Skip to content

Research at St Andrews

Amphioxus functional genomics and the origins of vertebrate gene regulation

Research output: Contribution to journalArticle

Author(s)

Ferdinand Marletaz, Panos Firbas, Ignacio Maeso, Juan Tena, Ozren Bogdanovic, Malcolm Perry, Chris Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael Acemel, Simon van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna Kozmikova & 41 others Jon Permanyer, Alexandra Louis, Beatriz Albuixech-Crespo, Yann Le Petillon, Anthony Leon Florian, Lucie Subirana, Piotr J. Balwierz, Paul Duckett, Ensieh Farahani, Jean Marc Aury, Sophie Mangenot, Patrick Wincker, Ricard Albalat, Elia Benito-Gutierrez, Cristian Canestro, Filipe Castro, Salvatore D'Aniello, David Ellard Keith Ferrier, Shengfeng Huang, Vincent Laudet, Gabriel Marais, Pierre Pontarotti, Michael Schubert, Herve Seitz, Ildiko Maureen Lara Somorjai, Tokiharu Takahashi, Olivier Mirabeau, Anlong Xu, Jr-Kai Yu, Piero Carninci, Juan Martinez-Morales, Hugues Crollius, Zbynek Kozmik, Matt Weirauch, Jordi Garcia-Fernandez, Ryan Lister, Boris Lenhard, Peter Holland, Hector Escriva, Jose Luis Gomez-Skarmeta, Manuel Irimia

School/Research organisations

Abstract

Vertebrates 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.
Close

Details

Original languageEnglish
Pages (from-to)64-70
Number of pages29
JournalNature
Volume564
Issue number7734
DOIs
StatePublished - 21 Nov 2018

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage

    Barton-Owen, T., Ferrier, D. E. K. & Somorjai, I. M. L. 20 Jun 2018 In : Scientific Reports. 8, 11 p., 9414

    Research output: Contribution to journalArticle

  2. Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

    Szabó, R. & Ferrier, D. E. K. 27 Dec 2018 In : BMC Evolutionary Biology. 18, 13 p., 203

    Research output: Contribution to journalArticle

  3. Transcriptional regulation of the Ciona Gsx gene in the neural plate

    Hudson, C., Esposito, R., Palladino, A., Staiano, L., Ferrier, D., Faure, E., Lemaire, P., Yasuo, H. & Spagnuolo, A. 21 Dec 2018 In : Developmental Biology. In press

    Research output: Contribution to journalArticle

  4. The evolution of ependymin-related proteins

    McDougall, C., Hammond, M., Dailey, S. C., Somorjai, I. M. L., Cummins, S. & Degnan, B. 4 Dec 2018 In : BMC Evolutionary Biology. 18, 13 p., 182

    Research output: Contribution to journalArticle

Related by journal

  1. Nature (Journal)

    Cresswell, W. (Reviewer)
    21 Dec 2017

    Activity: Publication peer-review and editorial workPeer review of manuscripts

  2. Nature (Journal)

    Cresswell, W. (Reviewer)
    11 Nov 2017

    Activity: Publication peer-review and editorial workPeer review of manuscripts

  3. Nature (Journal)

    Dritschel, D. G. (Editor)
    2005 → …

    Activity: Publication peer-review and editorial workEditor of research journal

  4. Nature (Journal)

    Samuel, I. D. W. (Editor)
    2005 → …

    Activity: Publication peer-review and editorial workEditor of research journal

Related by journal

  1. An absolute sodium abundance for a cloud-free 'hot Saturn' exoplanet

    Nikolov, N. , Sing, D. K. , Fortney, J. J. , Goyal, J. M. , Drummond, B. , Evans, T. M. , Gibson, N. P. , De Mooj, E. J. W. , Rustamkulov, Z. , Wakeford, H. R. , Smalley, B. , Burgasser, A. J. , Hellier, C. , Helling, C. , Mayne, N. J. , Madhusudhan, N. , Kataria, T. , Baines, J. , Carter, A. L. , Ballester, G. E. & 3 others Barstow, J. K., McCleery, J. & Spake, J. J. 7 May 2018 In : Nature. 557, p. 526-529

    Research output: Contribution to journalArticle

  2. CO2 storage and release in the deep Southern Ocean on millennial to centennial timescales

    Rae, J. W. B., Burke, A., Robinson, L. F., Adkins, J. F., Chen, T., Cole, C., Greenop, R., Li, T., Littley, E., Nita, D. C., Stewart, J. A. & Taylor, B. 24 Oct 2018 In : Nature. 562, p. 569-573

    Research output: Contribution to journalLetter

  3. Does the galaxy NGC1052-DF2 falsify Milgromian dynamics?

    Kroupa, P., Haghi, H., Javanmardi, B., Zonoozi, A. H., Müller, O., Banik, I., Wu, X., Zhao, H. & Dabringhausen, J. 12 Sep 2018 In : Nature. 561, p. E4-E5 2 p.

    Research output: Contribution to journalComment/debate

  4. Exciton-polariton topological insulator

    Klembt, S., Harder, T. H., Egorov, O. A., Winkler, K., Ge, R., Bandres, M. A., Emmerling, M., Worschech, L., Liew, T. C. H., Segev, M., Schneider, C. & Höfling, S. 8 Oct 2018 In : Nature. 16 p.

    Research output: Contribution to journalArticle

ID: 256331628