@article{oai:oist.repo.nii.ac.jp:00000934,
 author = {Marlétaz, Ferdinand and Firbas, Panos N. and Maeso, Ignacio and Tena, Juan J. and Bogdanovic, Ozren and Perry, Malcolm and Wyatt, Christopher D. R. and de la Calle-Mustienes, Elisa and Bertrand, Stephanie and Burguera, Demian and Acemel, Rafael D. and van Heeringen, Simon J. and Naranjo, Silvia and Herrera-Ubeda, Carlos and Skvortsova, Ksenia and Jimenez-Gancedo, Sandra and Aldea, Daniel and Marquez, Yamile and Buono, Lorena and Kozmikova, Iryna and Permanyer, Jon and Louis, Alexandra and Albuixech-Crespo, Beatriz and Le Petillon, Yann and Leon, Anthony and Subirana, Lucie and Balwierz, Piotr J. and Duckett, Paul Edward and Farahani, Ensieh and Aury, Jean-Marc and Mangenot, Sophie and Wincker, Patrick and Albalat, Ricard and Benito-Gutiérrez, Èlia and Cañestro, Cristian and Castro, Filipe and D’Aniello, Salvatore and Ferrier, David E. K. and Huang, Shengfeng and Laudet, Vincent and Marais, Gabriel A. B. and Pontarotti, Pierre and Schubert, Michael and Seitz, Hervé and Somorjai, Ildiko and Takahashi, Tokiharu and Mirabeau, Olivier and Xu, Anlong and Yu, Jr-Kai and Carninci, Piero and Martinez-Morales, Juan Ramon and Crollius, Hugues Roest and Kozmik, Zbynek and Weirauch, Matthew T. and Garcia-Fernàndez, Jordi and Lister, Ryan and Lenhard, Boris and Holland, Peter W. H. and Escriva, Hector and Gómez-Skarmeta, Jose Luis and Irimia, Manuel},
 issue = {7734},
 journal = {Nature},
 month = {Nov},
 note = {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.},
 pages = {64--70},
 title = {Amphioxus functional genomics and the origins of vertebrate gene regulation},
 volume = {564},
 year = {2018}
}