Widespread antisense transcription of Populus genome under drought.
Identifieur interne : 000C03 ( Main/Exploration ); précédent : 000C02; suivant : 000C04Widespread antisense transcription of Populus genome under drought.
Auteurs : Yinan Yuan [États-Unis] ; Su Chen [États-Unis]Source :
- Molecular genetics and genomics : MGG [ 1617-4623 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Antisense.
- genetics : Populus.
- methods : Gene Expression Profiling, Sequence Analysis, RNA.
- Droughts, Gene Expression Regulation, Plant, Genome, Plant, Introns, Molecular Sequence Annotation.
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.
DOI: 10.1007/s00438-018-1456-z
PubMed: 29876646
Affiliations:
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49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular genetics and genomics : MGG</title><idno type="eISSN">1617-4623</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Droughts (MeSH)</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Introns (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Populus (genetics)</term><term>RNA, Antisense (genetics)</term><term>Sequence Analysis, RNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN antisens (génétique)</term><term>Analyse de profil d'expression de gènes (méthodes)</term><term>Analyse de séquence d'ARN (méthodes)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Génome végétal (MeSH)</term><term>Introns (MeSH)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Sécheresses (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Antisense</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN antisens</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Droughts</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>Introns</term><term>Molecular Sequence Annotation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Annotation de séquence moléculaire</term><term>Génome végétal</term><term>Introns</term><term>Régulation de l'expression des gènes végétaux</term><term>Sécheresses</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29876646</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>13</Day></DateCompleted><DateRevised><Year>2019</Year><Month>03</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1617-4623</ISSN><JournalIssue CitedMedium="Internet"><Volume>293</Volume><Issue>4</Issue><PubDate><Year>2018</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol Genet Genomics</ISOAbbreviation></Journal><ArticleTitle>Widespread antisense transcription of Populus genome under drought.</ArticleTitle><Pagination><MedlinePgn>1017-1033</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00438-018-1456-z</ELocationID><Abstract><AbstractText>Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>Yinan</ForeName><Initials>Y</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-6772-3623</Identifier><AffiliationInfo><Affiliation>School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA. yinyuan@mtu.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Su</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>2012-67014-19445</GrantID><Agency>the National Institute of Food 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sort="Yuan, Yinan" uniqKey="Yuan Y" first="Yinan" last="Yuan">Yinan Yuan</name></noRegion><name sortKey="Chen, Su" sort="Chen, Su" uniqKey="Chen S" first="Su" last="Chen">Su Chen</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
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|clé= pubmed:29876646
|texte= Widespread antisense transcription of Populus genome under drought.
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