Abstract
The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no
Highlights
The use of CRISPR–Cas is ubiquitous in modern molecular biology
Many CRISPR–Cas applications require the generation of a frameshift mutation to disrupt gene function, which requires a DNA repair event in which the number of inserted or deleted nucleotides is not a multiple of three
In just a few years, CRISPR–Cas has become a powerful targeting tool for silencing and activating both DNA and RNA in a range of contexts, each of which requires the application of specific rules
Summary
The use of CRISPR–Cas is ubiquitous in modern molecular biology. First introduced as a tool for introducing repair-induced mutations in the genome, the emergence of catalytically dead or fused versions of the effector proteins has transformed CRISPR–Cas into a general purpose tool for targeting. All CRISPR–Cas applications use a sgRNA to direct the CRISPR effector (Cas) protein to its target. Many CRISPR–Cas applications require the generation of a frameshift mutation to disrupt gene function, which requires a DNA repair event in which the number of inserted or deleted nucleotides is not a multiple of three.
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