Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes

Abstract

Despite significant advances made in epigenetic research in recent decades, many questions remain unresolved, especially concerning cause and consequence of epigenetic marks with respect to gene expression modulation (GEM). Technologies allowing the targeting of epigenetic enzymes to predetermined DNA sequences are uniquely suited to answer such questions and could provide potent (bio)medical tools. Toward the goal of gene-specific GEM by overwriting epigenetic marks (Epigenetic Editing, EGE), instructive epigenetic marks need to be identified and their writers/erasers should then be fused to gene-specific DNA binding domains. The appropriate epigenetic mark(s) to change in order to efficiently modulate gene expression might have to be validated for any given chromatin context and should be (mitotically) stable. Various insights in such issues have been obtained by sequence-specific targeting of epigenetic enzymes, as is presented in this review. Features of such studies provide critical aspects for further improving EGE. An example of this is the direct effect of the edited mark versus the indirect effect of recruited secondary proteins by targeting epigenetic enzymes (or their domains). Proof-of-concept of expression modulation of an endogenous target gene is emerging from the few EGE studies reported. Apart from its promise in correcting disease-associated epi-mutations, EGE represents a powerful tool to address fundamental epigenetic questions.

Figure 1.

Targeted rewriting of epigenetic marks. Schematic figure shows the general concept of targeting epigenetic enzymes. In the middle, an example of a certain locus harboring a DBD recognition site (black triangle) is shown. Lollypops represent either unmethylated (open) or methylated (filled) CpGs. Histones and their tails are also represented. Histone tails can be post-translationally modified and as such are associated with a repressed chromatin state (represented by the filled black dots), or with an active chromatin state (represented by open black circles). The upper and lower figures show the induced change in gene expression by targeting a DBD fused to an epigenetic enzyme involved in changing the epigenetic composition (histone modifications or DNA methylation), thereby causing gene activation (top) and repression (bottom). In the epigenetic enzymes, CD = catalytic domains and RD = recruiting domains are indicated. Black arrows show the action of the CD of the epigenetic enzymes, dashed arrows show the possible recruitment of other proteins or capturing by other proteins (star, top; shape, bottom).

Figure 2.

Targeted gene expression regulation capacity by various domains of p300. This figure gives an overview of the domains of p300 that were targeted by fusion to a sequence-specific DBD. Full-length protein actively upregulated the expression of the target gene in all targeting studies reviewed here. The activating domains are shown above and the non-activating domains below the full-length protein. The first and second indicated domain, respectively, indicate the bromodomain and the HAT domain of p300 according to a conserved domain search on the NCBI website. Dashes in the full-length protein show the position of the commercially available ‘HAT domain’ of p300 (Millipore). Numbers indicate aa positions. Black-dashed lines represent a part of the enzyme deleted in the middle of a protein. References are indicated by the pattern of stripes or color within the domain box as explained in the legend. The table at the right side indicates whether the N-terminal activation domain, HAT domain and/or C-terminal activation domain are present in the related construct. Domains indicated with a star shape were more active than the full-length enzyme upon comparison within one study. Thin dotted lines connect two equal domains with different outcomes.