The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster

Environmental stimuli can have a significant impact on gene expression patterns and this impact is not always confined to a single cell cycle, but can sometimes persist through multiple divisions or even transgenerationally. Such phenomena are often classified as epigenetic because genetic mutations are not thought to behave in such a directed, nonrandom manner. Studies concerning epigenetics often overlook unstable variation in repetitive heterochromatic sequences as a potential mode of transgenerational inheritance. Although they constitute a large fraction of most eukaryotic genomes, technological limitations have greatly hindered our understanding of the functional importance of such sequences. Copy number variation in the unstable ribosomal RNA gene array (rDNA) -a specific class of repetitive sequence- modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila genome. The primary aim of this study was to identify an environmental source of rDNA instability and to characterize the phenotypic consequences of the variation generated by that instability. Using genetic, cytological, and molecular assays, I discovered that increased dietary yeast concentration results in rDNA instability and copy number reduction in the soma and germline. Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process. Previous studies suggest that rDNA deletions influence the regulation of a number of metabolically important genes. Supporting this, I found that variation in rDNA modulates the Drosophila starvation response and affects lipid metabolism. This effect is potentially mediated by differential rDNA transcription, suggesting a link between the cause of instability and its phenotypic outcome. Instability is not just thought to be a property of rDNA, but seems to occur via similar mechanisms in other repetitive sequences. I developed a novel polymerase chain reaction (PCR) technique to quantify simple pentameric sequence repeats and used it to discover previously uncharacterized natural and mutationally-induced variation on the heterochromatic Y chromosome. Taken together, these findings suggest a non-epigenetic mechanism through which the environment can influence gene expression patterns in a manner that is specific, heritable, and consequential