Amphioxus functional genomics and the origins of vertebrate gene regulation

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Title: Amphioxus functional genomics and the origins of vertebrate gene regulation
Authors: Marletaz, F
Firbas, PN
Maeso, I
Tena, JJ
Bogdanovic, O
Perry, M
Wyatt, CDR
De la Calle-Mustienes, E
Bertrand, S
Burguera, D
Acemel, RD
Van Heeringen, SJ
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, A
Subirana, L
Balwierz, PJ
Duckett, PE
Farahani, E
Aury, J-M
Mangenot, S
Wincker, P
Albalat, R
Benito-Gutierrez, E
Canestro, C
Castro, F
D'Aniello, S
Ferrier, DEK
Huang, S
Laudet, V
Marais, GAB
Pontarotti, P
Schubert, M
Seitz, H
Somorjai, I
Takahashi, T
Mirabeau, O
Xu, A
Yu, J-K
Carninci, P
Ramon Martinez-Morales, J
Crollius, HR
Kozmik, Z
Weirauch, MT
Garcia-Fernandez, J
Lister, R
Lenhard, B
Holland, PWH
Escriva, H
Luis Gomez-Skarmeta, J
Irimia, M
Item Type: Journal Article
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.
Issue Date: 6-Dec-2018
Date of Acceptance: 18-Oct-2018
ISSN: 0028-0836
Publisher: Nature Research
Start Page: 64
End Page: 70
Journal / Book Title: Nature
Volume: 564
Copyright Statement: © 2018 The Authors. 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
Sponsor/Funder: Commission of the European Communities
Biotechnology and Biological Sciences Research Council (BBSRC)
Wellcome Trust
Funder's Grant Number: 242048
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
MD Multidisciplinary
General Science & Technology
Publication Status: Published
Open Access location:
Online Publication Date: 2018-11-21
Appears in Collections:Clinical Sciences
Molecular Sciences

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