Genome-wide analysis of day/night DNA methylation differences in Populus nigra.
Identifieur interne : 000E68 ( Main/Exploration ); précédent : 000E67; suivant : 000E69Genome-wide analysis of day/night DNA methylation differences in Populus nigra.
Auteurs : Chang-Jun Ding [République populaire de Chine] ; Li-Xiong Liang [République populaire de Chine] ; Shu Diao [République populaire de Chine] ; Xiao-Hua Su [République populaire de Chine] ; Bing-Yu Zhang [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Populus.
- métabolisme : Feuilles de plante.
- physiologie : Populus.
- Adaptation physiologique, Génome végétal, Immunoprécipitation, Lumière, Méthylation de l'ADN, Obscurité, Rythme circadien.
English descriptors
- KwdEn :
- MESH :
- genetics : Populus.
- metabolism : Plant Leaves.
- physiology : Populus.
- Adaptation, Physiological, Circadian Rhythm, DNA Methylation, Darkness, Genome, Plant, Immunoprecipitation, Light.
Abstract
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.
DOI: 10.1371/journal.pone.0190299
PubMed: 29293569
PubMed Central: PMC5749751
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (MeSH)</term><term>Circadian Rhythm (MeSH)</term><term>DNA Methylation (MeSH)</term><term>Darkness (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Immunoprecipitation (MeSH)</term><term>Light (MeSH)</term><term>Plant Leaves (metabolism)</term><term>Populus (genetics)</term><term>Populus (physiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation physiologique (MeSH)</term><term>Feuilles de plante (métabolisme)</term><term>Génome végétal (MeSH)</term><term>Immunoprécipitation (MeSH)</term><term>Lumière (MeSH)</term><term>Méthylation de l'ADN (MeSH)</term><term>Obscurité (MeSH)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Rythme circadien (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Leaves</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Feuilles de plante</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adaptation, Physiological</term><term>Circadian Rhythm</term><term>DNA Methylation</term><term>Darkness</term><term>Genome, Plant</term><term>Immunoprecipitation</term><term>Light</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adaptation physiologique</term><term>Génome végétal</term><term>Immunoprécipitation</term><term>Lumière</term><term>Méthylation de l'ADN</term><term>Obscurité</term><term>Rythme circadien</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29293569</PMID><DateCompleted><Year>2018</Year><Month>02</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>1</Issue><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of day/night DNA methylation differences in Populus nigra.</ArticleTitle><Pagination><MedlinePgn>e0190299</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0190299</ELocationID><Abstract><AbstractText>DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ding</LastName><ForeName>Chang-Jun</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Li-Xiong</ForeName><Initials>LX</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Diao</LastName><ForeName>Shu</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Xiao-Hua</ForeName><Initials>XH</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bing-Yu</ForeName><Initials>BY</Initials><Identifier Source="ORCID">0000-0002-8291-277X</Identifier><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>01</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002940" MajorTopicYN="Y">Circadian Rhythm</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019175" MajorTopicYN="Y">DNA Methylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003624" MajorTopicYN="N">Darkness</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, 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