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Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

GSE54745 Homo sapiens; Mus musculus Genome binding/occupancy profiling by high throughput sequencing 18 samples Submitted 2014/04/20 Platform GPL13112Platform GPL11154
Summary
The bacterial CRISPR-Cas9 system has been widely adapted for RNA-guided genome editing and gene regulation in diverse organisms yet its in vivo target specificity is poorly understood. Here we provide the first genome-wide binding maps of nuclease-deactivated Cas9 loaded with guide RNAs in mammalian cells. We find a 5-nucleotide seed region in the guide RNA targets Cas9 to thousands of sites in the genome. Chromatin accessibility limits binding to the other hundreds of thousands sites with matching seed sequences, and consequently 70% of off-target binding sites are associated with genes. U-rich seeds have low numbers of off-target sites limited by both low guide RNA abundance and scarcity of complimentary sites in accessible chromatin. Unexpectedly, off-target sites show little evidence of cleavage, supporting a two-state model reminiscent of eukaryotic RNAi machinery where a short seed match triggers binding but extensive pairing is required for cleavage.
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Also filed as BioProject PRJNA237533 and SRA study SRP036833. Searching any of these in the dataset finder brings you back here.

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