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Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions

ABSTRACT: Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer-promoter pairs. Here we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as a novel activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer-promoter pairs. We find that these platforms display variable comparative expression levels in different human cell types and that their relative transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus, and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs), and that this eRNA induction is highly correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to show that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that contact frequencies between an enhancer and corresponding downstream promoter can be increased by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205858 | GEO | 2022/06/21

REPOSITORIES: GEO

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