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Amphioxus functional genomics and the origins of vertebrate gene regulation
- Source :
- Nature, Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩, Recercat. Dipósit de la Recerca de Catalunya, instname, Nature, Nature Publishing Group, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩, Nature, 564, pp. 64-70, Digital.CSIC. Repositorio Institucional del CSIC, Dipòsit Digital de la UB, Universidad de Barcelona, Repositório Científico de Acesso Aberto de Portugal, Repositório Científico de Acesso Aberto de Portugal (RCAAP), instacron:RCAAP, Digital.CSIC: Repositorio Institucional del CSIC, Consejo Superior de Investigaciones Científicas (CSIC), Nature, 564, 64-70, Takahashi, T & al, E 2018, ' Amphioxus functional genomics and the origins of vertebrate gene regulation ', Nature, vol. 564, pp. 64-70 . https://doi.org/10.1038/s41586-018-0734-6
- Publication Year :
- 2018
- Publisher :
- HAL CCSD, 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.<br />This research was funded primarily by the European Research Council (ERC) under the European Union’s Horizon 2020 and Seventh Framework Program FP7 research and innovation programs (ERC-AdG-LS8-740041 to J.L.G.-S., ERC-StG-LS2-637591 to M.I., a Marie Sklodowska-Curie Grant (658521) to I.M. and a FP7/2007-2013-ERC-268513 to P.W.H.H.), the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P to J.L.G.-S., RYC-2016-20089 to I.M., BFU2014-55076-P and BFU2017-89201-P to M.I. and BFU2014-55738-REDT to J.L.G.-S, M.I. and J.R.M.-M), the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208), the ‘Unidad de Excelencia María de Maetzu 2017-2021’(MDM-2016-0687), the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program FP7 under REA grant agreement number 607142 (DevCom) to J.L.G.-S., and the CNRS and the ANR (ANR16-CE12-0008-01) to H.E. O.B. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA; DE140101962).
- Subjects :
- Epigenomics
Branchiostoma
genetic analysis
animal cell
transcriptomics
0302 clinical medicine
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
vertebrate
zebra fish
histone modification
Branchiostoma lanceolatum
ComputingMilieux_MISCELLANEOUS
comparative study
Lancelets
Regulation of gene expression
DDC model
DNA methylation
adult
Vertebrate
Genomics
priority journal
Science & Technology - Other Topics
Molecular Developmental Biology
LANDSCAPES
whole genome duplication
Functional genomics
chordate evolution
CONSERVATION
embryo
gene sequence
PLURIPOTENCY
Article
animal tissue
03 medical and health sciences
regulatory genomics
biology.animal
genomics
Humans
genome
mouse
Science & Technology
Molecular Sequence Annotation
TRANSGENESIS
DNA Methylation
Ancestral expression
developmental stage
030104 developmental biology
hourglass model
Amfiox
Evolutionary biology
molecular genetics
chromatin
Subfunctionalization
transcriptome
030217 neurology & neurosurgery
CHROMATIN
0301 basic medicine
Branchiostoma Lanceolatum
Genome
specialization
Gene duplication
Vertebrats
Promoter Regions, Genetic
Whole-genome Duplication (WGD)
Multidisciplinary
gene control
BRANCHIOSTOMA-LANCEOLATUM
innovation
Multidisciplinary Sciences
female
SEQ
Vertebrates
[SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Phylotypic Period
General Science & Technology
invertebrate
QH426 Genetics
Biology
DNA DEMETHYLATION
male
evolution
Animals
controlled study
gene
QH426
multigene family
Body Patterning
Vertebrata
nonhuman
Amphioxus
ZEBRAFISH
gene duplication
embryo development
DAS
biology.organism_classification
EVOLUTION
[SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis
Gene Expression Regulation
gene expression
Molecular evolution
Transcriptome
Subjects
Details
- Language :
- English
- ISSN :
- 00280836, 14764687, and 14764679
- Database :
- OpenAIRE
- Journal :
- Nature, Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩, Recercat. Dipósit de la Recerca de Catalunya, instname, Nature, Nature Publishing Group, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩, Nature, 564, pp. 64-70, Digital.CSIC. Repositorio Institucional del CSIC, Dipòsit Digital de la UB, Universidad de Barcelona, Repositório Científico de Acesso Aberto de Portugal, Repositório Científico de Acesso Aberto de Portugal (RCAAP), instacron:RCAAP, Digital.CSIC: Repositorio Institucional del CSIC, Consejo Superior de Investigaciones Científicas (CSIC), Nature, 564, 64-70, Takahashi, T & al, E 2018, ' Amphioxus functional genomics and the origins of vertebrate gene regulation ', Nature, vol. 564, pp. 64-70 . https://doi.org/10.1038/s41586-018-0734-6
- Accession number :
- edsair.doi.dedup.....4beca909ac1323255e03fa32b70757ff