Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome
Identifieur interne : 002496 ( Ncbi/Curation ); précédent : 002495; suivant : 002497Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome
Auteurs : Magali Naville [France] ; Minaka Ishibashi [Australie] ; Marco Ferg [Allemagne] ; Hemant Bengani [Royaume-Uni] ; Silke Rinkwitz [Australie] ; Monika Krecsmarik [France] ; Thomas A. Hawkins [Royaume-Uni] ; Stephen W. Wilson [Royaume-Uni] ; Elizabeth Manning [Australie] ; Chandra S. R. Chilamakuri [Norvège] ; David I. Wilson [Royaume-Uni] ; Alexandra Louis [France] ; F. Lucy Raymond [Royaume-Uni] ; Sepand Rastegar [Allemagne] ; Uwe Str Hle [Allemagne] ; Boris Lenhard [Royaume-Uni] ; Laure Bally-Cuif [France] ; Veronica Van Heyningen [Royaume-Uni] ; David R. Fitzpatrick [Royaume-Uni] ; Thomas S. Becker [Australie, Norvège] ; Hugues Roest Crollius [France]Source :
- Nature Communications [ 2041-1723 ] ; 2015.
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Abstract
Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression.
Url:
DOI: 10.1038/ncomms7904
PubMed: 25908307
PubMed Central: 4423230
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PMC:4423230Le document en format XML
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-regulatory interactions on the human X chromosome</title>
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<country xml:lang="fr">Royaume-Uni</country>
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<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<author><name sortKey="Chilamakuri, Chandra S R" sort="Chilamakuri, Chandra S R" uniqKey="Chilamakuri C" first="Chandra S. R." last="Chilamakuri">Chandra S. R. Chilamakuri</name>
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<author><name sortKey="Wilson, David I" sort="Wilson, David I" uniqKey="Wilson D" first="David I." last="Wilson">David I. Wilson</name>
<affiliation wicri:level="1"><nlm:aff id="a10"><institution>University of Southampton and University Hospital Southampton NHS Foundation Trust, Centre for Human Development, Stem Cells and Regeneration, MP808, Faculty of Medicine, Southampton General Hospital</institution>
, Tremona Road, Southampton 16 6YD,<country>UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<author><name sortKey="Louis, Alexandra" sort="Louis, Alexandra" uniqKey="Louis A" first="Alexandra" last="Louis">Alexandra Louis</name>
<affiliation wicri:level="1"><nlm:aff id="a1"><institution>Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS</institution>
, 46 rue d'Ulm, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="a2"><institution>CNRS</institution>
, UMR 8197, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="a3"><institution>Inserm</institution>
, U1024, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lucy Raymond, F" sort="Lucy Raymond, F" uniqKey="Lucy Raymond F" first="F." last="Lucy Raymond">F. Lucy Raymond</name>
<affiliation wicri:level="1"><nlm:aff id="a11"><institution>Cambridge Institute for Medical Research, University of Cambridge</institution>
, Hills Road, Cambridge CB2 OXY,<country>UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Rastegar, Sepand" sort="Rastegar, Sepand" uniqKey="Rastegar S" first="Sepand" last="Rastegar">Sepand Rastegar</name>
<affiliation wicri:level="1"><nlm:aff id="a5"><institution>Institute of Toxicology and Genetics and European Zebrafish Resource Centre, Karlsruhe Institute of Technology</institution>
, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,<country>Germany</country>
</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Str Hle, Uwe" sort="Str Hle, Uwe" uniqKey="Str Hle U" first="Uwe" last="Str Hle">Uwe Str Hle</name>
<affiliation wicri:level="1"><nlm:aff id="a5"><institution>Institute of Toxicology and Genetics and European Zebrafish Resource Centre, Karlsruhe Institute of Technology</institution>
, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,<country>Germany</country>
</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lenhard, Boris" sort="Lenhard, Boris" uniqKey="Lenhard B" first="Boris" last="Lenhard">Boris Lenhard</name>
<affiliation wicri:level="1"><nlm:aff id="a12"><institution>Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus</institution>
