AI and CRISPR Precisely Control Gene Expression
Published:13 Sep.2023    Source:Columbia University School of Engineering and Applied Science
A new research showed that artificial intelligence can predict on- and off-target activity of CRISPR tools that target RNA instead of DNA. CRISPR is a gene editing technology which often works by targeting DNA using an enzyme called Cas9. In recent years, scientists discovered another type of CRISPR that instead targets RNA using an enzyme called Cas13. RNA-targeting CRISPRs can be used in a wide range of applications, including RNA editing and knocking down RNA to block expression of a particular gene. Researchers at NYU and the New York Genome Center created a platform for RNA-targeting CRISPR screens using Cas13 to better understand RNA regulation and to identify the function of non-coding RNAs.
A key goal of the study is to maximize the activity of RNA-targeting CRISPRs on the intended target RNA and minimize activity on other RNAs which could have detrimental side effects for the cell. Earlier studies of RNA-targeting CRISPRs focused only on on-target activity and mismatches; predicting off-target activity, particularly insertion and deletion mutations, has not been well-studied. Earlier research demonstrated how to design Cas13 guides that can knock down a particular RNA. With TIGER, we can now design Cas13 guides that strike a balance between on-target knockdown and avoiding off-target activity.

The researchers also demonstrated that TIGER's off-target predictions can be used to precisely modulate gene dosage -- the amount of a particular gene that is expressed -- by enabling partial inhibition of gene expression in cells with mismatch guides. The deep learning model can tell us not only how to design a guide RNA that knocks down a transcript completely, but can also 'tune' it -- for instance, having it produce only 70% of the transcript of a specific gene.