CRIBAR: a fast and flexible sgRNA design tool for CRISPR imaging

TL;DR

CRIBAR is a new tool for designing guide RNAs used in CRISPR imaging to track nucleic acids in real time with high precision.

Contribution

CRIBAR introduces a systematic and optimized approach for designing sgRNAs specifically for CRISPR imaging, improving targeting efficiency and reducing off-target effects.

Findings

CRIBAR generates sgRNA sets that maximize on-target binding sites for CRISPR imaging.

The tool effectively evaluates and minimizes potential off-target effects in silico.

CRIBAR enables CRISPR imaging in non-repetitive genomic regions.

Abstract

CRISPR imaging enables the real-time tracking of nucleic acids. Using guide RNAs (gRNAs) to direct fluorescent tags to target regions allows for precise nucleic acid monitoring via microscopy. The design of gRNAs largely affects the efficacy of CRISPR imaging. Currently, available gRNA design tools are developed primarily for gene editing, often producing individual gRNAs that target genes or regulatory elements.

In this study, we introduce CRIBAR, a computational tool developed to systematically design single-guide RNAs (sgRNAs) for CRISPR imaging applications. CRIBAR first generates sgRNA sets optimized to maximize the number of on-target binding sites and then evaluates the potential off-target effect. The results of the in silico experiment show that CRIBAR enables CRISPR imaging in non-repetitive regions.

CRIBAR is available as a software package at https://github.com/ucfcbb/CRIBAR and as a web server at http://genome.ucf.edu/CRIBAR.

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