CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [ChIP-seq]

We recently developed CHANGE-seq (Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing), a fast, streamlined, Tn5 tagmentation-based assay for measuring the genome-wide activity of Cas9 in vitro that is easily scalable to many targets and samples. In this study, we directly compare CIRCLE-seq to CHANGE-seq and systematically evaluate Cas9 genome-wide activity on 110 targets across 13 therapeutically-relevant loci leveraging CHANGE-seq. We validate the sensitivity of CHANGE-seq for identifying sites of bona fide cellular off-target mutations using GUIDE-seq and sensitive targeted tag sequencing. Additionally, we sought to evaluate the impact of chromatin accessibility on cellular off-target activity by comparing CHANGE-seq with matched GUIDE-seq cellular off-target, chromatin, and transcriptional profiles generated from the same human primary T-cells. Chromatin immunoprecipitation on 5-10 million cross-linked CD4+/CD8+ T-cells using antibody to H3K4me1 (Abcam, ab8895), H3K4me3 (Cell signaling, 9751), H3K9ac (Abcam, ab10812), H3K27me3(Abcam, ab6002), H3K27ac (Abcam, ab4729), H3K36me3 (Abcam, ab9050) or H3K9me3 (Abcam, ab8898) Please note that each processed data file was generated from both replicates and is linked to the corresponding *rep1 sample records.