Journal
NATURE
Volume 564, Issue 7734, Pages 64-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41586-018-0734-6
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Funding
- European Research Council (ERC) under the European Union [ERC-AdG-LS8-740041, ERC-StG-LS2-637591, 658521, FP7/2007-2013-ERC-268513]
- Spanish Ministerio de Economia y Competitividad [BFU2016-74961-P, RYC-2016-20089, BFU2014-55076-P, BFU2017-89201-P, BFU2014-55738-REDT]
- People Program (Marie Curie Actions) of the European Union's Seventh Framework Program FP7 under REA [607142]
- CNRS
- ANR [ANR16-CE12-0008-01]
- Australian Research Council Discovery Early Career Researcher Award (DECRA) [DE140101962]
- CERCA Programme/Generalitat de Catalunya
- Spanish Ministry of Economy, Industry and Competitiveness (MEIC)
- Centro de Excelencia Severo Ochoa 2013-2017 [SEV-2012-0208]
- Unidad de Excelencia Maria de Maetzu 2017-2021 [MDM-2016-0687]
- Australian Research Council [DE140101962] Funding Source: Australian Research Council
- Marie Curie Actions (MSCA) [658521] Funding Source: Marie Curie Actions (MSCA)
- BBSRC [BB/L00741X/1] Funding Source: UKRI
- MRC [MC_UP_1102/1] Funding Source: UKRI
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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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