CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

TLDR

CRISPR–Cas is a versatile genome editing system used across diverse organisms, originally for DNA mutations but now also targeting nucleic acids, and CHOPCHOP is a web tool that identifies sgRNA targets. This major update of CHOPCHOP expands its toolbox beyond knockouts. The update adds Cas13 RNA‑targeting with isoform and accessibility support, new DNA modes for activation/repression, enrichment for long‑read sequencing, and Cas9 repair outcome prediction, while enhancing visualization of isoforms and downstream ATG sites. CHOPCHOP now supports over 200 genomes and offers a command‑line script for large jobs and unsupported genomes. CHOPCHOP v3 is available at https://chopchop.cbu.uib.no.

Abstract

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