Causality in Epigenetics: Strategies for Targeted Epigenome Engineering of Transcriptional Regulation and Genome Topology

Abstract

Changes in epigenetic states are at the heart of normal developmental processes and also underlie many human diseases. Studies to date have established strong associations between histone post-translational modifications, genome topology, and gene expression patterns, yet have not established their causal linkage at individual loci. Genetic or chemical manipulations have been applied to chromatin and topological regulatory factors, however these approaches lead to global changes of epigenetic states, thus confounding the ability to deduce causality. Here I harness programmable DNA binding proteins fused to chromatin regulators to enable directed perturbation of histone modifications and topological insulators at single loci to interrogate their causal contribution to regulating gene expression. I present evidence to suggest that bivalent chromatin states are resistant to targeted modification by individual histone modifying enzymes. Further, I describe methods to disrupt topological insulators through locus- specific editing of epigenetic state. I apply these methods to model oncogenic insulator loss in glioma and recapitulate changes in topology and gene expression observed in patient tumors. These results show that epigenome engineering enables the study of causality in epigenetics and has implications for the correction of epigenetic states in disease, and rational control of biological information processing in future technologies.