Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle
Identifieur interne : 000B73 ( Main/Exploration ); précédent : 000B72; suivant : 000B74Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle
Auteurs : Cédric Meersseman [France] ; Rabia Letaief [France] ; Véronique Léjard [France] ; Emmanuelle Rebours [France] ; Gabriel Guillocheau [France] ; Diane Esquerré [France] ; Anis Djari [France] ; Amanda Chamberlain [Australie] ; Christy Vander Jagt [Australie] ; Christophe Klopp [France] ; Mekki Boussaha [France] ; Gilles Renand [France] ; Abderrahman Maftah [France] ; Daniel Petit [France] ; Dominique Rocha [France]Source :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Proteins.
- metabolism : Back Muscles.
- Animals, Cattle, Gene Expression Profiling, Gene Expression Regulation, Male, Pilot Projects, Polymorphism, Single Nucleotide, Promoter Regions, Genetic.
Abstract
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine
Url:
DOI: 10.1093/dnares/dsx004
PubMed: 28338730
PubMed Central: 5499805
Affiliations:
- Australie, France
- Limousin, Nouvelle-Aquitaine, Île-de-France
- Jouy-en-Josas, Limoges
- Université de Limoges
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Le document en format XML
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xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Jouy-en-Josas</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="dsx004-aff2">GMA, INRA, Université de Limoges, 87060 Limoges, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GMA, INRA, Université de Limoges, 87060 Limoges</wicri:regionArea><placeName><region type="region" nuts="2">Nouvelle-Aquitaine</region><region type="old region" nuts="2">Limousin</region><settlement type="city">Limoges</settlement><settlement type="city">Limoges</settlement></placeName><orgName type="university">Université de Limoges</orgName></affiliation></author><author><name sortKey="Letaief, Rabia" sort="Letaief, Rabia" uniqKey="Letaief R" first="Rabia" last="Letaief">Rabia Letaief</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Lejard, Veronique" sort="Lejard, Veronique" uniqKey="Lejard V" first="Véronique" last="Léjard">Véronique Léjard</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Rebours, Emmanuelle" sort="Rebours, Emmanuelle" uniqKey="Rebours E" first="Emmanuelle" last="Rebours">Emmanuelle Rebours</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Guillocheau, Gabriel" sort="Guillocheau, Gabriel" uniqKey="Guillocheau G" first="Gabriel" last="Guillocheau">Gabriel Guillocheau</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Esquerre, Diane" sort="Esquerre, Diane" uniqKey="Esquerre D" first="Diane" last="Esquerré">Diane Esquerré</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff3">GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan</wicri:regionArea><wicri:noRegion>31326 Castanet Tolosan</wicri:noRegion><wicri:noRegion>31326 Castanet Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Djari, Anis" sort="Djari, Anis" uniqKey="Djari A" first="Anis" last="Djari">Anis Djari</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff4">SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan</wicri:regionArea><wicri:noRegion>31362 Castanet-Tolosan</wicri:noRegion><wicri:noRegion>31362 Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Chamberlain, Amanda" sort="Chamberlain, Amanda" uniqKey="Chamberlain A" first="Amanda" last="Chamberlain">Amanda Chamberlain</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff5">Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="dsx004-aff6">AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation></author><author><name sortKey="Vander Jagt, Christy" sort="Vander Jagt, Christy" uniqKey="Vander Jagt C" first="Christy" last="Vander Jagt">Christy Vander Jagt</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff5">Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="dsx004-aff6">AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation></author><author><name sortKey="Klopp, Christophe" sort="Klopp, Christophe" uniqKey="Klopp C" first="Christophe" last="Klopp">Christophe