, Du Cane Road, London W12 0NN,<country>UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bally Cuif, Laure" sort="Bally Cuif, Laure" uniqKey="Bally Cuif L" first="Laure" last="Bally-Cuif">Laure Bally-Cuif</name>
<affiliation wicri:level="1"><nlm:aff id="a7"><institution>Paris-Saclay Institute for Neuroscience (Neuro-PSI), UMR9197 CNRS-Université Paris Sud</institution>
, Avenue de la Terrasse, Gif-sur-Yvette 91190,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Van Heyningen, Veronica" sort="Van Heyningen, Veronica" uniqKey="Van Heyningen V" first="Veronica" last="Van Heyningen">Veronica Van Heyningen</name>
<affiliation wicri:level="1"><nlm:aff id="a6"><institution>MRC Human Genetics Unit, MRC Institute of Medical Genetic and Molecular Medicine, University of Edinburgh</institution>
, Edinburgh EH4 2XU,<country>UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Fitzpatrick, David R" sort="Fitzpatrick, David R" uniqKey="Fitzpatrick D" first="David R." last="Fitzpatrick">David R. Fitzpatrick</name>
<affiliation wicri:level="1"><nlm:aff id="a6"><institution>MRC Human Genetics Unit, MRC Institute of Medical Genetic and Molecular Medicine, University of Edinburgh</institution>
, Edinburgh EH4 2XU,<country>UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Becker, Thomas S" sort="Becker, Thomas S" uniqKey="Becker T" first="Thomas S." last="Becker">Thomas S. Becker</name>
<affiliation wicri:level="1"><nlm:aff id="a4"><institution>Brain and Mind Research Institute, Sydney Medical School, University of Sydney</institution>
, Camperdown, New South Wales 2050,<country>Australia</country>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="a13"><institution>Department of Clinical Medicine, University of Bergen</institution>
, Bergen 5009,<country>Norway</country>
</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Roest Crollius, Hugues" sort="Roest Crollius, Hugues" uniqKey="Roest Crollius H" first="Hugues" last="Roest Crollius">Hugues Roest Crollius</name>
<affiliation wicri:level="1"><nlm:aff id="a1"><institution>Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS</institution>
, 46 rue d'Ulm, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="a2"><institution>CNRS</institution>
, UMR 8197, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="a3"><institution>Inserm</institution>
, U1024, Paris F-75005,<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Nature Communications</title>
<idno type="eISSN">2041-1723</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Animals, Genetically Modified</term>
<term>Chromosomes, Human, X (genetics)</term>
<term>Enhancer Elements, Genetic (genetics)</term>
<term>Evolution, Molecular</term>
<term>Gene Expression (genetics)</term>
<term>Gene Rearrangement (genetics)</term>
<term>Genetic Linkage (genetics)</term>
<term>Humans</term>
<term>Selection, Genetic (genetics)</term>
<term>Zebrafish</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animal génétiquement modifié</term>
<term>Animaux</term>
<term>Chromosomes X humains (génétique)</term>
<term>Danio zébré</term>
<term>Expression des gènes (génétique)</term>
<term>Humains</term>
<term>Liaison génétique (génétique)</term>
<term>Réarrangement des gènes (génétique)</term>
<term>Sélection génétique (génétique)</term>
<term>Éléments activateurs (génétique) (génétique)</term>
<term>Évolution moléculaire</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Human, X</term>
<term>Enhancer Elements, Genetic</term>
<term>Gene Expression</term>
<term>Gene Rearrangement</term>
<term>Genetic Linkage</term>
<term>Selection, Genetic</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes X humains</term>
<term>Expression des gènes</term>
<term>Liaison génétique</term>
<term>Réarrangement des gènes</term>
<term>Sélection génétique</term>
<term>Éléments activateurs (génétique)</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Animals, Genetically Modified</term>
<term>Evolution, Molecular</term>
<term>Humans</term>
<term>Zebrafish</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animal génétiquement modifié</term>
<term>Animaux</term>
<term>Danio zébré</term>
<term>Humains</term>
<term>Évolution moléculaire</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression.</p>
</div>
</front>
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