Direct comparison of CRISPR knockout and interference with Perturb-seq
Drepanos, L. M.; Escude Velasco, B.; Chase, A.; Srikanth, S.; Gatzen, M.; Rickner, H. D.; Dubinsky, D.; Navia, A. W.; Winter, P. S.; Shibue, T.; Yates, K. B.; Doench, J. G.
Show abstract
CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread adoption. Here, we establish benchmarking libraries for Cas9-based CRISPRko and CRISPRi screens using Perturb-seq as the read-out. For both modalities, we observe consistent transcriptional signatures among cells with the same genes perturbed, strong evidence of on-target signal. We also examine tradeoffs between modalities: while CRISPRi guides demonstrate heightened rates of off-target activity, we also observe artifacts stemming from the cellular response to double-stranded breaks with the use of CRISPRko. The libraries and analyses presented here will be a useful benchmarking and de-risking resource for any group preparing for a large-scale Perturb-seq screen.
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