New Directions for Epigenetics: Application of Engineered DNA-binding Molecules to Locus-specific Epigenetic Research

Epigenetic mechanisms are regulated by DNA and histone modifications, and these modifications are finely tuned by diverse molecules in a locus-specific manner. To obtain insight into these mechanisms, it is important to identify the factors involved in locus-specific epigenetic regulation, and it is also useful to artificially introduce desirable epigenetic modifications at a target locus and analyze their effect on its biological output. The recent advent of engineered DNA-binding molecules such as zinc finger proteins, transcription activator-like effector proteins, and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) (CRISPR/Cas) system has enabled us to specifically localize epigenetic modifiers, such as DNA methyltransferases and histone-modifying enzymes, to loci of interest. In addition, these engineered DNA-binding molecules can be used to tag specific loci to isolate them, followed by identification of interacting epigenetic modifiers. These approaches yield mechanistic insight into epigenetic pathogenesis of disorders and therapeutic applications. In this chapter, we describe applications of engineered DNA-binding molecules to epigenetic research.