Article

Coding exons function as tissue-specific enhancers of nearby genes

Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, CA 94143, USA.
Genome Research (Impact Factor: 13.85). 03/2012; 22(6):1059-68. DOI: 10.1101/gr.133546.111
Source: PubMed

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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    • "Three fragments (DMR, the SIX5 promoter, and the entire region) were cloned into the E1b GFP-Tol2 vector containing an E1b minimal promoter, followed by GFP (Li et al., 2010; Birnbaum et al., 2012). Briefly, the zebrafish were injected following standard procedures (Nusslein-Volhard and Dahm 2002) into at least 100 embryos/construct along with Tol2 mRNA (Kawakami, 2005) to facilitate genomic integration. "
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    • "Three fragments (DMR, the SIX5 promoter, and the entire region) were cloned into the E1b GFP-Tol2 vector containing an E1b minimal promoter, followed by GFP (Li et al., 2010; Birnbaum et al., 2012). Briefly, the zebrafish were injected following standard procedures (Nusslein-Volhard and Dahm 2002) into at least 100 embryos/construct along with Tol2 mRNA (Kawakami, 2005) to facilitate genomic integration. "
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