Amphioxus functional genomics and the origins of vertebrate gene regulation
Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
MC_UP_1102/1
Medical Research Council - United Kingdom
PubMed
30464347
PubMed Central
PMC6292497
DOI
10.1038/s41586-018-0734-6
PII: 10.1038/s41586-018-0734-6
Knihovny.cz E-zdroje
- MeSH
- anotace sekvence MeSH
- genomika * MeSH
- kopinatci embryologie genetika MeSH
- lidé MeSH
- metylace DNA MeSH
- obratlovci genetika MeSH
- promotorové oblasti (genetika) MeSH
- regulace genové exprese * MeSH
- rozvržení tělního plánu genetika MeSH
- transkriptom genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn Napoli Naples Italy
Biomedical Sciences Research Complex School of Biology University of St Andrews St Andrews UK
Centre for Genomic Regulation Barcelona Spain
Computational Regulatory Genomics MRC London Institute of Medical Sciences London UK
Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH USA
Department of Zoology University of Cambridge Cambridge UK
Department of Zoology University of Oxford Oxford UK
Harry Perkins Institute of Medical Research Nedlands Western Australia Australia
Institut de Biologie de l'ENS IBENS Ecole Normale Supérieure Paris France
Institute of Cellular and Organismic Biology Academia Sinica Taipei Taiwan
Institute of Clinical Sciences Faculty of Medicine Imperial College London London UK
Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic
Laboratoire de Biométrie et Biologie Evolutive CNRS and Université Lyon 1 Villeurbanne France
Laboratory for Transcriptome Technology RIKEN Center for Integrative Medical Sciences Yokohama Japan
RIKEN Center for Life Science Technologies Yokohama Japan
Sars International Centre for Marine Molecular Biology University of Bergen Bergen Norway
School of Life Sciences Beijing University of Chinese Medicine Beijing China
State Key Laboratory of Biocontrol School of Life Sciences Sun Yat sen University Guangzhou China
The Scottish Oceans Institute Gatty Marine Laboratory University of St Andrews St Andrews UK
UMR 9002 CNRS Institut de Génétique Humaine Université de Montpellier Montpellier France
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Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
ExOrthist: a tool to infer exon orthologies at any evolutionary distance