Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications

The Author(s) 2020.

Detalles Bibliográficos
Autores: Touceda-Suárez, María, Kita, Elizabeth M., Acemel, Rafael D., Firbas, Panos, Magri, Marta Silvia, Naranjo, Silvia, Tena, Juan J., Gómez-Skarmeta, José Luis, Maeso, Ignacio, Irimia, Manuel
Tipo de recurso: artículo
Fecha de publicación:2020
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/226235
Acceso en línea:http://hdl.handle.net/10261/226235
Access Level:acceso abierto
Palabra clave:Gene deserts
Origin of vertebrates
Genomic regulatory block
Whole-genome duplications
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dc.title.none.fl_str_mv Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
title Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
spellingShingle Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
Touceda-Suárez, María
Gene deserts
Origin of vertebrates
Genomic regulatory block
Whole-genome duplications
title_short Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
title_full Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
title_fullStr Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
title_full_unstemmed Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
title_sort Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
dc.creator.none.fl_str_mv Touceda-Suárez, María
Kita, Elizabeth M.
Acemel, Rafael D.
Firbas, Panos
Magri, Marta Silvia
Naranjo, Silvia
Tena, Juan J.
Gómez-Skarmeta, José Luis
Maeso, Ignacio
Irimia, Manuel
author Touceda-Suárez, María
author_facet Touceda-Suárez, María
Kita, Elizabeth M.
Acemel, Rafael D.
Firbas, Panos
Magri, Marta Silvia
Naranjo, Silvia
Tena, Juan J.
Gómez-Skarmeta, José Luis
Maeso, Ignacio
Irimia, Manuel
author_role author
author2 Kita, Elizabeth M.
Acemel, Rafael D.
Firbas, Panos
Magri, Marta Silvia
Naranjo, Silvia
Tena, Juan J.
Gómez-Skarmeta, José Luis
Maeso, Ignacio
Irimia, Manuel
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Research Council
European Commission
Ministerio de Ciencia, Innovación y Universidades (España)
Generalitat de Catalunya
Ministerio de Economía y Competitividad (España)
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Gene deserts
Origin of vertebrates
Genomic regulatory block
Whole-genome duplications
topic Gene deserts
Origin of vertebrates
Genomic regulatory block
Whole-genome duplications
description The Author(s) 2020.
publishDate 2020
dc.date.none.fl_str_mv 2020
2021
2021
2021
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url http://hdl.handle.net/10261/226235
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dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
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spelling Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome DuplicationsTouceda-Suárez, MaríaKita, Elizabeth M.Acemel, Rafael D.Firbas, PanosMagri, Marta SilviaNaranjo, SilviaTena, Juan J.Gómez-Skarmeta, José LuisMaeso, IgnacioIrimia, ManuelGene desertsOrigin of vertebratesGenomic regulatory blockWhole-genome duplicationsThe Author(s) 2020.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.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.Oxford University PressEuropean Research CouncilEuropean CommissionMinisterio de Ciencia, Innovación y Universidades (España)Generalitat de CatalunyaMinisterio de Economía y Competitividad (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2021202120202021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/226235reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/740041info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/ BFU2017-89201-PBFU2017-89201-P/AEI/10.13039/501100011033info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/RYC-2016-20089info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-099392-A-I00PGC2018-099392-A-I00/AEI/10.13039/501100011033info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2016-74961-Pinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2016-81887-REDTinfo:eu-repo/grantAgreement/EC/FP7/608959info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/MDM-2016-0687http://dx.doi.org/10.1093/molbev/msaa123Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2262352026-05-22T06:33:51Z
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