UC San Diego

This dissertation describes the use of high-throughput molecular biological techniques and bioinformatics to systematically locate and characterize transcriptional enhancers in the human genome. Enhancers are an important class of transcriptional regulatory elements, along with promoters, silencers, insulators, and locus control regions. Though critical to proper regulation of gene expression in space and time, enhancers have been difficult to locate in the human genome due to their widespread distribution and poorly understood sequence features. In this work, I discuss the discovery of physical features of enhancers that allow their distinct identification throughout the genome of human cells and the insights gained by the first genomewide analysis of human transcriptional enhancers. Chapter 1 introduces principles of transcriptional regulation and summarizes high-throughput technologies employed to locate transcriptional promoters. Chapter 2 details the discovery of distinct chromatin signatures for promoters and enhancers and the development of novel computational strategies to predict these regulatory elements in 1% of the human genome. Chapter 3 describes the extension of the enhancer prediction model to the entire human genome and insights gained from large-scale analysis of the characteristics of these enhancers. Chapter 4 discusses the development of a related high-throughput method, RiGS, designed to facilitate functional genomic screens in mammalian systems