names></name><name><surname>Ngo</surname><given-names>QM</given-names></name><etal></etal><article-title>Human DNA methylomes at base resolution show widespread epigenomic differences</article-title><source>Nature</source><year>2009</year><volume>462</volume><issue>7271</issue><fpage>315</fpage><lpage>322</lpage><pub-id pub-id-type="doi">10.1038/nature08514</pub-id><pub-id pub-id-type="pmid">19829295</pub-id></mixed-citation></ref><ref id="B10"><mixed-citation publication-type="journal"><name><surname>Xiang</surname><given-names>H</given-names></name><name><surname>Zhu</surname><given-names>J</given-names></name><name><surname>Chen</surname><given-names>Q</given-names></name><name><surname>Dai</surname><given-names>F</given-names></name><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Li</surname><given-names>M</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><name><surname>Zhang</surname><given-names>G</given-names></name><name><surname>Li</surname><given-names>D</given-names></name><name><surname>Dong</surname><given-names>Y</given-names></name><etal></etal><article-title>Single base-resolution methylome of the silkworm reveals a sparse epigenomic map</article-title><source>Nature biotechnology</source><year>2010</year><volume>28</volume><issue>5</issue><fpage>516</fpage><lpage>520</lpage><pub-id pub-id-type="doi">10.1038/nbt.1626</pub-id><pub-id pub-id-type="pmid">20436463</pub-id></mixed-citation></ref><ref id="B11"><mixed-citation publication-type="journal"><name><surname>Cao</surname><given-names>X</given-names></name><name><surname>Jacobsen</surname><given-names>SE</given-names></name><article-title>Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes</article-title><source>Proceedings of the National Academy of Sciences</source><year>2002</year><volume>99</volume><issue>Suppl 4</issue><fpage>16491</fpage><lpage>16498</lpage></mixed-citation></ref><ref id="B12"><mixed-citation publication-type="journal"><name><surname>Razin</surname><given-names>A</given-names></name><article-title>CpG methylation, chromatin structure and gene silencing-a three-way connection</article-title><source>The EMBO journal</source><year>1998</year><volume>17</volume><issue>17</issue><fpage>4905</fpage><lpage>4908</lpage><pub-id pub-id-type="doi">10.1093/emboj/17.17.4905</pub-id><pub-id pub-id-type="pmid">9724627</pub-id></mixed-citation></ref><ref id="B13"><mixed-citation publication-type="journal"><name><surname>Curradi</surname><given-names>M</given-names></name><name><surname>Izzo</surname><given-names>A</given-names></name><name><surname>Badaracco</surname><given-names>G</given-names></name><name><surname>Landsberger</surname><given-names>N</given-names></name><article-title>Molecular mechanisms of gene silencing mediated by DNA methylation</article-title><source>Molecular and cellular biology</source><year>2002</year><volume>22</volume><issue>9</issue><fpage>3157</fpage><lpage>3173</lpage><pub-id pub-id-type="doi">10.1128/MCB.22.9.3157-3173.2002</pub-id><pub-id pub-id-type="pmid">11940673</pub-id></mixed-citation></ref><ref id="B14"><mixed-citation publication-type="journal"><name><surname>Uthup</surname><given-names>TK</given-names></name><name><surname>Ravindran</surname><given-names>M</given-names></name><name><surname>Bini</surname><given-names>K</given-names></name><name><surname>Thakurdas</surname><given-names>S</given-names></name><article-title>Divergent DNA Methylation Patterns Associated with Abiotic Stress in Hevea brasiliensis</article-title><source>Molecular Plant</source><year>2011</year><volume>4</volume><issue>6</issue><fpage>996</fpage><lpage>1013</lpage><pub-id pub-id-type="doi">10.1093/mp/ssr039</pub-id><pub-id pub-id-type="pmid">21705581</pub-id></mixed-citation></ref><ref id="B15"><mixed-citation publication-type="journal"><name><surname>Labra</surname><given-names>M</given-names></name><name><surname>Ghiani</surname><given-names>A</given-names></name><name><surname>Citterio</surname><given-names>S</given-names></name><name><surname>Sgorbati</surname><given-names>S</given-names></name><name><surname>Sala</surname><given-names>F</given-names></name><name><surname>Vannini</surname><given-names>C</given-names></name><name><surname>Ruffini-Castiglione</surname><given-names>M</given-names></name><name><surname>Bracale</surname><given-names>M</given-names></name><article-title>Analysis