CpG cytosines within genomic DNA near the dCas9 binding site (CpG sites)

CpG cytosines located near dCas9 binding sites serve as the primary substrate for programmable epigenome editing tools. By utilizing a catalytically inactive Cas9 (dCas9) protein as a DNA-binding scaffold, effector domains such as DNA methyltransferases (e.g., DNMT3A) or ten-eleven translocation (TET) dioxygenases can be directed to specific genomic coordinates to modify the methylation state of these cytosines (Liu et al., 2016, Cell). This targeted modification allows for the precise control of gene expression by mimicking or reversing natural epigenetic processes that regulate transcription (Thakore et al., 2016, Nature Methods). In therapeutic contexts, these sites are targeted to silence oncogenes or reactivate tumor suppressor genes and genes affected by imprinting disorders (Pflueger et al., 2019, Nature Communications). Unlike traditional CRISPR-Cas9 gene editing, targeting CpG sites with dCas9 fusions does not induce double-strand breaks, potentially offering a safer profile for clinical applications by avoiding permanent sequence alterations (Goell & Hilton, 2021, Trends in Genetics). The ability to modulate these sites provides a powerful mechanism for treating diseases driven by epigenetic dysregulation rather than primary DNA sequence mutations.

Other names

CpG dinucleotidesCpG islandsDNA methylation sitesdCas9-targeted CpG sitesEpigenetic target sites

Targeted DNA methylation or demethylation via dCas9-mediated recruitment of epigenetic effector domains to specific genomic loci.