A cross-species transcriptomics approach to identify genes involved in leaf development.
Identifieur interne : 003A10 ( Main/Exploration ); précédent : 003A09; suivant : 003A11A cross-species transcriptomics approach to identify genes involved in leaf development.
Auteurs : Nathaniel Robert Street [Suède] ; Andreas Sjödin ; Max Bylesjö ; Petter Gustafsson ; Johan Trygg ; Stefan JanssonSource :
- BMC genomics [ 1471-2164 ] ; 2008.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Analyse en composantes principales (MeSH), Arabidopsis (génétique), Facteurs de transcription (génétique), Feuilles de plante (génétique), Gènes de plante (MeSH), Locus de caractère quantitatif (MeSH), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'espèce (MeSH), Séquençage par oligonucléotides en batterie (MeSH), Étiquettes de séquences exprimées (MeSH).
- MESH :
- génétique : Arabidopsis, Facteurs de transcription, Feuilles de plante, Populus.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Analyse en composantes principales, Gènes de plante, Locus de caractère quantitatif, Régulation de l'expression des gènes végétaux, Spécificité d'espèce, Séquençage par oligonucléotides en batterie, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Cluster Analysis (MeSH), Expressed Sequence Tags (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Plant Leaves (genetics), Populus (genetics), Principal Component Analysis (MeSH), Quantitative Trait Loci (MeSH), Species Specificity (MeSH), Transcription Factors (genetics).
- MESH :
- chemical , genetics : Transcription Factors.
- genetics : Arabidopsis, Plant Leaves, Populus.
- Cluster Analysis, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Oligonucleotide Array Sequence Analysis, Principal Component Analysis, Quantitative Trait Loci, Species Specificity.
Abstract
BACKGROUND
We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.
RESULTS
Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.
CONCLUSION
This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.
DOI: 10.1186/1471-2164-9-589
PubMed: 19061504
PubMed Central: PMC2621207
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Bylesjö</name></author><author><name sortKey="Gustafsson, Petter" sort="Gustafsson, Petter" uniqKey="Gustafsson P" first="Petter" last="Gustafsson">Petter Gustafsson</name></author><author><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:19061504</idno><idno type="pmid">19061504</idno><idno type="doi">10.1186/1471-2164-9-589</idno><idno type="pmc">PMC2621207</idno><idno type="wicri:Area/Main/Corpus">003723</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003723</idno><idno type="wicri:Area/Main/Curation">003723</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003723</idno><idno 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uniqKey="Bylesjo M" first="Max" last="Bylesjö">Max Bylesjö</name></author><author><name sortKey="Gustafsson, Petter" sort="Gustafsson, Petter" uniqKey="Gustafsson P" first="Petter" last="Gustafsson">Petter Gustafsson</name></author><author><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Cluster Analysis (MeSH)</term><term>Expressed Sequence Tags (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Plant Leaves (genetics)</term><term>Populus (genetics)</term><term>Principal Component Analysis (MeSH)</term><term>Quantitative Trait Loci (MeSH)</term><term>Species Specificity (MeSH)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Analyse en composantes principales (MeSH)</term><term>Arabidopsis (génétique)</term><term>Facteurs de transcription (génétique)</term><term>Feuilles de plante (génétique)</term><term>Gènes de plante (MeSH)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Plant Leaves</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Facteurs de transcription</term><term>Feuilles de plante</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Expressed Sequence Tags</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Oligonucleotide Array Sequence Analysis</term><term>Principal Component Analysis</term><term>Quantitative Trait Loci</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Analyse en composantes principales</term><term>Gènes de plante</term><term>Locus de caractère quantitatif</term><term>Régulation de l'expression des gènes végétaux</term><term>Spécificité d'espèce</term><term>Séquençage par oligonucléotides en batterie</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19061504</PMID><DateCompleted><Year>2009</Year><Month>01</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><PubDate><Year>2008</Year><Month>Dec</Month><Day>05</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>A cross-species transcriptomics approach to identify genes involved in leaf development.</ArticleTitle><Pagination><MedlinePgn>589</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-9-589</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel Robert</ForeName><Initials>NR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden. nathaniel.street@plantphys.umu.se</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sjödin</LastName><ForeName>Andreas</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Bylesjö</LastName><ForeName>Max</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Gustafsson</LastName><ForeName>Petter</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Trygg</LastName><ForeName>Johan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Stefan</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D017418">Meta-Analysis</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>12</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName 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Jansson</name><name sortKey="Sjodin, Andreas" sort="Sjodin, Andreas" uniqKey="Sjodin A" first="Andreas" last="Sjödin">Andreas Sjödin</name><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></noCountry><country name="Suède"><noRegion><name sortKey="Street, Nathaniel Robert" sort="Street, Nathaniel Robert" uniqKey="Street N" first="Nathaniel Robert" last="Street">Nathaniel Robert Street</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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