Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

214

190

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.

Section: Exonic Enhancers Of Nearby Genesmentioning

confidence: 99%

mentioning

confidence: 99%

Coding exons function as tissue-specific enhancers of nearby genes

Birnbaum¹,

Clowney²,

Agamy³

et al. 2012

214

190

“…S12). The presence of Sowah2 ''pseudoexons'' across deeply diverged tetrapod lineages was surprising, since nonfunctional pseudogenic sequences are expected to decay relatively rapidly, and could be suggestive of (ancestral) recruitment of these exons into a cis-regulatory role as CNRs (Dong et al 2010;Eichenlaub and Ettwiller 2011). However, the degree of degeneration of these pseudogenized remnants is very variable across lineages, with a patchy distribution of pseudoexon presence.…”

Section: Elephant Shark and Teleost Irx-linked Sowah Gene Cnrs Includmentioning

confidence: 99%

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

Maeso¹,

Irimia²,

Tena³

et al. 2012

Developmental genes are regulated by complex, distantly located cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois-Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois; however, teleost and elephant shark data demonstrate that this is a derived feature, and that many Iroquois-CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results highlight the importance of CRMs in imposing constraints to genome architecture, even across large phylogenetic distances, and of gene duplication-mediated genetic redundancy to disentangle these constraints, increasing genomic plasticity.

“…But, in fact, ORFs in many species simultaneously encode additional functional sequence elements within the codon sequence, often with strong evolutionary constraint on the synonymous sites Itzkovitz and Alon 2007). For example, mammalian ORFs are known to encode exonic splicing enhancers and silencers (Chen and Manley 2009), microRNA target sites (Lewis et al 2005;Hurst 2006), A-to-I recoding sites (Rueter et al 1999;Bass 2002), and transcriptional enhancers (Lang et al 2005;Nguyen et al 2007;Lampe et al 2008;Tümpel et al 2008;Dong et al 2010). Several previous studies have observed strong genome-wide trends toward increased evolutionary constraint on such overlapping functional elements, by averaging across many loci pooled together (Baek and Green 2005;Xing and Lee 2005;Chen et al 2006;Down et al 2006;Goren et al 2006;Parmley et al 2006;Robins et al 2008;Kural et al 2009).…”

mentioning

confidence: 99%

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

Lin¹,

Kheradpour²,

Washietl³

et al. 2011

The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes-especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contaiñ 2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.