PROJECT SUMMARY Transposable elements (TEs) are genomic parasites that can negatively impact host viability and fertility. They have been identified as the causes of inherited human disorders and cancers. Despite their detrimental effects, TEs are prevalent across eukaryotic genomes and exhibit dramatic variation in abundance and genomic positions within and between species. For instance, the proportion of vertebrate genomes occupied by TEs ranges from only 6% in pufferfish to 65% in salamander. Over 45% of the human genome harbors TEs, and any two people differ by at least a thousand TE insertions. However, it remains unclear what evolutionary forces drive TE variation and how that influences functions and, thereby, host health. Most studies of the harmful effects of TEs have centered on TE-mediated physical disruption of DNA and changes in DNA sequences. While such genetic disturbances have important consequences, this paradigm overlooks the detrimental epigenetic effects mediated by TEs, including biochemical modifications of chromatin and reorganization of three-dimensional (3D) genome structures. My recent pioneering studies revealed, on a genome-wide scale, that epigenetically silenced TEs can perturb the function of neighboring genes through cis spreading of silencing marks (cis epigenetic effects of TEs) and alter 3D genome organization (3D epigenetic effects of TEs). These exciting observations offer a possibility to answer long-unresolved questions about why there are between-species differences in TE content and how these differences affect genome function and evolution—the overarching goals of my research program. My laboratory uses Drosophila as a primary model and integrates evolutionary genomics and cell biology to decipher the functional and evolutionary significance of TE variation. One major goal of my research program is to determine how TE variation influences genome evolution through my newly discovered 3D epigenetic effects of TEs. My research group will use integrative genomic analysis at multiple levels (DNA, RNA, epigenetics, and 3D genome structures) to investigate our hypothesis that the 3D epigenetic effects mediated by TEs can produce varying 3D genome organization. We further predict that this TE-mediated variation in 3D genome structures can shape genome evolution by affecting fundamental genetic processes. In addition, my laboratory seeks to identify the molecular and evolutionary mechanisms contributing to between-species differences in TE content. We will use Drosophila genetics and transgenics to identify host genetic factors that modulate the epigenetic effects of TEs in cis and in 3D nuclear space. Furthermore, we will combine comparative evolutionary genomics and experimental evolution to investigate our hypothesis that between-species variation in these host genetic factors contributes to varying epigenetic effects of TEs and ultimately drives the evolution of divergent TE content across Drosophila species. ...