Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers

By Isaac B. Hilton, A. D'Ippolito, Christopher M. Vockley, Pratiksha I. Thakore, Gregory E. Crawford, Timothy E. Reddy, C. Gersbach. 2015

1,755 citations recorded by the source corpus.

Technologies that enable targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we describe a programmable, CRISPR-Cas9-based acetyltransferase consisting of the nuclease-null dCas9 protein fused to the catalytic core of the human acetyltransferase p300. The fusion protein catalyzes acetylation of histone H3 lysine 27 at its target sites, leading to robust transcriptional activation of target genes from promoters and both proximal and distal enhancers. Gene activation by the targeted acetyltransferase was highly specific across the genome. In contrast to previous dCas9-based activators, the acetyltransferase activates genes from enhancer regions and with an individual guide RNA. We also show that the core p300 domain can be fused to other programmable DNA-binding proteins. These results support targeted acetylation as a causal mechanism of transactivation and provide a robust tool for manipulating gene regulation.

Subfields: Molecular Biology

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, background): “For instance, the CRISPR system has been adjusted for targeted manipulation of posttranslational modifications to histones (46).”
Highly Specific Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements (2015, positive): “To identify off-target H3K9me3 sites, we first compared dCas9-KRAB + Cr4/Cr10 to dCas9-KRAB without a sgRNA (Supplementary Table 10 and 11).”
Editing DNA methylation in the mammalian genome (2016, positive): “…activator/suppressor, chromatin modifier, and green fluorescence protein to regulate gene expression, to modify chromatin, and to image genomic loci respectively (Chen et al., 2013; Gilbert et al., 2013; Hilton et al., 2015; Jinek et al., 2012; Konermann et al., 2015; Qi et al., 2013).”
CRISPR/Cas9 in Genome Editing and Beyond. (2016, methodology): “The studies (38, 39, 203) described above have demonstrated that dCas9 fusion proteins can act as sequence-specific, synthetic epigenome modifiers, which not only change local epigenetic status but also change the gene expression of relevant genes.”
Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation (2016, background): “Importantly, while several strategies have been described for CRISPR-mediated activation (Chavez et al., 2015; Gilbert et al., 2013; Hilton et al., 2015; Konermann et al., 2015; Maeder et al., 2013; PerezPinera et al., 2013; Tanenbaum et al., 2014; Zalatan et al., 2015), a recent comparison of…”
Crystal structure of Cpf1 in complex with guide RNA and target DNA (2016, background): “, 2015) to targeted modulation of histone marks (Hilton et al., 2015; Kearns et al., 2015).”
Delivering CRISPR: a review of the challenges and approaches (2018, background): “A fusion protein of dCas9 and acetyltransferase was developed by Hilton et al. (2015), catalyzing acetylation of histone H3 lysine 27 at target sites.”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “Consistent with the idea that coactivators are the workhorses behind enhancer-mediated transcriptional activation, RNAguided recruitment of the acetyltransferase domain of p300 fused to dCas9 is sufficient to bypass the requirement for TFs during enhancer activation in an endogenous chromosomal cont”
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering (2016, methodology): “In this new version we also offer a promoter-targeting mode (Figure 2) for experiments such as down-or upregulating gene expression using catalytically dead Cas9 (dCas9) or transcriptionally active dCas9 (e.g. dCas9-VP64), respectively (23– 25).”
Repurposing the CRISPR-Cas9 system for targeted DNA methylation (2016, background): “Finally, the choice of the targeting domain for both genome and epigenome editing seems to be shifting toward the CRISPR-Cas9 system (8,15), which is not surprising because of the ease of targeting by guide RNAs even to multiple sites (25) and insensitivity to CpG methylation.”