Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology

Abstract

CRISPR-Cas (Clustered, Regularly Interspaced, Short Palindromic Repeats – CRISPR-associated (Cas)) RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several laboratories have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to shRNA screening. At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.

Keywords

CRISPR-Cas9 / genome editing / gRNA design / off-target analysis / gRNA efficacy

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Acknowledgements

I would like to thank Dr. Scot Wolfe at Department of Molecular, Cell and Cancer Biology in University of Massachusetts Medical School for his critical review of the manuscript and his excellent suggestions.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg