The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells

Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes in eukaryotic cells. Little is known about the factors responsible for dislodging Cas9 or how they influence genome engineering. Unbiased detection through proximity labeling of transient protein interactions in cell-free Xenopus laevis egg extract identified the dimeric histone chaperone facilitates chromatin transcription (FACT) as an interactor of substrate-bound Cas9. FACT is both necessary and sufficient to displace dCas9, and FACT immunodepletion converts Cas9’s activity from multi-turnover to single turnover. In human cells, FACT depletion extends dCas9 residence times, delays genome editing, and alters the balance between indel formation and homology-directed repair. FACT knockdown also increases epigenetic marking by dCas9-based transcriptional effectors with a concomitant enhancement of transcriptional modulation. FACT thus shapes the intrinsic cellular response to Cas9-based genome manipulation most likely by determining Cas9 residence times. [Display omitted] •Histone chaperone FACT is necessary and sufficient to remove Cas9 from DNA in vitro•FACT turns Cas9 from single turnover to multi-turnover•FACT depletion in human cells delays Cas9 DSB repair and alters editing outcomes•FACT depletion increases dCas9 residence to increase epigenetic marking and CRISPRi S. pyogenes Cas9 binds very tightly to DNA. It has been unclear how cells remove Cas9 from the genome. Wang et al. determine that the histone chaperone complex FACT displaces Cas9 from its substrate in eukaryotic systems. FACT knockdown potentiates CRISPR-based tools and alters Cas9 gene editing outcomes.