Klopp</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff4">SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan</wicri:regionArea><wicri:noRegion>31362 Castanet-Tolosan</wicri:noRegion><wicri:noRegion>31362 Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Boussaha, Mekki" sort="Boussaha, Mekki" uniqKey="Boussaha M" first="Mekki" last="Boussaha">Mekki Boussaha</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Renand, Gilles" sort="Renand, Gilles" uniqKey="Renand G" first="Gilles" last="Renand">Gilles Renand</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author><author><name sortKey="Maftah, Abderrahman" sort="Maftah, Abderrahman" uniqKey="Maftah A" first="Abderrahman" last="Maftah">Abderrahman Maftah</name><affiliation wicri:level="4"><nlm:aff id="dsx004-aff2">GMA, INRA, Université de Limoges, 87060 Limoges, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GMA, INRA, Université de Limoges, 87060 Limoges</wicri:regionArea><wicri:noRegion>87060 Limoges</wicri:noRegion><orgName type="university">Université de Limoges</orgName><placeName><settlement type="city">Limoges</settlement><region type="region" nuts="2">Limousin</region></placeName></affiliation></author><author><name sortKey="Petit, Daniel" sort="Petit, Daniel" uniqKey="Petit D" first="Daniel" last="Petit">Daniel Petit</name><affiliation wicri:level="4"><nlm:aff id="dsx004-aff2">GMA, INRA, Université de Limoges, 87060 Limoges, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GMA, INRA, Université de Limoges, 87060 Limoges</wicri:regionArea><wicri:noRegion>87060 Limoges</wicri:noRegion><orgName type="university">Université de Limoges</orgName><placeName><settlement type="city">Limoges</settlement><region type="region" nuts="2">Limousin</region></placeName></affiliation></author><author><name sortKey="Rocha, Dominique" sort="Rocha, Dominique" uniqKey="Rocha D" first="Dominique" last="Rocha">Dominique Rocha</name><affiliation wicri:level="1"><nlm:aff id="dsx004-aff1">GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion><wicri:noRegion>78350 Jouy-en-Josas</wicri:noRegion></affiliation></author></analytic><series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><idno type="ISSN">1340-2838</idno><idno type="eISSN">1756-1663</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Back Muscles (metabolism)</term><term>Cattle</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation</term><term>Male</term><term>Pilot Projects</term><term>Polymorphism, Single Nucleotide</term><term>Promoter Regions, Genetic</term><term>Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Bovins</term><term>Muscles du dos (métabolisme)</term><term>Mâle</term><term>Polymorphisme de nucléotide simple</term><term>Projets pilotes</term><term>Protéines (génétique)</term><term>Régions promotrices (génétique)</term><term>Régulation de l'expression des gènes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Back Muscles</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Muscles du dos</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cattle</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation</term><term>Male</term><term>Pilot Projects</term><term>Polymorphism, Single Nucleotide</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Bovins</term><term>Mâle</term><term>Polymorphisme de nucléotide simple</term><term>Projets pilotes</term><term>Régions promotrices (génétique)</term><term>Régulation de l'expression des gènes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine <italic>Longissimus thoracis</italic> and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated <italic>in vitro</italic> 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Adachi, N" uniqKey="Adachi N">N. Adachi</name></author><author><name sortKey="Lieber, M" uniqKey="Lieber M">M. Lieber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Takai, D" uniqKey="Takai D">D. Takai</name></author><author><name sortKey="Jones, P A" uniqKey="Jones P">P.A. Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Trinklein, N D" uniqKey="Trinklein N">N.D. Trinklein</name></author><author><name sortKey="Aldred, S F" uniqKey="Aldred S">S.F. 