Dose-Dependent Activation of Gene Expression Is Achieved Using CRISPR and Small Molecules That Recruit Endogenous Chromatin Machinery

Gene expression can be activated or suppressed using CRISPR/Cas9 systems. However, tools that enable dose dependent activation of gene expression without the use of exogenous transcription regulatory proteins are lacking. We created a technology termed chemical epigenetic modifiers (CEMs) which can regulate the expression of target genes by recruiting components of the endogenous chromatin regulatory machinery, eliminating the need for exogenous transcriptional effectors. The system has two parts: catalytically inactive Cas9 (dCas9) in complex with FK506 binding protein (FKBP), and a CEM consisting of FK506 linked to a molecule that interacts with cellular epigenetic machinery. We show that CEMs upregulate gene expression at target endogenous loci up to 20-fold or more depending on the gene. We also demonstrate dose-dependent control of transcriptional activation, function across multiple diverse genes, reversibility of CEM activity, and genome wide specificity of our best-in-class system.