Coding exons function as tissue-specific enhancers of nearby genes

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 ChIPseq 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.

Functional and topological characteristics of mammalian regulatory domains

“…4; Foxg1, Fig. 4B; Twist1, Ruf et al 2011;Birnbaum et al 2012), further supports the notion that regulatory control is exerted by coordinated, and not individual action, of enhancers. It indicates that this integration is orchestrated at the level of the regulatory domain, not at endogenous gene promoters (Marini c et al 2013).…”

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development

“…These elements are sometimes referred to as eExons. One recent paper (Birnbaum et al, 2012) found that four of seven potential eExons tested functioned to control the expression of nearby genes. Another paper found that enhancers in coding regions target their own gene (Ritter et al, 2012).…”

Clinical, genetic, and molecular aspects of split‐hand/foot malformation: An update

“…Interestingly, two enhancers controlling limb expression are located far centromeric to Dlx5/6, residing within exons 15 and 17 of Dync1i1 [Birnbaum et al, 2012a]. Moreover, one of these was shown to physically associate with the Dlx5/6 promoter regions in mouse limbs.…”

“…Moreover, one of these was shown to physically associate with the Dlx5/6 promoter regions in mouse limbs. These exonic enhancers, termed "eExons," have been implicated in human SHFM based on their locations relative to various translocation and inversion breakpoints that are presumed to disrupt their interactions with DLX5/6 [Birnbaum et al, 2012a]. Additional analysis of rearrangements at this locus has led to the delineation of a minimal 1.2 Mb critical region in which other DLX5/6 enhancers might reside [Birnbaum et al, 2012b].…”