ArticleGenome research2014
Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Conserved sex-biased DNA methylation patterns target key developmental genes and reproductive function in two Poeciliidae species.G3 (Bethesda, Md.) · 2026Article
- Functional genomics analysis of developing zebrafish and human endoderm reveals highly conservedGenome research · 2026Article
- Cell fate specification modes shape transcriptome evolution in the highly conserved spiral cleavage.EMBO reports · 2025Article
- Genetic analysis of medaka fish illuminates conserved and divergent roles of Pax6 in vertebrate eye development.Frontiers in cell and developmental biology · 2024Article
- Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species.Nucleic acids research · 2023Article
- ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect,Frontiers in genetics · 2023Article
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nature genetics · 2022Article
- The revolutionary developmental biology of Wilhelm His, Sr.Biological reviews of the Cambridge Philosophical Society · 2022Review
- Theories, laws, and models in evo-devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2022Review
- The bowfin genome illuminates the developmental evolution of ray-finned fishes.Nature genetics · 2021Article
- Modeling transcriptional regulation of model species with deep learning.Genome research · 2021Article
- Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis.Genome research · 2020Article
- Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions.Nature communications · 2019Article
- EpiAlignment: alignment with both DNA sequence and epigenomic data.Nucleic acids research · 2019Article
- Fluorescent Light Incites a Conserved Immune and Inflammatory Genetic Response within Vertebrate Organs (Genes · 2019Article
- Article
- Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development.Nature communications · 2018Article
- Evolutionary emergence of theProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies.Evolution letters · 2018Article
- CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments.Biology direct · 2016Article
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11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer's formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115-200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan.
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