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: 14.63). 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.

Download full-text

Full-text

Available from: Mee Kim
  • Source
    • "2B, table S4, Supplementary Material online). Interestingly, we found further distinguishing characteristics within coding clusters⎯specifically that many protein-coding TSAR clusters (e.g., those in UBE4A, DNAH2, HEATR1, SUPT16H, and WDFY3) are evolving rapidly at synonymous sites, which might indicate changes in translational efficiency and expression (Warnecke and Hurst 2007; Mitarai et al. 2008) or regulatory elements overlapping exons (Birnbaum et al. 2012). Very few protein-coding TSAR clusters have high rates of nonsynonymous substitution (fig. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Mammals have evolved remarkably different sensory, reproductive, metabolic, and skeletal systems. To explore the genetic basis for these differences, we developed a comparative genomics approach to scan whole-genome multiple sequence alignments to identify regions that evolved rapidly in an ancestral lineage but are conserved within extant species. This pattern suggests that ancestral changes in function were maintained in descendants. After applying this test to therian mammals, we identified 4797 accelerated regions, many of which are non-coding and located near developmental transcription factors. We then used mouse transgenic reporter assays to test if non-coding accelerated regions are enhancers and to determine how therian-specific substitutions affect their activity in vivo. We discovered enhancers with expression specific to the therian version in brain regions involved in the hormonal control of milk ejection, uterine contractions, blood pressure, temperature, and visual processing. This work underscores the idea that changes in developmental gene expression are important for mammalian evolution, and it pinpoints candidate genes for unique aspects of mammalian biology.
    Preview · Article · Dec 2015 · Molecular Biology and Evolution
  • Source
    • "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. "

    Full-text · Dataset · Jul 2015
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    ABSTRACT: CTG repeat expansion in DMPK, the cause of myotonic dystrophy type 1 (DM1), frequently results in hypermethylation and reduced SIX5 expression. The contribution of hypermethylation to disease pathogenesis and the precise mechanism by which SIX5 expression is reduced are unknown. Using 14 different DM1-affected human embryonic stem cell (hESC) lines, we characterized a differentially methylated region (DMR) near the CTGs. This DMR undergoes hypermethylation as a function of expansion size in a way that is specific to undifferentiated cells and is associated with reduced SIX5 expression. Using functional assays, we provide evidence for regulatory activity of the DMR, which is lost by hypermethylation and may contribute to DM1 pathogenesis by causing SIX5 haplo-insufficiency. This study highlights the power of hESCs in disease modeling and describes a DMR that functions both as an exon coding sequence and as a regulatory element whose activity is epigenetically hampered by a heritable mutation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Full-text · Article · Jul 2015 · Stem Cell Reports
Show more