ArticleBMC genomics2015
Functionally conserved enhancers with divergent sequences in distant vertebrates.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.HGG advances · 2026Article
- Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse.bioRxiv : the preprint server for biology · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Polygenic basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence.bioRxiv : the preprint server for biology · 2025Article
- Functional characterization of transcriptional enhancers in an Anopheles genetic locus controlling natural resistance to the malaria parasite, Plasmodium falciparum.Epigenetics & chromatin · 2025Article
- Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.Science (New York, N.Y.) · 2023Article
- Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers.Nature communications · 2022Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Enhancer RNAs are an important regulatory layer of the epigenome.Nature structural & molecular biology · 2020Review
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Transposable elements are the primary source of novelty in primate gene regulation.Genome research · 2017Article
- Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas.Nature medicine · 2017Article
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Authors and funding
8 authors.
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Abstract
backgroundTo examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.
resultsWe searched for sequences that were conserved within groups of closely related species but not between groups of more distant species, and were associated with an epigenetic mark of enhancer activity. To facilitate inferring orthology between non-conserved sequences, we limited our search to introns whose orthology could be unambiguously established by mapping the bracketing exons. We show that a subset of these non-conserved but syntenic sequences from the mouse and zebrafish genomes have homologous functions in a zebrafish transgenic enhancer assay. The conserved expression patterns driven by these enhancers are probably associated with short transcription factor-binding motifs present in the divergent sequences.
conclusionsWe have identified numerous potential enhancers with divergent sequences but a conserved function. These results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution; evidence for selection at the sequence level is not a necessary criterion to define a gene regulatory element.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.