of Cytosine Methylation Pattern in Response to Water Deficit in Pea Root Tips</article-title><source>Plant Biology</source><year>2002</year><volume>4</volume><issue>6</issue><fpage>694</fpage><lpage>699</lpage><pub-id pub-id-type="doi">10.1055/s-2002-37398</pub-id></mixed-citation></ref><ref id="B16"><mixed-citation publication-type="journal"><name><surname>Colaneri</surname><given-names>AC</given-names></name><name><surname>Jones</surname><given-names>AM</given-names></name><article-title>Genome-Wide Quantitative Identification of DNA Differentially Methylated Sites in Arabidopsis Seedlings Growing at Different Water Potential</article-title><source>PloS one</source><year>2013</year><volume>8</volume><issue>4</issue><fpage>e59878</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0059878</pub-id><pub-id pub-id-type="pmid">23577076</pub-id></mixed-citation></ref><ref id="B17"><mixed-citation publication-type="other"><name><surname>Wang</surname><given-names>W-S</given-names></name><name><surname>Pan</surname><given-names>Y-J</given-names></name><name><surname>Zhao</surname><given-names>X-Q</given-names></name><name><surname>Dwivedi</surname><given-names>D</given-names></name><name><surname>Zhu</surname><given-names>L-H</given-names></name><name><surname>Ali</surname><given-names>J</given-names></name><name><surname>Fu</surname><given-names>B-Y</given-names></name><name><surname>Li</surname><given-names>Z-K</given-names></name><article-title>Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)</article-title><source>Journal of experimental botany</source><year>2010</year></mixed-citation></ref><ref id="B18"><mixed-citation publication-type="journal"><name><surname>Yu</surname><given-names>Y</given-names></name><name><surname>Yang</surname><given-names>X</given-names></name><name><surname>Wang</surname><given-names>H</given-names></name><name><surname>Shi</surname><given-names>F</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>J</given-names></name><name><surname>Li</surname><given-names>L</given-names></name><name><surname>Wang</surname><given-names>D</given-names></name><name><surname>Liu</surname><given-names>B</given-names></name><article-title>Cytosine Methylation Alteration in Natural Populations of <italic>Leymus chinensis </italic>Induced by Multiple Abiotic Stresses</article-title><source>PloS one</source><year>2013</year><volume>8</volume><issue>2</issue><fpage>e55772</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0055772</pub-id><pub-id pub-id-type="pmid">23418457</pub-id></mixed-citation></ref><ref id="B19"><mixed-citation publication-type="journal"><name><surname>Rico</surname><given-names>L</given-names></name><name><surname>Ogaya</surname><given-names>R</given-names></name><name><surname>Barbeta</surname><given-names>A</given-names></name><name><surname>Peñuelas</surname><given-names>J</given-names></name><article-title>Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change</article-title><source>Plant Biol (Stuttg)</source><year>2013</year><volume>16</volume><issue>2</issue><fpage>419</fpage><lpage>427</lpage><pub-id pub-id-type="pmid">23889779</pub-id></mixed-citation></ref><ref id="B20"><mixed-citation publication-type="other"><name><surname>Griffiths</surname><given-names>H</given-names></name><name><surname>Parry</surname><given-names>MA</given-names></name><article-title>Plant responses to water stress</article-title><source>Annals of Botany</source><year>2002</year><issue>89</issue><fpage>801</fpage><lpage>802</lpage><pub-id pub-id-type="pmid">12102505</pub-id></mixed-citation></ref><ref id="B21"><mixed-citation