CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations
Year: 2020
Type: article
Abstract: CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of guide RNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.
Source: G3 Genes Genomes Genetics
Authors: Hayley R. Stoneman, Russell L. Wrobel, Michael Place, Michael Graham, David J. Krause, Matteo De Chiara, Gianni Liti, Joseph Schacherer, Robert Landick, Audrey P. Gasch, Trey K. Sato, Chris Todd Hittinger
Institutions: University of Wisconsin–Madison, Great Lakes Bioenergy Research Center, Centre National de la Recherche Scientifique, Inserm, Université Côte d'Azur, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Institut Universitaire de France, Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,709
Funders: National Science Foundation, U.S. Department of Energy, U.S. Department of Agriculture, Pew Charitable Trusts, Wisconsin Alumni Research Foundation, National Institute of Food and Agriculture, Office of Science, Great Lakes Bioenergy Research Center, Division of Graduate Education, Biological and Environmental Research
OpenAlex ID: W3088778547