CAREER Deciphering how enhancers encode tissue-specificity and phenotypes

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Our genome is 3 billion letters of DNA which encode the tools (proteins) and instructions for making every single cell within our body. These instructions for building us are embedded within genomic sequences called enhancers, which act as switches to turn on the production of proteins in particular cell types at particular times, allowing a fertilized egg to develop into a complex organism. Changes in the enhancer sequence can alter where proteins are made, causing dramatic effects, such as extra toes, loss of fins, or even novel functions that allow an organism to exist in a new environment. Indeed, changes within enhancers underlie the majority of differences between individuals and contribute to the diversity of species on our planet. Yet these elements are poorly understood. This research will develop cutting-edge approaches to test millions of versions of enhancers for function to understand how changes in the enhancer sequence can alter when and where proteins are made. These findings will help uncover how genomes encode the instructions for making us and how changes within enhancers can lead to changes in the function and structure of an organism. Middle school students from a Title I school will contribute to this research by conducting experiments in the classroom and on the university campus. Supporting underprivileged students from a young age and giving them access to research and higher education experiences is essential to help students see college as an attainable goal, engage in science, and strive for educational goals. Enhancers are genomic elements that control the timing and location of gene expression; as such, enhancers ensure the successful development and integrity of an organism. Although we can identify putative enhancers in genomes with relative ease, we have little understanding of how the underlying sequence encodes gene expression. This lack of knowledge is a major problem as sequence changes within enhancers are thought to underlie the majority of phenotypic diversity. The goal of this proposal is to develop a deep understanding of how enhancers encode tissue-specific expression patterns, how transcription factors interact specifically with enhancer sequences, and the mechanisms by which enhancer variants alter phenotypes. To achieve these goals, this research will use a creative combination of high-throughput enhancer assays in developing vertebrate embryos (chick), binding assays, and transgenic approaches in mice. These assays will be implemented in the context of limb development as this is an ideal system in which to study how enhancers encode tissue-specific expression patterns and how changes in these patterns impact organismal integrity. These studies will uncover overarching principles governing the relationship between enhancer sequence and tissue-specific expression and provide a mechanistic understanding of how sequence changes within enhancers alter phenotypes. The broader impacts will involve middle school students from a Title I school contributing to this research by conducting experiments in the classroom and on the university campus.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.