Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle
Identifieur interne : 002245 ( Pmc/Curation ); précédent : 002244; suivant : 002246Genetic 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.
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
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<author><name sortKey="Djari, Anis" sort="Djari, Anis" uniqKey="Djari A" first="Anis" last="Djari">Anis Djari</name>
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<author><name sortKey="Chamberlain, Amanda" sort="Chamberlain, Amanda" uniqKey="Chamberlain A" first="Amanda" last="Chamberlain">Amanda Chamberlain</name>
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<author><name sortKey="Vander Jagt, Christy" sort="Vander Jagt, Christy" uniqKey="Vander Jagt C" first="Christy" last="Vander Jagt">Christy Vander Jagt</name>
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<author><name sortKey="Klopp, Christophe" sort="Klopp, Christophe" uniqKey="Klopp C" first="Christophe" last="Klopp">Christophe Klopp</name>
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<author><name sortKey="Boussaha, Mekki" sort="Boussaha, Mekki" uniqKey="Boussaha M" first="Mekki" last="Boussaha">Mekki Boussaha</name>
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<author><name sortKey="Renand, Gilles" sort="Renand, Gilles" uniqKey="Renand G" first="Gilles" last="Renand">Gilles Renand</name>
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<author><name sortKey="Maftah, Abderrahman" sort="Maftah, Abderrahman" uniqKey="Maftah A" first="Abderrahman" last="Maftah">Abderrahman Maftah</name>
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<author><name sortKey="Petit, Daniel" sort="Petit, Daniel" uniqKey="Petit D" first="Daniel" last="Petit">Daniel Petit</name>
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<author><name sortKey="Rocha, Dominique" sort="Rocha, Dominique" uniqKey="Rocha D" first="Dominique" last="Rocha">Dominique Rocha</name>
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<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>
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id>
<journal-id journal-id-type="iso-abbrev">DNA Res</journal-id>
<journal-id journal-id-type="publisher-id">dnares</journal-id>
<journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title>
</journal-title-group>
<issn pub-type="ppub">1340-2838</issn>
<issn pub-type="epub">1756-1663</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">28338730</article-id>
<article-id pub-id-type="pmc">5499805</article-id>
<article-id pub-id-type="doi">10.1093/dnares/dsx004</article-id>
<article-id pub-id-type="publisher-id">dsx004</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Full Papers</subject>
</subj-group>
<subj-group subj-group-type="category-oup-series"><subject>Editor's Choice</subject>
</subj-group>
</article-categories>
<title-group><article-title>Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Meersseman</surname>
<given-names>Cédric</given-names>
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<xref ref-type="aff" rid="dsx004-aff1">1</xref>
<xref ref-type="aff" rid="dsx004-aff2">2</xref>
</contrib>
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<given-names>Rabia</given-names>
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<given-names>Véronique</given-names>
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<given-names>Emmanuelle</given-names>
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<given-names>Gabriel</given-names>
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<given-names>Diane</given-names>
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<xref ref-type="aff" rid="dsx004-aff4">4</xref>
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<given-names>Amanda</given-names>
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<xref ref-type="aff" rid="dsx004-aff5">5</xref>
<xref ref-type="aff" rid="dsx004-aff6">6</xref>
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<given-names>Christophe</given-names>
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<xref ref-type="aff" rid="dsx004-aff4">4</xref>
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<given-names>Mekki</given-names>
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<xref ref-type="aff" rid="dsx004-aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Renand</surname>
<given-names>Gilles</given-names>
</name>
<xref ref-type="aff" rid="dsx004-aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Maftah</surname>
<given-names>Abderrahman</given-names>
</name>
<xref ref-type="aff" rid="dsx004-aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Petit</surname>
<given-names>Daniel</given-names>
</name>
<xref ref-type="aff" rid="dsx004-aff2">2</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Rocha</surname>
<given-names>Dominique</given-names>
</name>
<xref ref-type="aff" rid="dsx004-aff1">1</xref>
<xref ref-type="corresp" rid="dsx004-cor1"></xref>
<pmc-comment>dominique.rocha@inra.fr </pmc-comment>
</contrib>
</contrib-group>
<aff id="dsx004-aff1"><label>1</label>
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France</aff>
<aff id="dsx004-aff2"><label>2</label>
GMA, INRA, Université de Limoges, 87060 Limoges, France</aff>
<aff id="dsx004-aff3"><label>3</label>
GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France</aff>
<aff id="dsx004-aff4"><label>4</label>
SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France</aff>
<aff id="dsx004-aff5"><label>5</label>
Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia</aff>
<aff id="dsx004-aff6"><label>6</label>
AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia</aff>
<author-notes><corresp id="dsx004-cor1"><label>*</label>
To whom correspondence should be addressed. Tel. +33 134 652 432. Fax. +33 134 652 478. Email: <email>dominique.rocha@inra.fr</email>
</corresp>
<fn id="dsx004-FM1"><p>Edited by Dr. Takao Sekiya</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>6</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="epub" iso-8601-date="2017-02-23"><day>23</day>
<month>2</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>23</day>
<month>2</month>
<year>2017</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the . </pmc-comment>
<volume>24</volume>
<issue>3</issue>
<fpage>221</fpage>
<lpage>233</lpage>
<history><date date-type="received"><day>02</day>
<month>9</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>24</day>
<month>1</month>
<year>2017</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</copyright-statement>
<copyright-year>2016</copyright-year>
<license license-type="cc-by-nc" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<self-uri xlink:href="dsx004.pdf"></self-uri>
<abstract><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>
</abstract>
<kwd-group kwd-group-type="author"><kwd>bidirectional promoter</kwd>
<kwd>cattle genome</kwd>
<kwd>genetic variability</kwd>
<kwd>muscle</kwd>
</kwd-group>
<funding-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">French National Institute for Agricultural Research and the Limousin Regional Council</named-content>
<named-content content-type="funder-identifier">10.13039/501100001665</named-content>
</funding-source>
</award-group>
</funding-group>
<counts><page-count count="13"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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