Entering edit mode
6.0 years ago
fr
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210
Is anyone aware of genome-wide CRISPR/Cas9 screens where gene expression is quantified? Meaning, after targeting a gene, what is the average gene expression change for all genes (microarray, RNAseq, etc.)?
Thanks in advance
I did not understand this part
It depends on how functional that gene in that particular cell-type.
Absolutely, that is exactly what I wanted to see! :)
I am not aware but it would be great to do that via whole genome phased sequencing and then RNA-seq. Indirectly, the information may already exist, as, if you excise a disease allele, you may be restoring the wild-type state, and, thus, the affected gene and pathways could return to their normal state. Very difficult to know exactly.
Yeah... An important challenge is that for whole-genome targeting, even if you consider only the 20k protein-coding genes, even microarray analyses become expensive. Especially if you consider any replicates
I still did not understand what would be the goal behind this type of experiments.
For many reasons, it would be great to have this sort of gene expression response to genome-wide screens. E.g. assessing pathway adaptation or response to knockout, finding potential therapeutic targets, determining gene essentiality. Though the last point may be somewhat addressed using existing datasets
I get that, but given the complexity of the genome, complex enhancer regulation, temporal expression of genes, cellular specificity, gene-regulatory networks etc etc, I could not image if someone will be able to do this. I remember a paper about cell survival CRISPR analysis, I will search for that paper. That might answer a part of this question.
I agree with geek_y. I think that you would only see 'global' / 'major' alterations in the transcription profile by modifying key genes like TP53, ESR1, MYC, p210, etc.