Known CRISPR KO effects on gene expression

Question

[j.gleixner]

I am looking for genes whose knockout with CRISPR/Cas9 (Indels) has known, strong effects on the expression of other genes.

Ideally the knockout has no strong growth phenotype and is robust ( in the sense that it is similar across many cell lines) or at least observed in HAP1 (or another CML (derived) cell line). These genes are to be used as positive controls in a Perturb-seq/CROPseq like study.

Did you ever run across such a gene in your RNAseq analyses?

Answer 1

[Jean-Karim Heriche]

Related to robustness of the KO, you may also want to consider that cells often seem to find ways of re-expressing the knocked-out gene as described in this paper (and a couple others which I can't find now).

[j.gleixner]

Thanks. I edited the question to clarify that by robust I mean that the mean effect across cells does not depend on the cell line used; variation due to different editing outcomes are fine. While very relevant to the topic the paper you point to sequenced only one (two for MFT2) clone for each gene (in technical replicates) so does not allow to to attribute variation gene expression to the targeted gene (besides perhaps for MFT2 perhaps).