The CRISPR/Cas System

The epigenome is a heritable layer of information not encoded in the DNA sequence of the genome, but in chemical modifications of DNA or histones. These chemical modifications, together with transcription factors, operate as spatiotemporal regulators of genome activity. Dissecting epigenome function requires controlled site-specific alteration of epigenetic information. Such control can be obtained using designed DNA-binding platforms associated with effector domains to function as targeted transcription factors or epigenetic modifiers. Here, we review the use of dCas9 as a novel and versatile tool for fundamental studies on epigenetic landscapes, chromatin structure and transcription regulation, and the potential of this approach in basic research in these fields. Introduction The epigenome is a layer of information that, together with transcription factors, defines the celltype-specific gene expression pattern of a genome. By definition, epigenetic information is mitotically and/or meiotically heritable, but not directly encoded in the DNA sequence (Bird, 2007; Berger et al., 2009). Epigenetic information consists of covalent chemical modifications [post-translational modification of histone proteins that include, but are not limited to, methyl, acetyl, phosphoryl and ubiquitin groups (Turner, 2012) and methylation of cytosine bases (Vardimon et al., 1982; Schübeler, 2015)] that alter the structure and physicochemical properties of DNA or DNA-bound histones (Bird, 2002; Kouzarides, 2007). Epigenetic modification states are dynamic by nature and depend on enzymes transferring or removing these modifications (Holliday, 1987; Cubas et al., 1999; Chong and Whitelaw, 2004; Youngson and Whitelaw, 2008). The epigenetic state of a genomic region is determined by combinations of modifications, but how exactly the resulting code is determined remains poorly understood (Gardner et al., 2011). These states correlate with gene expression and chromatin structure, and link the modification pattern of DNA and histones of genomic regions to states of development and differentiation (Holliday, 2006; Henikoff and Shilatifard, 2011; Zhou et al., 2011; Turner, 2012; Smith and Meissner, 2013). A variety of diseases has been linked to mutations in epigenetic maintenance enzymes or to misregulation of genes following aberrations in the epigenetic code (Kelly et al., 2010; Baylin and Jones, 2011; Plass et al., 2013). Epigenome editing could develop into a tool used to revert aberrations in this code that lead to disease. Due to the lack of knowledge of rare modifications and the combinatorics of DNA and histone modifications, it is unclear by what exact mechanisms epigenetic signals lead to downstream effects on gene regulation and chromatin conformation and whether as yet unknown