SM-Epigen · Revealing the Epigenetic Regulatory Network with Single-Molecule Precision

Genes and genomic elements are packaged by chromatin structures that regulate their activity. The fundamental unit of chromatin is the nucleosome, composed of an octamer of histones. The large numbers of histone modifications, chromatin remodelers and transcription factors (TFs) that interact with our genome has fuelled speculation that multiple elements act combinatorially to direct specific outcomes. However, the field lacks technologies for detection and analysis of such combinations, thus impeding our ability to test this hypothesis and shed light on human genome regulation. Our recent proof-of-principle for a single-molecule system for mapping combinatorial chromatin modifications holds the technological solution. This powerful method can identify directly unique combinations of epigenetic marks and reveal regulatory modules that can only be ascertained by single-molecule studies.The proposed project will scale-up and advance our technology to establish robust high-throughput systems for investigating combinatorial chromatin and TF interactions and identify their genomic locations, thus bridging the gap between single-molecule proteomics and genomics. We will apply it to address basic questions in epigenetic regulation during early development, and define the network of interactions between histone marks, DNA methylation and the core TFs in stem cells and differentiated cells. We will also harness our 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.Successful implementation and dissemination of these novel systems will yield a transformative new technology for functional genomics that will unravel the chromatin language during early development. This work will open new research directions at the interface of genomics and proteomics, and pave the way for the development of therapeutic and diagnostic tools.