Rapid and Reversible Epigenome Editing By Endogenous Chromatin Regulators

Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed a CRISPR-Cas9-based system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci (FIRE-Cas9). We enhanced the dCas9/MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. By tagging MS2 proteins with Fkbp, we can recruit Frb-fused chromatin regulators to a given locus within minutes of Rapamycin addition. We find that mSWI/SNF BAF complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information that allows modeling of epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.