A tool for CRISPR-Cas9 gRNA evaluation based on computational models of gene expression

CRISPR based technologies have revolutionized all biomedical fields as it enables efficient genomic editing. These technologies are often used to silence genes by inducing mutations that are expected to nullify their expression. To this end, dozens of computational tools have been developed to design gRNAs, CRISPRs gene-targeting molecular guide, with high cutting efficiency and no off-target effect. However, these tools do not consider the induced mutations effect on the genes expression, which is the actual objective that should be optimized. This fact can often lead to failures in the design, as an efficient cutting of the DNA does not ensure the desired effect in protein production. Therefore, we developed EXPosition, a computational tool for gRNA design. It is the first tool designed to improve the true objective of using CRISPR: the effect it has on gene expression. To this end, we used predictive deep-learning models for the relevant gene expression steps: transcription, splicing, and translation initiation. We validated our tool by demonstrating that it can classify sites as "silencing" or "non-silencing" better than models that consider only the cutting efficiency. We believe that this tool will significantly improve both the efficiency and accuracy of genome editing endeavors. EXPosition is available at http://www.cs.tau.ac.il/~tamirtul/EXPosition.