How do genetic changes in enhancer sequences alter gene expression during animal development? How such changes contribute to phenotypic differences between species?
All biological processes, from animal development and homeostasis to the onset of diseases, rely on gene regulation. The instructions for tissue-specific gene expression are encoded by a class of cis-regulatory genomic elements called enhancers. Genetic changes in enhancer sequences are responsible for most of the phenotypic differences between and within species as well as the genetic etiology of various human diseases. Uncovering the mechanisms of enhancer function, therefore, has broad implications, from understanding developmental and evolutionary processes to predicting and treating diseases. We address these issues from a unique perspective by studying natural genetic variations in enhancers that contributed to phenotypic evolution between closely related species of flies. Our goal is to generate a comprehensive, mechanistic understanding of how genetic changes in enhancer sequences alter gene expression during animal development to contribute to phenotypic evolution.