ArticleNucleic acids research2020
Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes.bioRxiv : the preprint server for biology · 2026Article
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.iScience · 2025Article
- Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS.Bioinformatics (Oxford, England) · 2024Article
- Green synthesis of chlorella-derived carbon dots and their fluorescence imaging in zebrafish.RSC advances · 2024Article
- From sequence to consequence: Deciphering the complex cisregulatory landscape.Journal of biosciences · 2024Article
- Zebrafish regulatory genomic resources for disease modelling and regeneration.Disease models & mechanisms · 2023Article
- Tracking Targets of Dynamic Super-EnhancersEnvironmental health perspectives · 2023Article
- Review
- A unifying statistical framework to discover disease genes from GWASs.Cell genomics · 2023Article
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nature genetics · 2022Article
- Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.Genome biology · 2022Article
- Classification of non-coding variants with high pathogenic impact.PLoS genetics · 2022Article
- Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness.Genome research · 2022Article
- Review
- Role of Non-Coding Regulatory Elements in the Control of GR-Dependent Gene Expression.International journal of molecular sciences · 2021Article
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
- The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations.Current biology : CB · 2021Article
- Heart Enhancers: Development and Disease Control at a Distance.Frontiers in genetics · 2021Review
- Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.Nature communications · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The spatiotemporal expression of genes is controlled by enhancer sequences that bind transcription factors. Identifying the target genes of enhancers remains difficult because enhancers regulate gene expression over long genomic distances. To address this, we used an evolutionary approach to build two genome-wide maps of predicted enhancer-gene associations in the human and zebrafish genomes. Evolutionary conserved sequences were linked to their predicted target genes using PEGASUS, a bioinformatics method that relies on evolutionary conservation of synteny. The analysis of these maps revealed that the number of predicted enhancers linked to a gene correlate with its expression breadth. Comparison of both maps identified hundreds of putative vertebrate ancestral regulatory relationships from which we could determine that predicted enhancer-gene distances scale with genome size despite strong positional conservation. The two maps represent a resource for further studies, including the prioritization of sequence variants in whole genome sequence of patients affected by genetic diseases.
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