Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene

Abstract

Abstract Evolutionary changes in enhancers, which control gene expression, often contribute to phenotypic evolution. Here, Kalay et al. examine how enhancer activities are encoded within non-coding sequences surrounding the pigmentation gene yellow from three Drosophila species... Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila  yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5′ intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni. We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.