CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

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.

Figure 1.

The workflow of CHOPCHOP when targeting RNA for knock-down. The CHOPCHOP homepage (upper box) require four types of input: (i) target, (ii) species, (iii) CRISPR effector and (iv) the purpose of the experiment. Default options will be adequate for most users, but advanced options can be revealed using the ‘Options’ button. The results of the search (lower box) are displayed along with all isoforms of the target gene. The target color indicates the quality of each sgRNA or nickase pair (green [best] to red [worst]). Below the graphic representation an interactive table allows for exploring each guide in greater detail.