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Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

2017-09Journal article Open access
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dc.contributor.authorBaudouin-Gonzalez, Luís
dc.contributor.authorSantos, Marília A.
dc.contributor.authorTempesta, Camille
dc.contributor.authorSucena, Élio
dc.contributor.authorRoch, Fernando
dc.contributor.authorTanaka, Kohtaro
dc.date.accessioned2017-11-09T18:07:12Z
dc.date.available2018-10-01T00:30:08Z
dc.date.issued2017-09
dc.descriptionThe deposited article is a post-print version and has peer review. The deposited article version contains attached the supplementary materials within the pdf.pt_PT
dc.description.abstractPairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 million years ago. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level in order to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression.pt_PT
dc.description.sponsorshipFundação Calouste Gulbenkian/Instituto Gulbenkian de Ciência; Toulouse RIO Imaging platform; Bloomington Drosophila Stock Center (Indiana, USA); Developmental Studies Hybridoma Bank (Iowa, USA); Drosophila Genomics Resource Center (Indiana, USA); NIH grant: (2P0OD010949); Agence Nationale de la Recherche grant: (ANR-13-ISV7-0001-01); Fundação para a Ciência e a Tecnologia grants: (SFRH/BPD/75139/2010, FCT-ANR/BIA-ANM/0003/2013, FCT-EXPL/BEX-GMG/2197/2013).pt_PT
dc.description.versioninfo:eu-repo/semantics/acceptedVersionpt_PT
dc.identifier.citationLuís Baudouin-Gonzalez, Marília A. Santos, Camille Tempesta, Élio Sucena, Fernando Roch, Kohtaro Tanaka; Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates, Molecular Biology and Evolution, , msx237, https://doi.org/10.1093/molbev/msx237pt_PT
dc.identifier.doi10.1093/molbev/msx237pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.7/803
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherOxford University Presspt_PT
dc.relation2P0OD010949pt_PT
dc.relationANR-13-ISV7-0001-01pt_PT
dc.relation.publisherversionhttps://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msx237pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectcis-regulatory evolutionpt_PT
dc.subjectenhancerpt_PT
dc.subjectDrosophilapt_PT
dc.subjectgene duplicationpt_PT
dc.subjectgene regulationpt_PT
dc.titleDiverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicatespt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/SFRH/SFRH%2FBPD%2F75139%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/FCT-ANR%2FBIA-ANM%2F0003%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/EXPL%2FBEX-GMG%2F2197%2F2013/PT
oaire.citation.endPage42pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleMolecular Biology and Evolutionpt_PT
oaire.fundingStreamSFRH
oaire.fundingStream3599-PPCDT
oaire.fundingStream3599-PPCDT
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.embargofctThe deposited article has 13 months of embargo period in terms of access, because of the journal's policies and the publisher's copyright policy. Since the paper has not been published yet, the library service put in this upload an embargo period superior than 6 months, as a securing measure.pt_PT
rcaap.rightsembargoedAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublication5a35965c-cc7d-4d59-847f-d805908f4aac
relation.isProjectOfPublicationdc1b3096-3901-45b4-98a4-27febbfefb91
relation.isProjectOfPublication28942fa4-02e9-47c8-8770-d16563de7ba1
relation.isProjectOfPublication.latestForDiscovery5a35965c-cc7d-4d59-847f-d805908f4aac

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