Dietary impacts on organismal health through altering epigenetic silencing of transposable elements

PROJECT SUMMARY Transposable elements (TEs) are widespread genomic parasites that occupy nearly half of the human genome. The selfish replication and movement of TEs are generally harmful to organisms, and eukaryotic hosts primarily defend against these adverse effects by depositing repressive epigenetic marks at TEs to silence them. Our recent investigations suggest an evolved balance of this process—the epigenetic silencing of TEs needs to be strong enough to reduce TEs’ harmful replicative movement, yet weak enough to avoid inadvertent spreading of repressive marks to TE-adjacent functional sequences. Interestingly, growing evidence shows that epigenetic modifications can be altered by diet, because dietary metabolites and nutrients can act as substrates, cofactors, or inhibitors for enzymes responsible for such epigenetic modifications. However, a critical knowledge gap remains regarding how diet-mediated changes in epigenetic modifications may influence the epigenetic silencing of TEs and, thus, organismal health. We hypothesize that dietary changes can negatively impact organismal health by perturbing the evolved balance of TE epigenetic silencing through both weakened and enhanced TE silencing. We will leverage TE natural variation and combine that with functional genomics and experimental genetics to address our evolution-driven hypothesis. Drosophila will be used as a model system for its ease of handling for large screens, its shared mechanisms of epigenetic regulation with mammals, and its unique TE features that offer an informative model for human TEs. We will conduct large screens to identify dietary factors that alter the balance of TE epigenetic silencing and the involved epigenetic modifying enzymes. This effort will use our newly developed fluorescence reporter system that enables efficient quantification of the strength of TE silencing (Aim 1). We will perform epigenomic and transcriptomic analyses of wildtype strains fed control and altered diets to characterize varying dietary responses of TEs across the genome. This genome-wide profiling will use natural polymorphism of TEs and compare the epigenetic states of homologous sequences with and without a TE insertion, pinpointing diet- mediated changes at individual TEs. Using these functional genomic data under altered diets, we will also investigate the predicted functional outcomes of perturbed TE silencing—elevated TE activity due to weakened silencing or excessive spreading of repressive marks to TE-adjacent genes due to enhanced silencing (Aim 2). Finally, by using pharmaceutical intervention to revert the functional outcomes of perturbed TE silencing, we will directly quantify dietary fitness impacts that are mediated by altered TE silencing (Aim 3). By exploring dietary factors that influence how organisms defend against TEs, and the subsequent impacts on genome function and organismal fitness, this project will reveal previously unknown mechanisms by which diet acts through epigenetic modifications to influence individual health. Our findings will provide a novel perspective for gauging the full impacts of the ongoing and rapid shifts in human diets on our health.