Are CRISPR knockouts better than RNAi knockdowns?

The ability to completely remove functional forms of a gene, to control for off-target effects, and to perform robust, reproducible experiments certainly make gene editing desirable for performing loss of function analyses. But, there is still a strong case for using RNAi, not least as an orthogonal approach to support gene editing data. There are also the following use cases: If clonal, knockout cell lines cannot be isolated then knockdown achieved by RNAi in a pool may be better than that achieved by CRISPR-Cas9. Generation of knockout cells requires the cells to be in culture for an extended period of time, and the constitutive gene knockout can activate compensatory mechanisms that may impair the phenotype. RNAi knockdown by contrast results in an acute depletion that may reveal additional gene functions. Given the challenges and time lines associated with generating genomic knockouts it often makes sense to have back up options and supporting experiments in place. At Horizon, we believe that our Hap1 Knockout Cell Lines provide an excellent solution for scientists looking for a proof of concept knockout model to bolster RNAi data, or to work with while a model in a specific cell line is generated.