Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole-genome duplications

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  • dc.contributor.author Touceda-Suárez, María
  • dc.contributor.author Kita, Elizabeth M.
  • dc.contributor.author Acemel, Rafael D.
  • dc.contributor.author Firbas, Panos N.
  • dc.contributor.author Magri, Marta S.
  • dc.contributor.author Naranjo, Silvia
  • dc.contributor.author Tena, Juan J.
  • dc.contributor.author Gómez Skarmeta, José Luis
  • dc.contributor.author Maeso, Ignacio
  • dc.contributor.author Irimia Martínez, Manuel
  • dc.date.accessioned 2020-10-20T05:53:26Z
  • dc.date.available 2020-10-20T05:53:26Z
  • dc.date.issued 2020
  • dc.description.abstract We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic regulatory blocks, GRBs). We showed that the majority of GRBs identified in the last common ancestor of chordates have been maintained as a single copy in humans. We found evidence that dismantling of the duplicated GRB copies occurred early in vertebrate evolution often through the differential retention of the regulatory gene but loss of the bystander gene's exonic sequences. Despite the large evolutionary scale, the presence of duplicated highly conserved noncoding regions provided unambiguous proof for this scenario for multiple ancient GRBs. Remarkably, the dismantling of ancient GRB duplicates has contributed to the creation of large gene deserts associated with regulatory genes in vertebrates, providing a potentially widespread mechanism for the origin of these enigmatic genomic traits.
  • dc.description.sponsorship The research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC-StG-LS2-637591 to M.I. and ERC-AdG-LS8-740041 to J.L.G.-S.), the Spanish Ministry of Science and Innovation (BFU2017-89201-P to M.I., RYC-2016-20089 and PGC2018-099392-A-I00 to I.M., BFU2016-74961-P to J.L.G.-S., and BFU2016-81887-REDT/AEI to J.L.G.-S. and M.I.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 608959, the “Centro de Excelencia Severo Ochoa 2013-2017” (SEV-2012-0208), and the “Unidad de Excelencia María de Maetzu 2017-2021” (MDM-2016-0687). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya and of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Touceda-Suárez M, Kita EM, Acemel RD, Firbas PN, Magri MS, Naranjo S et al. Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole-genome duplications. Mol Biol Evol. 2020 Oct 1; 37(10): 2857-2864. DOI: 10.1093/molbev/msaa123
  • dc.identifier.doi http://dx.doi.org/10.1093/molbev/msaa123
  • dc.identifier.issn 0737-4038
  • dc.identifier.uri http://hdl.handle.net/10230/45512
  • dc.language.iso eng
  • dc.publisher Oxford University Press (OUP)
  • dc.relation.ispartof Molecular Biology and Evolution. 2020 Oct 1;37(10):2857-64
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/637591
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/740041
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/608959
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-89201-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/ PGC2018-099392-A-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/RYC-2016-20089
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-74961-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-81887-REDT/AEI
  • dc.rights © María Touceda -Suárez et al. 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium,provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
  • dc.subject.other Genòmica
  • dc.subject.other Genètica
  • dc.subject.other Vertebrats
  • dc.title Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole-genome duplications
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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