publication-type="journal"><name><surname>Xu</surname><given-names>X</given-names></name><name><surname>Yang</surname><given-names>F</given-names></name><name><surname>Xiao</surname><given-names>X</given-names></name><name><surname>Zhang</surname><given-names>S</given-names></name><name><surname>Korpelainen</surname><given-names>H</given-names></name><name><surname>Li</surname><given-names>C</given-names></name><article-title>Sex-specific responses of Populus cathayana to drought and elevated temperatures</article-title><source>Plant, cell & environment</source><year>2008</year><volume>31</volume><issue>6</issue><fpage>850</fpage><lpage>860</lpage><pub-id pub-id-type="doi">10.1111/j.1365-3040.2008.01799.x</pub-id></mixed-citation></ref><ref id="B22"><mixed-citation publication-type="journal"><name><surname>Regier</surname><given-names>N</given-names></name><name><surname>Streb</surname><given-names>S</given-names></name><name><surname>Cocozza</surname><given-names>C</given-names></name><name><surname>Schaub</surname><given-names>M</given-names></name><name><surname>Cherubini</surname><given-names>P</given-names></name><name><surname>Zeeman</surname><given-names>SC</given-names></name><name><surname>Frey</surname><given-names>B</given-names></name><article-title>Drought tolerance of two black poplar (Populus nigra L.) clones: contribution of carbohydrates and oxidative stress defence</article-title><source>Plant, cell & environment</source><year>2009</year><volume>32</volume><issue>12</issue><fpage>1724</fpage><lpage>1736</lpage><pub-id pub-id-type="doi">10.1111/j.1365-3040.2009.02030.x</pub-id></mixed-citation></ref><ref id="B23"><mixed-citation publication-type="journal"><name><surname>Hayatsu</surname><given-names>H</given-names></name><name><surname>Tsuji</surname><given-names>K</given-names></name><name><surname>Negishi</surname><given-names>K</given-names></name><article-title>Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis</article-title><source>Nucleic Acids Symposium Series</source><year>2006</year><volume>50</volume><issue>1</issue><fpage>69</fpage><lpage>70</lpage><pub-id pub-id-type="doi">10.1093/nass/nrl034</pub-id><pub-id pub-id-type="pmid">17150821</pub-id></mixed-citation></ref><ref id="B24"><mixed-citation publication-type="journal"><name><surname>Zhang</surname><given-names>GJ</given-names></name><name><surname>Guo</surname><given-names>GW</given-names></name><name><surname>Hu</surname><given-names>XD</given-names></name><name><surname>Zhang</surname><given-names>Y</given-names></name><name><surname>Li</surname><given-names>QY</given-names></name><name><surname>Li</surname><given-names>RQ</given-names></name><name><surname>Zhuang</surname><given-names>RH</given-names></name><name><surname>Lu</surname><given-names>ZK</given-names></name><name><surname>He</surname><given-names>ZQ</given-names></name><name><surname>Fang</surname><given-names>XD</given-names></name><article-title>Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome</article-title><source>Genome research</source><year>2010</year><volume>20</volume><issue>5</issue><fpage>646</fpage><lpage>654</lpage><pub-id pub-id-type="doi">10.1101/gr.100677.109</pub-id><pub-id pub-id-type="pmid">20305017</pub-id></mixed-citation></ref><ref id="B25"><mixed-citation publication-type="journal"><name><surname>Du</surname><given-names>Z</given-names></name><name><surname>Zhou</surname><given-names>X</given-names></name><name><surname>Ling</surname><given-names>Y</given-names></name><name><surname>Zhang</surname><given-names>Z</given-names></name><name><surname>Su</surname><given-names>Z</given-names></name><article-title>agriGO: a GO analysis toolkit for the agricultural community</article-title><source>Nucleic acids research</source><year>2010</year><volume>38</volume><issue>suppl 2</issue><fpage>W64</fpage><lpage>W70</lpage><pub-id pub-id-type="pmid">20435677</pub-id></mixed-citation></ref><ref id="B26"><mixed-citation publication-type="journal"><name><surname>Horiuchi</surname><given-names>T</given-names></name><name><surname>Aigaki</surname><given-names>T</given-names></name><article-title>Alternative trans-splicing: a novel mode of pre-mRNA processing</article-title><source>Biology of the