Please use this identifier to cite or link to this item: https://hdl.handle.net/10216/120382
Author(s): Marlétaz F.
Firbas P.N.
Maeso I.
Tena J.J.
Bogdanovic O.
Perry M.
Wyatt C.D.R.
de la Calle-Mustienes E.
Bertrand S.
Burguera D.
Acemel R.D.
van Heeringen S.J.
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 P.J.
Duckett P.E.
Farahani E.
Aury J.-M.
Mangenot S.
Wincker P.
Albalat R.
Benito-Gutiérrez È.
Cañestro C.
Castro F.
D’Aniello S.
Ferrier D.E.K.
Huang S.
Laudet V.
Marais G.A.B.
Pontarotti P.
Schubert M.
Seitz H.
Somorjai I.
Takahashi T.
Mirabeau O.
Xu A.
Yu J.-K.
Carninci P.
Martinez-Morales J.R.
Crollius H.R.
Kozmik Z.
Weirauch M.T.
Garcia-Fernàndez J.
Lister R.
Lenhard B.
Holland P.W.H.
Escriva H.
Gómez-Skarmeta J.L.
Irimia M.
Title: Amphioxus functional genomics and the origins of vertebrate gene regulation
Publisher: Nature Publishing Group
Issue Date: 2018
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. © 2018, Springer Nature Limited.
Subject: transcriptome
comparative study
developmental stage
evolution
gene
gene expression
genetic analysis
genomics
innovation
invertebrate
specialization
vertebrate
adult
animal cell
animal tissue
Article
Branchiostoma
chromatin
controlled study
developmental stage
DNA methylation
embryo
embryo development
female
functional genomics
gene control
gene duplication
gene expression
gene sequence
genome
histone modification
male
molecular genetics
mouse
multigene family
nonhuman
priority journal
zebra fish
Branchiostoma lanceolatum
Vertebrata
URI: https://hdl.handle.net/10216/120382
Source: Nature, vol. 564(7734), p. 64-70
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:CIIMAR - Artigo em Revista Científica Internacional

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