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Journal Articles Nature Year : 2018

Amphioxus functional genomics and the origins of vertebrate gene regulation

1 OIST - Okinawa Institute of Science and Technology Graduate University
2 Department of Zoology [Oxford]
3 Centro Andaluz de Biología del Desarrollo
4 UNSW - University of New South Wales [Sydney]
5 UWA - The University of Western Australia
6 Imperial College London
7 UPF - Universitat Pompeu Fabra [Barcelona]
8 BIOM - Biologie intégrative des organismes marins
9 BIST - Barcelona Institute of Science and Technology
10 UPO - Universidad Pablo de Olavide [Sevilla]
11 Radboud University [Nijmegen]
12 University of Barcelona
13 Garvan Institute of medical research
14 IMG / CAS - Institute of Molecular Genetics of the Czech Academy of Sciences
15 IBENS - Institut de biologie de l'ENS Paris
16 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
17 UMR 8030 - Génomique métabolique
18 Department of Genetics and IrBio
19 CAM - University of Cambridge [UK]
20 Universidade do Porto = University of Porto
21 SZN - Stazione Zoologica Anton Dohrn
22 University of St Andrews [Scotland]
23 SYSU - Sun Yat-sen University [Guangzhou]
24 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
25 MEPHI - Microbes évolution phylogénie et infections
26 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
27 IGH - Institut de génétique humaine
28 University of Manchester [Manchester]
29 PSL - Université Paris Sciences et Lettres
30 Academia Sinica
31 RIKEN CLST - RIKEN Center for Life Science Technologies
32 UC - University of Cincinnati
33 UiB - University of Bergen
34 University of Oxford
Alexandra Louis
Patrick Wincker
Herve Seitz
Ildiko Somorjai
Jr-Kai Yu
  • Function : Author

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.
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hal-02000511 , version 1 (17-04-2019)

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Ferdinand Marletaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, et al.. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩. ⟨hal-02000511⟩
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