Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
Identifieur interne : 003D40 ( Main/Exploration ); précédent : 003D39; suivant : 003D41Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
Auteurs : Stefanie De Bodt [Belgique] ; Guenter Theissen ; Yves Van De PeerSource :
- Molecular biology and evolution [ 0737-4038 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MADS Domain Proteins.
- classification : Populus.
- genetics : Arabidopsis, Populus, Promoter Regions, Genetic.
- Conserved Sequence, Gene Duplication, Genetic Speciation, Genome, Plant, Phylogeny.
Abstract
The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization.
DOI: 10.1093/molbev/msk016
PubMed: 16581940
Affiliations:
Links toward previous steps (curation, corpus...)
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(génétique)</term><term>Régions promotrices (génétique) (génétique)</term><term>Spéciation génétique (MeSH)</term><term>Séquence conservée (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MADS Domain Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Populus</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Populus</term><term>Protéines à domaine MADS</term><term>Régions promotrices (génétique)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term><term>Gene Duplication</term><term>Genetic Speciation</term><term>Genome, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Duplication de gène</term><term>Génome 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However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16581940</PMID><DateCompleted><Year>2006</Year><Month>08</Month><Day>03</Day></DateCompleted><DateRevised><Year>2008</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0737-4038</ISSN><JournalIssue CitedMedium="Print"><Volume>23</Volume><Issue>6</Issue><PubDate><Year>2006</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.</ArticleTitle><Pagination><MedlinePgn>1293-303</MedlinePgn></Pagination><Abstract><AbstractText>The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>De Bodt</LastName><ForeName>Stefanie</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Theissen</LastName><ForeName>Guenter</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Van de Peer</LastName><ForeName>Yves</ForeName><Initials>Y</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>03</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D026161">MADS Domain Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D049810" MajorTopicYN="N">Genetic Speciation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026161" MajorTopicYN="N">MADS Domain Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>4</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>8</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>4</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16581940</ArticleId><ArticleId IdType="pii">msk016</ArticleId><ArticleId IdType="doi">10.1093/molbev/msk016</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Belgique</li></country><region><li>Province de Flandre-Orientale</li><li>Région flamande</li></region><settlement><li>Gand</li></settlement><orgName><li>Université de Gand</li></orgName></list><tree><noCountry><name sortKey="Theissen, Guenter" sort="Theissen, Guenter" uniqKey="Theissen G" first="Guenter" last="Theissen">Guenter Theissen</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></noCountry><country name="Belgique"><region name="Région flamande"><name sortKey="De Bodt, Stefanie" sort="De Bodt, Stefanie" uniqKey="De Bodt S" first="Stefanie" last="De Bodt">Stefanie De Bodt</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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