Cell</source><year>2006</year><volume>98</volume><issue>2</issue><fpage>135</fpage><lpage>140</lpage><pub-id pub-id-type="doi">10.1042/BC20050002</pub-id><pub-id pub-id-type="pmid">16417469</pub-id></mixed-citation></ref><ref id="B27"><mixed-citation publication-type="journal"><name><surname>Akiva</surname><given-names>P</given-names></name><name><surname>Toporik</surname><given-names>A</given-names></name><name><surname>Edelheit</surname><given-names>S</given-names></name><name><surname>Peretz</surname><given-names>Y</given-names></name><name><surname>Diber</surname><given-names>A</given-names></name><name><surname>Shemesh</surname><given-names>R</given-names></name><name><surname>Novik</surname><given-names>A</given-names></name><name><surname>Sorek</surname><given-names>R</given-names></name><article-title>Transcription-mediated gene fusion in the human genome</article-title><source>Genome research</source><year>2006</year><volume>16</volume><issue>1</issue><fpage>30</fpage><lpage>36</lpage><pub-id pub-id-type="pmid">16344562</pub-id></mixed-citation></ref><ref id="B28"><mixed-citation publication-type="journal"><name><surname>Filichkin</surname><given-names>SA</given-names></name><name><surname>Priest</surname><given-names>HD</given-names></name><name><surname>Givan</surname><given-names>SA</given-names></name><name><surname>Shen</surname><given-names>R</given-names></name><name><surname>Bryant</surname><given-names>DW</given-names></name><name><surname>Fox</surname><given-names>SE</given-names></name><name><surname>Wong</surname><given-names>WK</given-names></name><name><surname>Mockler</surname><given-names>TC</given-names></name><article-title>Genome-wide mapping of alternative splicing in Arabidopsis thaliana</article-title><source>Genome research</source><year>2010</year><volume>20</volume><issue>1</issue><fpage>45</fpage><lpage>58</lpage><pub-id pub-id-type="doi">10.1101/gr.093302.109</pub-id><pub-id pub-id-type="pmid">19858364</pub-id></mixed-citation></ref><ref id="B29"><mixed-citation publication-type="journal"><name><surname>Mazzucotelli</surname><given-names>E</given-names></name><name><surname>Mastrangelo</surname><given-names>AA</given-names></name><name><surname>Crosatti</surname><given-names>C</given-names></name><name><surname>Guerra</surname><given-names>D</given-names></name><name><surname>Stanca</surname><given-names>AM</given-names></name><name><surname>Cattivelli</surname><given-names>L</given-names></name><article-title>Abiotic stress response in plants: When post-transcriptional and post-translational regulations control transcription</article-title><source>Plant Sci</source><year>2008</year><volume>174</volume><issue>4</issue><fpage>420</fpage><lpage>431</lpage><pub-id pub-id-type="doi">10.1016/j.plantsci.2008.02.005</pub-id></mixed-citation></ref><ref id="B30"><mixed-citation publication-type="journal"><name><surname>Palusa</surname><given-names>SG</given-names></name><name><surname>Ali</surname><given-names>GS</given-names></name><name><surname>Reddy</surname><given-names>ASN</given-names></name><article-title>Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses</article-title><source>The Plant Journal</source><year>2007</year><volume>49</volume><issue>6</issue><fpage>1091</fpage><lpage>1107</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2006.03020.x</pub-id><pub-id pub-id-type="pmid">17319848</pub-id></mixed-citation></ref><ref id="B31"><mixed-citation publication-type="journal"><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Wang</surname><given-names>X</given-names></name><name><surname>He</surname><given-names>K</given-names></name><name><surname>Ma</surname><given-names>Y</given-names></name><name><surname>Su</surname><given-names>N</given-names></name><name><surname>He</surname><given-names>H</given-names></name><name><surname>Stolc</surname><given-names>V</given-names></name><name><surname>Tongprasit</surname><given-names>W</given-names></name><name><surname>Jin</surname><given-names>W</given-names></name><name><surname>Jiang</surname><given-names>J</given-names></name><article-title>High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression</article-title><source>The