ArticleGenome research2012
Coding exons function as tissue-specific enhancers of nearby genes.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
142 citing papers in PubMed.
- Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.Genome biology and evolution · 2026Article
- The G→C rs590352 in the Protein-Coding Region of ATXN7L3B Gene Upregulates Its Expression In Vivo.Biochemical genetics · 2026Article
- Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment.Nature communications · 2026Article
- The exonic SNP rs11676272-C risk allele mediates diet-induced obesity and reduces enhancer activation.EMBO reports · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- Signal control during tissue regeneration in adult animals.Nature reviews. Molecular cell biology · 2026Review
- Distinct precursor landscape of subcutaneous and visceral fat in development and aging.Cell reports · 2026Review
- Introducing the EpGEpigenomes · 2025Article
- MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis.Genes & development · 2025Article
- Prediction of Enhancer RNAs in Chicken Genome.International journal of molecular sciences · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.Science (New York, N.Y.) · 2025Article
- The Function and Regulation of celsr1a in Skeletal Age-associated Homeostasis and Repair in Zebrafish.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
- Article
- Mapping of chromatin architecture and enhancer-promoter interactions in the cochlea.Frontiers in molecular biosciences · 2025Article
- Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14).Leukemia · 2025Article
- The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence.Science advances · 2024Article
- A Foxf1-Wnt-Nr2f1 cascade promotes atrial cardiomyocyte differentiation in zebrafish.PLoS genetics · 2024Article
- Article
- A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.BMC medical genomics · 2024Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
Enhancers are essential gene regulatory elements whose alteration can lead to morphological differences between species, developmental abnormalities, and human disease. Current strategies to identify enhancers focus primarily on noncoding sequences and tend to exclude protein coding sequences. Here, we analyzed 25 available ChIP-seq data sets that identify enhancers in an unbiased manner (H3K4me1, H3K27ac, and EP300) for peaks that overlap exons. We find that, on average, 7% of all ChIP-seq peaks overlap coding exons (after excluding for peaks that overlap with first exons). By using mouse and zebrafish enhancer assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enhancers of their neighboring genes and that the exonic sequence is necessary for enhancer activity. Using ChIP, 3C, and DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhancer marks and physically interacts with Dlx5/6 promoter regions 900 kb away. In addition, its removal by chromosomal abnormalities in humans could cause split hand and foot malformation 1 (SHFM1), a disorder associated with DLX5/6. These results demonstrate that DNA sequences can have a dual function, operating as coding exons in one tissue and enhancers of nearby gene(s) in another tissue, suggesting that phenotypes resulting from coding mutations could be caused not only by protein alteration but also by disrupting the regulation of another gene.
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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.