ArticleBMC genomics2013
Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes.Genome biology · 2025Article
- Cis-regulatory control of mammalian Trps1 gene expression.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2024Article
- Identification of ancestral gnathostome Gli3 enhancers with activity in mammals.Development, growth & differentiation · 2024Article
- Advancing human disease research with fish evolutionary mutant models.Trends in genetics : TIG · 2022Review
- Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers.Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.Genome biology · 2019Article
- Dichotomy in redundant enhancers points to presence of initiators of gene regulation.BMC genomics · 2018Article
- Diversification of four human HOX gene clusters by step-wise evolution rather than ancient whole-genome duplications.Development genes and evolution · 2015Review
- The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.Genome biology and evolution · 2015Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
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7 authors.
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Abstract
backgroundHuman genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution.
resultsThis study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Furthermore, we used human-rodent comparison for a set of 159 orthologous enhancer pairs to infer that the central nervous system (CNS) specific gene expression is closely associated with the cooperative interaction among at least eight distinct transcription factors: SOX5, HFH, SOX17, HNF3β, c-FOS, Tal1beta-E47S, MEF and FREAC.
conclusionsIn conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine.
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