Amphioxus functional genomics and the origins of vertebrate gene regulation
Ferdinand Marletaz
(1, 2)
,
Panos N. Firbas
(3)
,
Ignacio Maeso
(3)
,
Juan J. Tena
(3)
,
Ozren Bogdanovic
(4, 5)
,
Malcolm Perry
(6)
,
Christopher D. R. Wyatt
(7)
,
Elisa de La Calle-Mustienes
(3)
,
Stephanie Bertrand
(8)
,
Demian Burguera
(9)
,
Rafael D. Acemel
(10)
,
Simon J. Van Heeringen
(11)
,
Silvia Naranjo
(10)
,
Carlos Herrera-Ubeda
(12)
,
Ksenia Skvortsova
(13)
,
Sandra Jimenez-Gancedo
(10)
,
Daniel Aldea
(8)
,
Yamile Marquez
(9)
,
Lorena Buono
(10)
,
Iryna Kozmikova
(14)
,
Jon Permanyer
(9)
,
Alexandra Louis
(15)
,
Beatriz Albuixech-Crespo
(12)
,
Yann Le Petillon
(8)
,
Anthony Leon
(8)
,
Lucie Subirana
(8)
,
Piotr J. Balwierz
(6)
,
Paul Edward Duckett
(13)
,
Ensieh Farahani
(10)
,
Jean-Marc Aury
(16)
,
Sophie Mangenot
(17)
,
Patrick Wincker
(17)
,
Ricard Albalat
(18)
,
Elia Benito-Gutierrez
(19)
,
Cristian Canestro
(18)
,
Filipe Castro
(20)
,
Salvatore d'Aniello
(21)
,
David E. K. Ferrier
(22)
,
Shengfeng Huang
(23)
,
Vincent Laudet
(8)
,
Gabriel A. B. Marais
(24)
,
Pierre Pontarotti
(25)
,
Michael Schubert
(26)
,
Herve Seitz
(27)
,
Ildiko Somorjai
(22)
,
Tokiharu Takahashi
(28)
,
Olivier Mirabeau
(29)
,
Anlong Xu
(23)
,
Jr-Kai Yu
(30)
,
Piero Carninci
(31)
,
Juan Ramon Martinez-Morales
(10)
,
Hugues Roest Crollius
(15)
,
Zbynek Kozmik
(14)
,
Matthew T. Weirauch
(32)
,
Jordi Garcia-Fernandez
(12)
,
Ryan Lister
(5)
,
Boris Lenhard
(6, 33)
,
Peter W. H. Holland
(34)
,
Hector Escriva
(8)
,
Jose Luis Gomez-Skarmeta
(10)
,
Manuel Irimia
(9, 7)
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
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
Stephanie Bertrand
- Fonction : Auteur
- PersonId : 737130
- IdHAL : stephaniebertrandescriva
- ORCID : 0000-0002-0689-0126
- IdRef : 189498889
Alexandra Louis
- Fonction : Auteur
- PersonId : 748563
- IdHAL : alexandra-louis
- ORCID : 0000-0001-7032-5650
- IdRef : 067130488
Jean-Marc Aury
- Fonction : Auteur
- PersonId : 756899
- IdHAL : jean-marc-aury
- ORCID : 0000-0003-1718-3010
Patrick Wincker
- Fonction : Auteur
- PersonId : 757160
- IdHAL : patrick-wincker
- ORCID : 0000-0001-7562-3454
Gabriel A. B. Marais
- Fonction : Auteur
- PersonId : 178781
- IdHAL : gabriel-marais
- ORCID : 0000-0003-2134-5967
- IdRef : 069939527
Pierre Pontarotti
- Fonction : Auteur
- PersonId : 741162
- IdHAL : pontarotti
- ORCID : 0000-0001-7202-3648
- IdRef : 14869196X
Michael Schubert
- Fonction : Auteur
- PersonId : 174777
- IdHAL : michael-schubert
- ORCID : 0000-0002-2341-712X
- IdRef : 155401750
Herve Seitz
- Fonction : Auteur
- PersonId : 179402
- IdHAL : herve-seitz
- ORCID : 0000-0001-8172-5393
- IdRef : 08373838X
Ildiko Somorjai
- Fonction : Auteur
- PersonId : 755509
- ORCID : 0000-0003-3956-7541
Olivier Mirabeau
- Fonction : Auteur
- PersonId : 940863
- IdHAL : olivier-mirabeau
- ORCID : 0000-0002-4048-1385
Hugues Roest Crollius
- Fonction : Auteur
- PersonId : 175223
- IdHAL : hugues-roest-crollius
- ORCID : 0000-0002-8209-173X
- IdRef : 134614461
Hector Escriva
- Fonction : Auteur
- PersonId : 740114
- IdHAL : hector-escriva
- ORCID : 0000-0001-7577-5028
- IdRef : 155403885
Résumé
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.
Domaines
Maladies infectieuses| Origine | Fichiers éditeurs autorisés sur une archive ouverte |
|---|
Loading...
