SINGLE-MOLECULE SYSTEMS TO DECODE EPIGENETIC INTERACTIONS
Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but are poorly addressed by existing technologies. We recently published a novel high-throughput single-molecule imaging technology to decode combinatorial modifications on millions of individual nucleosomes (Shema et al., Science, 2016). We apply this technology to elucidate the epigenetic events that drive tumorigenesis in cancers carrying mutations in critical epigenetic pathways. Specifically, we study two cancer models with disruption of Polycomb regulation: (i) Pediatric gliomas harboring point mutations in the histone H3 Lysine 27, the Polycomb catalytic target; and (ii) Breast cancer models with upregulation of EZH2, the Polycomb catalytic subunit. We combine the single-molecule proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. Our single-molecule epigenetic profiling technology is a transformative new tool for functional genomics with the potential to unravel the contribution of epigenetic alterations to tumorigenesis. We also harness this technology to reveal the tissue-of-origin of cell-free DNA circulating in our blood in the form of nucleosomes, and apply it to devise novel strategies for early detection of cancer and other diseases.