Functionally conserved enhancers with divergent sequences in distant vertebrates.

Song Yang,Alexander Poliakov,Nir Oksenberg,Dario Boffelli,Inna Dubchak,Nadav Ahituv,Sachiko Takayama,Seok-Jin Heo

doi:10.1186/s12864-015-2070-7

Abstract

BackgroundTo examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.ResultsWe searched for sequences that were conserved within groups of closely related species but not between groups of more distant species, and were associated with an epigenetic mark of enhancer activity. To facilitate inferring orthology between non-conserved sequences, we limited our search to introns whose orthology could be unambiguously established by mapping the bracketing exons. We show that a subset of these non-conserved but syntenic sequences from the mouse and zebrafish genomes have homologous functions in a zebrafish transgenic enhancer assay. The conserved expression patterns driven by these enhancers are probably associated with short transcription factor-binding motifs present in the divergent sequences.ConclusionsWe have identified numerous potential enhancers with divergent sequences but a conserved function. These results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution; evidence for selection at the sequence level is not a necessary criterion to define a gene regulatory element.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2070-7) contains supplementary material, which is available to authorized users.

Highlights

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence
We have identified numerous potential enhancers with divergent sequences but a conserved activity; these results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution
We used a combination of comparative genomics and epigenomics to search for potential enhancers within this set of orthologous introns, following the steps illustrated in Fig. 1 and described in Methods

Summary

Introduction

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species. Enhancers are not spatially restricted to the region proximal to the gene’s transcription start site but can be located anywhere, including in introns or exons of distal genes. The spatial and temporal pattern of activity of an enhancer is controlled by the type of epigenetic modifications attached to it, and by the combinatorial binding of transcription factors to specific binding sites in the enhancer’s sequence [1]. Stabilizing selection can explain why the function of some enhancers is conserved in related species while their sequences are not. Ludwig et al showed that the sequence of the even-skipped stripe 2 enhancer was not conserved in two Drosophila species because of transcription factor binding site (TFBS) turnover, but that

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