Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner

Abstract

Histone modifications reflect gene activity, but the relationship between cause and consequence of transcriptional control is heavily debated. Recent developments in rewriting local histone codes of endogenous genes elucidated instructiveness of certain marks in regulating gene expression. Maintenance of such repressive epigenome editing is controversial, while stable reactivation is still largely unexplored. Here we demonstrate sustained gene re-expression using two types of engineered DNA-binding domains fused to a H3K4 methyltransferase. Local induction of H3K4me3 is sufficient to allow re-expression of silenced target genes in various cell types. Maintenance of the re-expression is achieved, but strongly depends on the chromatin microenvironment (that is, DNA methylation status). We further identify H3K79me to be essential in allowing stable gene re-expression, confirming its role in epigenetic crosstalk for stable reactivation. Our approach uncovers potent epigenetic modifications to be directly written onto genomic loci to stably activate any given gene.

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities

“…A recent study by Cano-Rodriguez and colleagues used a combination of different CMEs to investigate the key events necessary for stable reactivation of silenced genes [27]. Their results showed that if there is H3K79 methylation and no (or low) DNA methylation present at the promoter, targeting the PDRM9 H3K4 methyltransferase is enough to achieve stable gene activation.…”

“…In this situation, stable gene activation is improved when both PRDM9 (H3K4 methylation) and Dot1L (K79 methylation) are co-targeted in combination with DNA demethylation. Results of these studies underlie the importance of knowing the local chromatin environment at the target loci and point out that combinatorial epigenome editing techniques will be important to reveal the true functional interdependency of these modifications as well as their interactions with chromatin proteins and the surrounding DNA sequence [12, 27, 28]. …”

“…In contrast, full-length Suv39H1 or G9a fusions to ZFs did not repress the promoter, potentially due to sequestration of the HMTs at other genomic locations through binding interactions of the full length proteins [30]. Several other related studies developed EEs by coupling catalytic domains of CMEs to ZFs [27, 29, 31–36], to transcription activator-like effectors (TALEs) [29, 37–39] and to dCas9 [27, 29]. However, an important point to note is that it is still unclear if using the minimal catalytic domains of CMEs improves specificity in all cases, and if they do so by removing other binding surfaces, increasing catalytic activity by reducing steric hindrances, or both.…”

Cancer induction and suppression with transcriptional control and epigenome editing technologies

“…Collectively, CRISPR-based epigenome editing can be performed with the gene-specific CRISPR-dCas9 reagent, consisting of synthesis-friendly sgRNA and generic Cas9; thus, the creation of the materials is rather simple and cost-effective compared with the ZFand TALE-based tools. This feature is practically quite advantageous, and the technical development of epigenome editing has rapidly been evolving with CRISPR-dCas9 platform [40][41][42][43][44].…”

“…Since there are a wide variety of histone modifications mediated by numerous effectors, programmable enzymes targeting histone tags are also variable compared to those for the DNA modification; e.g., histone demethylase (LSD1 [34,42]), histone methyltransferases (PRDM9 [40], G9a [30,33,50,65] and SUV39H1 [30,33]), and histone acetyltransferase (p300) [66].…”