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Sadowski</name></author><author><name sortKey="Henry, R W" uniqKey="Henry R">R.W. Henry</name></author><author><name sortKey="Lobo, S M" uniqKey="Lobo S">S.M. Lobo</name></author><author><name sortKey="Hernandez, N" uniqKey="Hernandez N">N. Hernandez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, Q" uniqKey="Zhou Q">Q. Zhou</name></author><author><name sortKey="Boyer, T G" uniqKey="Boyer T">T.G. Boyer</name></author><author><name sortKey="Berk, A J" uniqKey="Berk A">A.J. Berk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martinez, E" uniqKey="Martinez E">E. Martinez</name></author><author><name sortKey="Chiang, C M" uniqKey="Chiang C">C.M. Chiang</name></author><author><name sortKey="Ge, H" uniqKey="Ge H">H. Ge</name></author><author><name sortKey="Roeder, R G" uniqKey="Roeder R">R.G. Roeder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, Z L" uniqKey="Hu Z">Z.L. Hu</name></author><author><name sortKey="Fritz, E R" uniqKey="Fritz E">E.R. Fritz</name></author><author><name sortKey="Reecy, J M" uniqKey="Reecy J">J.M. Reecy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karim, L" uniqKey="Karim L">L. Karim</name></author><author><name sortKey="Takeda, H" uniqKey="Takeda H">H. Takeda</name></author><author><name sortKey="Lin, L" uniqKey="Lin L">L. Lin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li></country><region><li>Limousin</li><li>Nouvelle-Aquitaine</li><li>Île-de-France</li></region><settlement><li>Jouy-en-Josas</li><li>Limoges</li></settlement><orgName><li>Université de Limoges</li></orgName></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Meersseman, Cedric" sort="Meersseman, Cedric" uniqKey="Meersseman C" first="Cédric" last="Meersseman">Cédric Meersseman</name></region><name sortKey="Boussaha, Mekki" sort="Boussaha, Mekki" uniqKey="Boussaha M" first="Mekki" last="Boussaha">Mekki Boussaha</name><name sortKey="Djari, Anis" sort="Djari, Anis" uniqKey="Djari A" first="Anis" last="Djari">Anis Djari</name><name sortKey="Esquerre, Diane" sort="Esquerre, Diane" uniqKey="Esquerre D" first="Diane" last="Esquerré">Diane Esquerré</name><name sortKey="Guillocheau, Gabriel" sort="Guillocheau, Gabriel" uniqKey="Guillocheau G" first="Gabriel" last="Guillocheau">Gabriel Guillocheau</name><name sortKey="Klopp, Christophe" sort="Klopp, Christophe" uniqKey="Klopp C" first="Christophe" last="Klopp">Christophe Klopp</name><name sortKey="Lejard, Veronique" sort="Lejard, Veronique" uniqKey="Lejard V" first="Véronique" last="Léjard">Véronique Léjard</name><name sortKey="Letaief, Rabia" sort="Letaief, Rabia" uniqKey="Letaief R" first="Rabia" last="Letaief">Rabia Letaief</name><name sortKey="Maftah, Abderrahman" sort="Maftah, Abderrahman" uniqKey="Maftah A" first="Abderrahman" last="Maftah">Abderrahman Maftah</name><name sortKey="Meersseman, Cedric" sort="Meersseman, Cedric" uniqKey="Meersseman C" first="Cédric" last="Meersseman">Cédric Meersseman</name><name sortKey="Petit, Daniel" sort="Petit, Daniel" uniqKey="Petit D" first="Daniel" last="Petit">Daniel Petit</name><name sortKey="Rebours, Emmanuelle" sort="Rebours, Emmanuelle" uniqKey="Rebours E" first="Emmanuelle" last="Rebours">Emmanuelle Rebours</name><name sortKey="Renand, Gilles" sort="Renand, Gilles" uniqKey="Renand G" first="Gilles" last="Renand">Gilles Renand</name><name sortKey="Rocha, Dominique" sort="Rocha, Dominique" uniqKey="Rocha D" first="Dominique" last="Rocha">Dominique Rocha</name></country><country name="Australie"><noRegion><name sortKey="Chamberlain, Amanda" sort="Chamberlain, Amanda" uniqKey="Chamberlain A" first="Amanda" last="Chamberlain">Amanda Chamberlain</name></noRegion><name sortKey="Chamberlain, Amanda" sort="Chamberlain, Amanda" uniqKey="Chamberlain A" first="Amanda" last="Chamberlain">Amanda Chamberlain</name><name sortKey="Vander Jagt, Christy" sort="Vander Jagt, Christy" uniqKey="Vander Jagt C" first="Christy" last="Vander Jagt">Christy Vander Jagt</name><name sortKey="Vander Jagt, Christy" sort="Vander Jagt, Christy" uniqKey="Vander Jagt C" first="Christy" last="Vander Jagt">Christy Vander Jagt</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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