Characterization of silencer element-associated chromatin

Abstract

Gene regulation is a carefully controlled process that is essential for development and cellular function. Transcriptional enhancers increase the expression of target genes, while transcriptional silencers decrease their expression. Until very recently, silencers have received much less attention than have enhancers. Recently, thousands of silencers have been identified by large-scale reporter assays in several species, but despite this large collection of examples, silencers as a class are difficult to predict based on histone modifications or other chromatin signatures. They are largely unannotated by commonly assayed histone marks and many do not contain known repressor binding sites. A subset are marked by the polycomb repressive mark H3K27me3, but that constitutes only a small subset of silencers and the mark is not specific to silencers. In chapter 2, I present my work on a system to isolate chromatin for unbiased proteomic analysis. In chapter 3, I present a survey of many repressive histone marks in Drosophila mesoderm and S2 cells and find that none are significantly enriched in silencers, disputing a previously published report of H4K20me1 enrichment. In chapter 4, I explore future directions for determining the chromatin state of silencers and possible models of silencer function. Overall, this dissertation provides a comprehensive overview of known transcriptional silencers and their characteristics and details the development of a locus-specific proteomic method.