Plant Cell Online</source><year>2008</year><volume>20</volume><issue>2</issue><fpage>259</fpage><lpage>276</lpage><pub-id pub-id-type="doi">10.1105/tpc.107.056879</pub-id></mixed-citation></ref><ref id="B32"><mixed-citation publication-type="journal"><name><surname>Zemach</surname><given-names>A</given-names></name><name><surname>McDaniel</surname><given-names>IE</given-names></name><name><surname>Silva</surname><given-names>P</given-names></name><name><surname>Zilberman</surname><given-names>D</given-names></name><article-title>Genome-wide evolutionary analysis of eukaryotic DNA methylation</article-title><source>Science</source><year>2010</year><volume>328</volume><issue>5980</issue><fpage>916</fpage><lpage>919</lpage><pub-id pub-id-type="doi">10.1126/science.1186366</pub-id><pub-id pub-id-type="pmid">20395474</pub-id></mixed-citation></ref><ref id="B33"><mixed-citation publication-type="journal"><name><surname>Perez-Rodriguez</surname><given-names>P</given-names></name><name><surname>Riano-Pachon</surname><given-names>DM</given-names></name><name><surname>Correa</surname><given-names>LG</given-names></name><name><surname>Rensing</surname><given-names>SA</given-names></name><name><surname>Kersten</surname><given-names>B</given-names></name><name><surname>Mueller-Roeber</surname><given-names>B</given-names></name><article-title>PlnTFDB: updated content and new features of the plant transcription factor database</article-title><source>Nucleic acids research</source><year>2010</year><volume>38</volume><issue>Database</issue><fpage>D822</fpage><lpage>827</lpage><pub-id pub-id-type="doi">10.1093/nar/gkp805</pub-id><pub-id pub-id-type="pmid">19858103</pub-id></mixed-citation></ref><ref id="B34"><mixed-citation publication-type="journal"><name><surname>Thornburg</surname><given-names>BG</given-names></name><name><surname>Gotea</surname><given-names>V</given-names></name><name><surname>Makalowski</surname><given-names>W</given-names></name><article-title>Transposable elements as a significant source of transcription regulating signals</article-title><source>Gene</source><year>2006</year><volume>365</volume><fpage>104</fpage><lpage>110</lpage><pub-id pub-id-type="pmid">16376497</pub-id></mixed-citation></ref><ref id="B35"><mixed-citation publication-type="journal"><name><surname>Vining</surname><given-names>KJ</given-names></name><name><surname>Pomraning</surname><given-names>KR</given-names></name><name><surname>Wilhelm</surname><given-names>LJ</given-names></name><name><surname>Priest</surname><given-names>HD</given-names></name><name><surname>Pellegrini</surname><given-names>M</given-names></name><name><surname>Mockler</surname><given-names>TC</given-names></name><name><surname>Freitag</surname><given-names>M</given-names></name><name><surname>Strauss</surname><given-names>SH</given-names></name><article-title>Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression</article-title><source>Bmc Genomics</source><year>2012</year><volume>13</volume><fpage>27</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-13-27</pub-id><pub-id pub-id-type="pmid">22251412</pub-id></mixed-citation></ref><ref id="B36"><mixed-citation publication-type="journal"><name><surname>Li</surname><given-names>XY</given-names></name><name><surname>Wang</surname><given-names>XF</given-names></name><name><surname>He</surname><given-names>K</given-names></name><name><surname>Ma</surname><given-names>YQ</given-names></name><name><surname>Su</surname><given-names>N</given-names></name><name><surname>He</surname><given-names>H</given-names></name><name><surname>Stolc</surname><given-names>V</given-names></name><name><surname>Tongprasit</surname><given-names>W</given-names></name><name><surname>Jin</surname><given-names>WW</given-names></name><name><surname>Jiang</surname><given-names>JM</given-names></name><etal></etal><article-title>High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression</article-title><source>Plant