期刊
BIOINFORMATICS
卷 34, 期 1, 页码 16-23出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx564
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资金
- Energy and Education Research Center (SEERC) seed fund at the University of Tennessee, Knoxville
- National Science Foundation [1553250, 1511881, 1360867]
- BioEnergy Science Center (BESC), a U.S. Department of Energy Bioenergy Research Center - Office of Biological and Environmental Research in the DOE Office of Science [DE-AC05-000R22725]
- DARPA YFA award [D17AP00023]
- Directorate For Engineering
- Div Of Chem, Bioeng, Env, & Transp Sys [1511881, 1360867] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1553250] Funding Source: National Science Foundation
Motivation: Genetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions. Results: To accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CRISPR Associated Software for Pathway Engineering and Research (CASPER), for identifying on-and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, P<0.05) over the conventional methods for predicting on-and off-target activities, respectively. Further we used CASPER to develop novel applications in genome editing: multitargeting analysis (i.e. simultaneous multiple-site modification on a target genome with a sole guide-RNA requirement) and multispecies population analysis (i.e. guide-RNA design for genome editing across a consortium of organisms). Our analysis on a selection of industrially relevant organisms revealed a number of non-unique target sites associated with genes and transposable elements that can be used as potential sites for multitargeting. The analysis also identified shared and unshared targets that enable genome editing of single or multiple genomes in a consortium of interest. We envision CASPER as a useful platform to enhance the precise CRISPR genome editing for metabolic engineering and synthetic biology applications. Availability and implementation: https://github.com/TrinhLab/CASPER. Contact: ctrinh@utk.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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