CBE Dissertation Defense: “Visualizing Genetics: Quantifying Gene Expression Through Genetic and Epigenetic Modifications”

“Visualizing Genetics: Quantifying Gene Expression Through Genetic and Epigenetic Modifications”

Abstract:

Precise control over gene expression is essential for proper development of an organism. However, genes are regulated in a variety of ways, the mechanisms of which are not well understood. This thesis explores gene regulation at two different levels: genetic control and epigenetic control. Genetic control focuses on components of the genome such as enhancers, promoters, gene composition, and gene length. Each of these facets can potentially affect either the timing, amount, or location of gene expression. Epigenetic control looks at how different DNA markers, which do not modify the DNA sequence, are able to manipulate gene production. Using quantitative live-imaging in Drosophila embryos and immunofluorescence staining in human fibroblasts, we are able to capture and analyze the impact each of these factors have on gene expression. In genetic control, we see that enhancers play a dominant role in controlling expression, specifically through the individual transcription factor binding sites within an enhancer. Based on the binding affinity and type of binding site, the enhancer can influence when genes are active as well as the amount of mRNA produced. The level of mRNA production is also influenced by the rate of RNA polymerase II (Pol II) elongation. The speed that Pol II moves along a gene body can impact how much mRNA is made within a certain developmental time period. We find that not only do enhancers play a role in controlling Pol II elongation rate, but the composition of the gene itself also contributes to modulating the rate of elongation. In epigenetic control, there are many different markers interacting with DNA. Here we identified H3K9me3 as a key epigenetic modification that controls DNA compaction, and thus can silence a large number of genes. As a result, specific epigenetic markers can ultimately control gene expression and dramatically impact a cell’s ability to reprogram itself. Slight changes in gene regulatory mechanisms can cause extreme changes in gene expression and ensuring that organisms develop properly is contingent upon having a better understanding of how different factors influence expression.