Grant: CIHR Fellowship

Enhancers are short stretches of DNA that control when and where expression of their target genes are turned on during development. Super-enhancers are diverse clusters of enhancers that drive expression of genes important for cellular differentiation. Many mutations implicated in diverse neurodevelopmental disorders impact enhancers - and are particularly enriched in super-enhancers active in disease-relevant cell types. Despite the rapidly growing catalog of enhancer variants implicated in these disorders, we have no way to accurately predict how these mutations impact gene expression to increase risk because we do not understand the mechanisms super-enhancers use to drive gene expression. Here, I will use high-throughput genome editing to decipher the functional architecture and regulatory grammar of super-enhancers. In Aim 1, I will use complementary multiplex genome editing approaches to dissect the relative contributions and redundancy of individual enhancers to the overall function of super-enhancers driving neuronal differentiation. In Aim 2, I will apply novel methods to generate thousands of synthetic super-enhancers and quantify their effects on target gene expression. Specifically, I will investigate the effects of shuffling the order, spacing, repetition, and combinations of the individual enhancers that comprise each super enhancer on gene expression programs critical for neural differentiation. This research will reveal several general principles of super-enhancer functional architecture and regulatory grammar, enabling more accurate predictions of the impacts of noncoding variants on gene expression and disease risk. This will lead to more accurate diagnostics and design of more precise cell-type specific expression systems for research and disease treatment. Importantly, this research represents a general framework that can be adapted to rapidly assess the function of any large regulatory sequence in diverse cell types relevant to myriad diseases.