CAREER: Phenotypic and developmental effects of enhancer variation on cichlid craniofacial evolution

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Genes are precisely turned on and off by their regulatory elements. This project examines how altered gene regulation can generate changes in animal development, specifically in the facial skeleton. This work will identify regulatory elements through genome analysis, quantify how altered gene regulation during embryonic development changes facial shape, and assess the effects of DNA mutations on regulatory function using microscopy. Given that (1) 85% of disease-causing mutations affect gene regulation and (2) changes to gene regulation are predicted to be a major source of evolutionary diversity, this work will provide insights into how DNA changes can produce both natural variation in animal development and disease in humans. Educational activities will improve factors key in retention of undergraduate and K-12 students in STEM disciplines. This will be accomplished through (1) mentorship of undergraduates and (2) creation of inquiry-based activities for the middle school classroom that will be implemented in local schools and distributed to educators nationally. Understanding the functional impact of genetic variation in cis-regulation is a major gap in our understanding of the generation of phenotypic diversity. The research objective of this project is to analyze the phenotypic function of non-coding, gene regulatory enhancers within the context of craniofacial evolution in cichlid fishes, a textbook example of an adaptive radiation. The specific aims are to (1) utilize four complementary genomic strategies to comprehensively identify candidate enhancers with genetic variation, (2) quantify phenotypic and transcriptional effects of modulating enhancer activity using CRISPR-Cas9, and (3) empirically assess the effect of genetic variation on enhancer activity. With a focus on the functional effect of enhancers in vivo in terms of activity, transcriptional regulation, and effect on phenotype, this work will address a major gap in knowledge of the genotype-phenotype relationship. These data will provide empirical information for those designing models of the grammar of gene regulation, a framework to significantly accelerate the discovery and systematic documentation of causal genetic variations in non-coding DNA, and experimental evidence for a central theory of Evolutionary Developmental Biology (Evo-Devo).This project is jointly funded by the Developmental Systems Cluster of IOS, and by the Established Program to Stimulate Competitive Research (EPSCoR)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.