Understanding Regulatory Logic in Evolution and Disease With High Throughput Screening

Abstract

Understanding gene regulation by cis-regulatory elements is central to the studyof human evolution and disease. Most genetic changes that separate humans and chimpanzees and most identified disease-associated variation falls within the noncoding genome. Using high-throughput transcriptional enhancer assays, I make contributions to both these fields. First, to understand genomic mechanisms by which co-regulatory networks form, I define families of noncoding elements based on sequence similarity and cell type-specific activity in humans. I identify segmental duplications as the major mechanism establishing these families, creating over one thousand networks of elements with open chromatin in embryonic stem cells. Using functional genomic assays, I find that segmentally duplicated elements can form novel human gene regulatory connections. Upon duplication, I observe proximalacting elements gaining the ability to regulate distally-located genes and observe transcriptional enhancers rewiring to regulate genes present at the locus outside the segmental duplication. Second, I characterize how cardiac disease-associated genetic variation impairs regulatory activity in two enhancers using a cardiomyocyte model. I show that the impacted enhancers regulate the gene CDKN1A, involved in cell cycle regulation. I hypothesize that the disease variants in these elements ultimately decrease CDKN1A expression leading to the cardiac phenotype. In summary, I leverage high-throughput enhancer assays to further understanding of how gene regulation is altered across evolutionary time and impaired in disease.