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Amphioxus functional genomics and the origins of vertebrate gene regulation
Bibliographic Information
- Other Title
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- Amphioxus functional genomics and the origins of vertebrate gene duplication.
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Description
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.
Journal
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- Nature
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Nature 564 (7734), 64-70, 2018-11-21
Nature Research
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Keywords
- CHROMATIN
- Epigenomics
- genetic analysis
- animal cell
- Branchiostoma Lanceolatum
- specialization
- [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
- vertebrate
- zebra fish
- Vertebrats
- histone modification
- Branchiostoma lanceolatum
- Promoter Regions, Genetic
- comparative study
- Whole-genome Duplication (WGD)
- Lancelets
- DNA methylation
- adult
- Functional genomics
- gene control
- Genomics
- BRANCHIOSTOMA-LANCEOLATUM
- innovation
- Multidisciplinary Sciences
- Phylotypic period
- female
- SEQ
- priority journal
- Vertebrates
- Science & Technology - Other Topics
- Molecular Developmental Biology
- Whole-genome duplications
- LANDSCAPES
- Phylotypic Period
- functional genomics
- General Science & Technology
- invertebrate
- CONSERVATION
- embryo
- 612
- QH426 Genetics
- gene sequence
- PLURIPOTENCY
- Article
- animal tissue
- Promoter Regions
- DNA DEMETHYLATION
- Genetic
- male
- evolution
- genomics
- Animals
- Humans
- controlled study
- gene
- QH426
- Branchiostoma
- genome
- mouse
- multigene family
- Body Patterning
- Vertebrata
- nonhuman
- Science & Technology
- Amphioxus
- ZEBRAFISH
- gene duplication
- 940
- DAS
- embryo development
- Molecular Sequence Annotation
- TRANSGENESIS
- DNA Methylation
- Ancestral expression
- EVOLUTION
- developmental stage
- Amfiox
- Gene Expression Regulation
- molecular genetics
- gene expression
- chromatin
- Molecular evolution
- Transcriptome
- transcriptome
Details 詳細情報について
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- CRID
- 1050282677683902720
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- NII Article ID
- 120006647254
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- ISSN
- 00280836
- 14764687
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- PubMed
- 30464347
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- Text Lang
- en
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- Article Type
- journal article
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- Data Source
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- IRDB
- Crossref
- CiNii Articles
- OpenAIRE