Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marlétaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry, Christopher D.R. Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael D. Acemel, Simon J. van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna KozmikovaJon Permanyer, Alexandra Louis, Beatriz Albuixech-Crespo, Yann Le Petillon, Anthony Leon, Lucie Subirana, Piotr J. Balwierz, Paul Edward Duckett, Ensieh Farahani, Jean Marc Aury, Sophie Mangenot, Patrick Wincker, Ricard Albalat, Èlia Benito-Gutiérrez, Cristian Cañestro, Filipe Castro, Salvatore D’Aniello, David E.K. Ferrier, Shengfeng Huang, Vincent Laudet, Gabriel A.B. Marais, Pierre Pontarotti, Michael Schubert, Hervé Seitz, Ildiko Somorjai, Tokiharu Takahashi, Olivier Mirabeau, Anlong Xu, Jr Kai Yu, Piero Carninci, Juan Ramon Martinez-Morales, Hugues Roest Crollius, Zbynek Kozmik, Matthew T. Weirauch, Jordi Garcia-Fernàndez, Ryan Lister, Boris Lenhard, Peter W.H. Holland, Hector Escriva, Jose Luis Gómez-Skarmeta, Manuel Irimia

Research output: Contribution to journalArticlepeer-review

159 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)64-70
Number of pages7
JournalNature
Volume564
Issue number7734
DOIs
Publication statusPublished - 6 Dec 2018

Fingerprint

Dive into the research topics of 'Amphioxus functional genomics and the origins of vertebrate gene regulation'. Together they form a unique fingerprint.

Cite this