Chromatin modifications play crucial roles in gene regulation and DNA repair. Importantly, epigenetic marks such as histone modifications and DNA methylation have been implicated in transcriptional repression of retrotransposons. Repression of retrotransposons is critical for preventing transpositions and aberrant activities of host genes. Covalent binding of the vitamin biotin to histones, mediated by holocarboxylase synthetase, is one of the very few chromatin modifications that directly depend on nutrient supply in the diet. In this dissertation I demonstrate that chromosome stability depends on biotin. I show that binding of biotin to K9 in histone H2A and K12 in histone H4 is the mechanism that causes repression of retrotransposons. I also provide evidence that silencing of retrotransposons by histone biotinylation is mediated by increased transcription of anti-sense RNA. This observation suggests that RNAi is involved in the silencing of retrotransposons by histone biotinylation. In another project of my dissertation, I developed an avidin-based assay to quantify activities of histone debiotinylases. This assay is a useful tool to achieve one of the long-term goals of our laboratory, i.e., the identification of histone debiotinylases in human cells. Identification of histone debiotinylases is a critical step to understand the regulation of histone biotinylation. Finally, I used mass spectrometry to identify novel biotinylation sites in human histones, and to identify histone marks that co-occur with biotinylation in a single histone molecule. This dissertation provides novel insights into the effects of nutrient status on cancer risk by a diet-dependent epigenetic mechanism of gene regulation, and it offers novel tools for the study of biological functions of histone biotinylation
