Functional Epigenomics In Insects Using Next-Generation Sequencing Methods

DNA methylation is a widespread epigenetic modification implicated in many important processes such as development, disease, and genomic imprinting. In well-studied mammalian systems, DNA methylation at gene promoters acts as a transcriptional repressor including playing a critical role in X chromosome inactivation. Despite the importance and prevalence of DNA methylation, essential model organisms such as D. melanogaster and C. elegans have experienced lineage-specific losses of genomic DNA methylation. This thesis focuses on a comprehensive epigenomics survey and investigation of the Hymenopteran insect order, a group of insects including wasps, bees and ants that have retained functional DNA methylation systems. This diverse group of insects allows us to gain new insights in to the function role of DNA methylation, especially in the context of gene expression regulation. I will first provide a general survey of the epigenetic landscape of insects, which have a completely different pattern compared to mammals, and offer a new approach to quantifying and analyzing DNA methylation in these organisms. Next, I investigate changes to DNA methylation and gene expression that accompany a bacterial infection and a drastic shift from sexual to asexual reproduction in a parasitoid wasp. I will then examine how the intricate honey bee society gives rise to allele-specific methylation and its potential relationship to allele-specific expression. Finally, I explore the importance of DNA methylation along with other promoter elements in regulating gene expression variation.Ph.D