Cell</source><year>2008</year><volume>20</volume><issue>2</issue><fpage>259</fpage><lpage>276</lpage><pub-id pub-id-type="doi">10.1105/tpc.107.056879</pub-id><pub-id pub-id-type="pmid">18263775</pub-id></mixed-citation></ref><ref id="B37"><mixed-citation publication-type="journal"><name><surname>Shukla</surname><given-names>S</given-names></name><name><surname>Kavak</surname><given-names>E</given-names></name><name><surname>Gregory</surname><given-names>M</given-names></name><name><surname>Imashimizu</surname><given-names>M</given-names></name><name><surname>Shutinoski</surname><given-names>B</given-names></name><name><surname>Kashlev</surname><given-names>M</given-names></name><name><surname>Oberdoerffer</surname><given-names>P</given-names></name><name><surname>Sandberg</surname><given-names>R</given-names></name><name><surname>Oberdoerffer</surname><given-names>S</given-names></name><article-title>CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing</article-title><source>Nature</source><year>2011</year><volume>479</volume><issue>7371</issue><fpage>74</fpage><lpage>79</lpage><pub-id pub-id-type="doi">10.1038/nature10442</pub-id><pub-id pub-id-type="pmid">21964334</pub-id></mixed-citation></ref><ref id="B38"><mixed-citation publication-type="journal"><name><surname>Chodavarapu</surname><given-names>RK</given-names></name><name><surname>Feng</surname><given-names>SH</given-names></name><name><surname>Bernatavichute</surname><given-names>YV</given-names></name><name><surname>Chen</surname><given-names>PY</given-names></name><name><surname>Stroud</surname><given-names>H</given-names></name><name><surname>Yu</surname><given-names>YC</given-names></name><name><surname>Hetzel</surname><given-names>JA</given-names></name><name><surname>Kuo</surname><given-names>F</given-names></name><name><surname>Kim</surname><given-names>J</given-names></name><name><surname>Cokus</surname><given-names>SJ</given-names></name><etal></etal><article-title>Relationship between nucleosome positioning and DNA methylation</article-title><source>Nature</source><year>2010</year><volume>466</volume><issue>7304</issue><fpage>388</fpage><lpage>392</lpage><pub-id pub-id-type="doi">10.1038/nature09147</pub-id><pub-id pub-id-type="pmid">20512117</pub-id></mixed-citation></ref><ref id="B39"><mixed-citation publication-type="journal"><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Yazaki</surname><given-names>J</given-names></name><name><surname>Sundaresan</surname><given-names>A</given-names></name><name><surname>Cokus</surname><given-names>S</given-names></name><name><surname>Chan</surname><given-names>SW</given-names></name><name><surname>Chen</surname><given-names>H</given-names></name><name><surname>Henderson</surname><given-names>IR</given-names></name><name><surname>Shinn</surname><given-names>P</given-names></name><name><surname>Pellegrini</surname><given-names>M</given-names></name><name><surname>Jacobsen</surname><given-names>SE</given-names></name><etal></etal><article-title>Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis</article-title><source>Cell</source><year>2006</year><volume>126</volume><issue>6</issue><fpage>1189</fpage><lpage>1201</lpage><pub-id pub-id-type="doi">10.1016/j.cell.2006.08.003</pub-id><pub-id pub-id-type="pmid">16949657</pub-id></mixed-citation></ref><ref id="B40"><mixed-citation publication-type="journal"><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Zhu</surname><given-names>J</given-names></name><name><surname>Hu</surname><given-names>F</given-names></name><name><surname>Ge</surname><given-names>S</given-names></name><name><surname>Ye</surname><given-names>M</given-names></name><name><surname>Xiang</surname><given-names>H</given-names></name><name><surname>Zhang</surname><given-names>G</given-names></name><name><surname>Zheng</surname><given-names>X</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><name><surname>Zhang</surname><given-names>S</given-names></name><etal></etal><article-title>Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression</article-title><source>Bmc