Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

<p>Abstract</p> <p>Background</p> <p>Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in <it>cis-</it>regulatory elements (<it>cis-</it>changes) or from changes in the expression pattern or function of transcription factors (<it>trans-</it>changes). While isolated examples of <it>trans-</it>changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear.</p> <p>Results</p> <p>Here, we attempt to examine the prevalence of <it>trans-</it>effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for <it>trans-</it>changes in the evolution of gene expression.</p> <p>Conclusions</p> <p>In total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the <it>trans</it> environment may play a significant role in the evolution of gene expression in vertebrates.</p

Functional analysis of limb enhancers in the developing fin

Despite diverging ~365 million years ago, tetrapod limbs and pectoral fins express similar genes that could be regulated by shared regulatory elements. In this study, we set out to analyze the ability of enhancers to maintain tissue specificity in these two divergent structures. We tested 22 human sequences that were previously reported as mouse limb enhancers for their enhancer activity in zebrafish (Danio rerio). Using a zebrafish enhancer assay, we found that 10/22 (45 %) were positive for pectoral fin activity. Analysis of the various criteria that correlated with positive fin activity found that both spatial limb activity and evolutionary conservation are not good predictors of fin enhancer activity. These results suggest that zebrafish enhancer assays may be limited in detecting human limb enhancers, and this limitation does not improve by the use of limb spatial expression or evolutionary conservation