Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii) in zebrafish and mice

Ryan B Macdonald,Luc Poitras,Mélanie Debiais-Thibaud,Marc Ekker,Byrappa Venkatesh,Kyle Martin,Boon-Hui Tay

doi:10.1186/1471-2148-10-157

Abstract

BackgroundThe phylogenetic position of the elephant shark (Callorhinchus milii ) is particularly relevant to study the evolution of genes and gene regulation in vertebrates. Here we examine the evolution of Dlx homeobox gene regulation during vertebrate embryonic development with a particular focus on the forebrain. We first identified the elephant shark sequence orthologous to the URE2 cis -regulatory element of the mouse Dlx1/Dlx2 locus (herein named CmURE2). We then conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse.ResultsThe CmURE2 sequence shows a high percentage of identity with its mouse and zebrafish counterparts but is overall more similar to mouse URE2 (MmURE2) than to zebrafish URE2 (DrURE2). In transgenic zebrafish and mouse embryos, CmURE2 displayed enhancer activity in the forebrain that overlapped with that of DrURE2 and MmURE2. However, we detected notable differences in the activity of the three sequences in the diencephalon. Outside of the forebrain, CmURE2 shows enhancer activity in areas such as the pharyngeal arches and dorsal root ganglia where its' counterparts are also active.ConclusionsOur transgenic assays show that part of the URE2 enhancer activity is conserved throughout jawed vertebrates but also that new characteristics have evolved in the different groups. Our study demonstrates that the elephant shark is a useful outgroup to study the evolution of regulatory mechanisms in vertebrates and to address how changes in the sequence of cis -regulatory elements translate into changes in their regulatory activity.

Highlights

The phylogenetic position of the elephant shark (Callorhinchus milii ) is relevant to study the evolution of genes and gene regulation in vertebrates
cis -regulatory elements (CREs) regulating Dlx expression can be found outside the intergenic region and we reported one such CRE named Upstream regulatory element 2 (URE2), located approximately 12 kb upstream of the mouse Dlx1 gene [18]
DrURE2 is located in a similar position upstream of the dlx1a gene but the unique metapl1 ortholog is found in synteny with dlx2b on chromosome 1

Summary

Introduction

The phylogenetic position of the elephant shark (Callorhinchus milii ) is relevant to study the evolution of genes and gene regulation in vertebrates. We first identified the elephant shark sequence orthologous to the URE2 cis -regulatory element of the mouse Dlx1/Dlx locus ( named CmURE2). We conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse. The growing wealth of metazoan genome sequence data has provided evidence for the conservation of sequences outside the coding regions of genes, the Conserved Non-coding Elements (CNEs) that tend to be located close to developmental genes [2,3]. Whether the conservation of CNE sequence is necessary for any conservation of CNE regulatory activity remains debateable. Recent studies have identified regulatory sequences with very little sequence conservation that have the ability to activate transcription in highly similar tissues [4,5,6,7]. A great effort has been made in systematically characterizing the CNEs in the mouse genome allowing for comparison with other model and non-model organisms [11]

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Conclusion