Genomics</source><year>2012</year><volume>13</volume><fpage>300</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-13-300</pub-id><pub-id pub-id-type="pmid">22747568</pub-id></mixed-citation></ref><ref id="B41"><mixed-citation publication-type="journal"><name><surname>Kapitonov</surname><given-names>VV</given-names></name><name><surname>Jurka</surname><given-names>J</given-names></name><article-title>A universal classification of eukaryotic transposable elements implemented in Repbase</article-title><source>Nat Rev Genet</source><year>2008</year><volume>9</volume><issue>5</issue><fpage>411</fpage><lpage>412</lpage><pub-id pub-id-type="doi">10.1038/nrg2165-c1</pub-id><pub-id pub-id-type="pmid">18421312</pub-id></mixed-citation></ref><ref id="B42"><mixed-citation publication-type="journal"><name><surname>Schwartz</surname><given-names>D</given-names></name><name><surname>Dennis</surname><given-names>E</given-names></name><article-title>Transposase activity of the Ac controlling element in maize is regulated by its degree of methylation</article-title><source>Mol Gen Genet</source><year>1986</year><volume>205</volume><issue>3</issue><fpage>476</fpage><lpage>482</lpage><pub-id pub-id-type="doi">10.1007/BF00338085</pub-id></mixed-citation></ref><ref id="B43"><mixed-citation publication-type="journal"><name><surname>Banks</surname><given-names>JA</given-names></name><name><surname>Masson</surname><given-names>P</given-names></name><name><surname>Fedoroff</surname><given-names>N</given-names></name><article-title>Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element</article-title><source>Genes & Development</source><year>1988</year><volume>2</volume><issue>11</issue><fpage>1364</fpage><lpage>1380</lpage><pub-id pub-id-type="doi">10.1101/gad.2.11.1364</pub-id><pub-id pub-id-type="pmid">2463208</pub-id></mixed-citation></ref><ref id="B44"><mixed-citation publication-type="journal"><name><surname>Martienssen</surname><given-names>RA</given-names></name><name><surname>Colot</surname><given-names>V</given-names></name><article-title>DNA methylation and epigenetic inheritance in plants and filamentous fungi</article-title><source>Science</source><year>2001</year><volume>293</volume><issue>5532</issue><fpage>1070</fpage><lpage>1074</lpage><pub-id pub-id-type="doi">10.1126/science.293.5532.1070</pub-id><pub-id pub-id-type="pmid">11498574</pub-id></mixed-citation></ref><ref id="B45"><mixed-citation publication-type="journal"><name><surname>Kato</surname><given-names>M</given-names></name><name><surname>Miura</surname><given-names>A</given-names></name><name><surname>Bender</surname><given-names>J</given-names></name><name><surname>Jacobsen</surname><given-names>SE</given-names></name><name><surname>Kakutani</surname><given-names>T</given-names></name><article-title>Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis</article-title><source>Current Biology</source><year>2003</year><volume>13</volume><issue>5</issue><fpage>421</fpage><lpage>426</lpage><pub-id pub-id-type="doi">10.1016/S0960-9822(03)00106-4</pub-id><pub-id pub-id-type="pmid">12620192</pub-id></mixed-citation></ref><ref id="B46"><mixed-citation publication-type="journal"><name><surname>Bourque</surname><given-names>G</given-names></name><name><surname>Leong</surname><given-names>B</given-names></name><name><surname>Vega</surname><given-names>VB</given-names></name><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Lee</surname><given-names>YL</given-names></name><name><surname>Srinivasan</surname><given-names>KG</given-names></name><name><surname>Chew</surname><given-names>JL</given-names></name><name><surname>Ruan</surname><given-names>Y</given-names></name><name><surname>Wei</surname><given-names>CL</given-names></name><name><surname>Ng</surname><given-names>HH</given-names></name><etal></etal><article-title>Evolution of the mammalian transcription factor binding repertoire via transposable elements</article-title><source>Genome research</source><year>2008</year><volume>18</volume><issue>11</issue><fpage>1752</fpage><lpage>1762</lpage><pub-id 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