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dc.contributor.authorMarletaz, Ferdinand
dc.contributor.authorFirbas, Panos
dc.contributor.authorMaeso, Ignacio
dc.contributor.authorTena, Juan
dc.contributor.authorBogdanovic, Ozren
dc.contributor.authorPerry, Malcolm
dc.contributor.authorWyatt, Chris
dc.contributor.authorde la Calle-Mustienes, Elisa
dc.contributor.authorBertrand, Stephanie
dc.contributor.authorBurguera, Demian
dc.contributor.authorAcemel, Rafael
dc.contributor.authorvan Heeringen, Simon
dc.contributor.authorNaranjo, Silvia
dc.contributor.authorHerrera-Ubeda, Carlos
dc.contributor.authorSkvortsova, Ksenia
dc.contributor.authorJimenez-Gancedo, Sandra
dc.contributor.authorAldea, Daniel
dc.contributor.authorMarquez, Yamile
dc.contributor.authorBuono, Lorena
dc.contributor.authorKozmikova, Iryna
dc.contributor.authorPermanyer, Jon
dc.contributor.authorLouis, Alexandra
dc.contributor.authorAlbuixech-Crespo, Beatriz
dc.contributor.authorLe Petillon, Yann
dc.contributor.authorLeon Florian, Anthony
dc.contributor.authorSubirana, Lucie
dc.contributor.authorBalwierz, Piotr J.
dc.contributor.authorDuckett, Paul
dc.contributor.authorFarahani, Ensieh
dc.contributor.authorAury, Jean Marc
dc.contributor.authorMangenot, Sophie
dc.contributor.authorWincker, Patrick
dc.contributor.authorAlbalat, Ricard
dc.contributor.authorBenito-Gutierrez, Elia
dc.contributor.authorCanestro, Cristian
dc.contributor.authorCastro, Filipe
dc.contributor.authorD'Aniello, Salvatore
dc.contributor.authorFerrier, David Ellard Keith
dc.contributor.authorHuang, Shengfeng
dc.contributor.authorLaudet, Vincent
dc.contributor.authorMarais, Gabriel
dc.contributor.authorPontarotti, Pierre
dc.contributor.authorSchubert, Michael
dc.contributor.authorSeitz, Herve
dc.contributor.authorSomorjai, Ildiko Maureen Lara
dc.contributor.authorTakahashi, Tokiharu
dc.contributor.authorMirabeau, Olivier
dc.contributor.authorXu, Anlong
dc.contributor.authorYu, Jr-Kai
dc.contributor.authorCarninci, Piero
dc.contributor.authorMartinez-Morales, Juan
dc.contributor.authorCrollius, Hugues
dc.contributor.authorKozmik, Zbynek
dc.contributor.authorWeirauch, Matt
dc.contributor.authorGarcia-Fernandez, Jordi
dc.contributor.authorLister, Ryan
dc.contributor.authorLenhard, Boris
dc.contributor.authorHolland, Peter
dc.contributor.authorEscriva, Hector
dc.contributor.authorGomez-Skarmeta, Jose Luis
dc.contributor.authorIrimia, Manuel
dc.identifier.citationMarletaz , F , Firbas , P , Maeso , I , Tena , J , Bogdanovic , O , Perry , M , Wyatt , C , de la Calle-Mustienes , E , Bertrand , S , Burguera , D , Acemel , R , van Heeringen , S , Naranjo , S , Herrera-Ubeda , C , Skvortsova , K , Jimenez-Gancedo , S , Aldea , D , Marquez , Y , Buono , L , Kozmikova , I , Permanyer , J , Louis , A , Albuixech-Crespo , B , Le Petillon , Y , Leon Florian , A , Subirana , L , Balwierz , P J , Duckett , P , Farahani , E , Aury , J M , Mangenot , S , Wincker , P , Albalat , R , Benito-Gutierrez , E , Canestro , C , Castro , F , D'Aniello , S , Ferrier , D E K , Huang , S , Laudet , V , Marais , G , Pontarotti , P , Schubert , M , Seitz , H , Somorjai , I M L , Takahashi , T , Mirabeau , O , Xu , A , Yu , J-K , Carninci , P , Martinez-Morales , J , Crollius , H , Kozmik , Z , Weirauch , M , Garcia-Fernandez , J , Lister , R , Lenhard , B , Holland , P , Escriva , H , Gomez-Skarmeta , J L & Irimia , M 2018 , ' Amphioxus functional genomics and the origins of vertebrate gene regulation ' , Nature , vol. 564 , no. 7734 , pp. 64-70 .
dc.identifier.otherPURE: 256331628
dc.identifier.otherPURE UUID: da3789be-c515-49c1-a1db-2a3fec7625e2
dc.identifier.otherScopus: 85057742554
dc.identifier.otherORCID: /0000-0003-3247-6233/work/51010288
dc.identifier.otherORCID: /0000-0001-5243-6664/work/51010299
dc.identifier.otherWOS: 000452269400041
dc.descriptionThis research was funded primarily by the European Research Council (ERC) under the European Union’s Horizon 2020 and Seventh Framework Program FP7 research and innovation programs (ERC-AdG-LS8-740041 to J.L.G.-S., ERC-StG-LS2-637591 to M.I., a Marie Sklodowska-Curie Grant (658521) to I.M. and a FP7/2007-2013-ERC-268513 to P.W.H.H.), the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P to J.L.G.-S., RYC-2016-20089 to I.M., BFU2014-55076-P and BFU2017-89201-P to M.I. and BFU2014-55738-REDT to J.L.G.-S, M.I. and J.R.M.-M), the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208), the ‘Unidad de Excelencia María de Maetzu 2017-2021’(MDM-2016-0687), the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program FP7 under REA grant agreement number 607142 (DevCom) to J.L.G.-S., and the CNRS and the ANR (ANR16-CE12-0008-01) to H.E. O.B. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA; DE140101962). 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. Additional sources of funding for all authors are listed in Supplementary Information.en
dc.description.abstractVertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.
dc.rightsCopyright © 2018 The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
dc.subjectQH426 Geneticsen
dc.titleAmphioxus functional genomics and the origins of vertebrate gene regulationen
dc.typeJournal articleen
dc.contributor.sponsorEuropean Commissionen
dc.contributor.sponsorThe Leverhulme Trusten
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.contributor.institutionUniversity of St Andrews. Marine Alliance for Science & Technology Scotlanden
dc.contributor.institutionUniversity of St Andrews. Scottish Oceans Instituteen
dc.contributor.institutionUniversity of St Andrews. Biomedical Sciences Research Complexen
dc.description.statusPeer revieweden

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