Abstract
Gene editing has great therapeutic impact, being of interest for many scientists worldwide. Clustered regularly interspaced short palindromic repeats (CRISPR) technology has been adapted for gene editing to serve as an efficient, rapid, and cost-effective tool. To fulfill CRISPR experiment’s goals, two components are important: an endonuclease and a gRNA. The most commonly used endonucleases are Cpf1 and Cas9 and are described in depth in this chapter. The gRNA targets the genome site to be edited, giving great importance to its design to obtain increased efficiency and decreased off-target events. In this chapter, we describe different tools to design suitable gRNAs for a variety of experimental purposes.
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References
Mojica FJM, Díez-Villaseñor C, García-Martínez J, Almendros C (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155:733–740
Zhang F, Wen Y, Guo X (2014) CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet 23:R40–R46
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
Nishimasu H, Nureki O (2017) Structures and mechanisms of CRISPR RNA-guided effector nucleases. Curr Opin Struct Biol 43:68–78
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826
Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7
Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE et al (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154:1380–1389
Wen W-S, Yuan Z-M, Ma S-J, Xu J, Yuan D-T (2016) CRISPR-Cas9 systems: versatile cancer modelling platforms and promising therapeutic strategies. Int J Cancer 138:1328–1336
Kim HK, Song M, Lee J, Vipin Menon A, Jung S, Kang Y-M et al (2016) In vivo high-throughput profiling of CRISPR–Cpf1 activity. Nat Methods 14:153–159
Friedland AE, Baral R, Singhal P, Loveluck K, Shen S, Sanchez M et al (2015) Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol 16:257. https://doi.org/10.1186/s13059-015-0817-8
Wong N, Liu W, Wang X (2015) WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 16:218
Haeussler M, Concordet J-P (2016) Genome editing with CRISPR-Cas9: can it get any better? J Genet Genomics 43:239–250
Moreno-Mateos MA, Vejnar CE, Beaudoin J-D, Fernandez JP, Mis EK, Khokha MK et al (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 12:982–988
Malina A, Cameron CJF, Robert F, Blanchette M, Dostie J, Pelletier J (2015) PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing. Nat Commun 6:10124
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud J-B et al (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF et al (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34:184–191
Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ et al (2015) Identification and characterization of essential genes in the human genome. Science 350:1096–1101
Abadi S, Yan WX, Amar D, Mayrose I (2017) A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput Biol. Public Library of Science 13:e1005807
Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM et al (2016) Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol. NIH Public Access 34:869
Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Keith Joung J et al (2013) High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. NIH Public Access 31:822
Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S et al (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. Cold Spring Harbor Laboratory Press 24:132
Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351:84–88
Zhang XH, Tee LY, Wang XG, Huang QS, Yang SH (2015) Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids. Cell Press 4:e264. https://doi.org/10.1038/mtna.2015.37
Jeffry D, Sander JKJ (2014) CRISPR-Cas systems for genome editing, regulation and targeting. Nat Biotechnol. NIH Public Access 32:347
Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P et al (2013) Optimization of scarless human stem cell genome editing. Nucleic Acids Res 41:9049–9061
Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE (2016) Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 34:339–344
Shrock E, Güell M (2017) CRISPR in animals and animal models. Prog Mol Biol Transl Sci. Academic Press 152:95–114
Guell M, Yang L, Church GM (2014) Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30:2968–2970
Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE et al (2016) Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol 34:695–697
Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V et al (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187–197
Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK (2017) CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods 14:607–614
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Pallarès Masmitjà, M., Knödlseder, N., Güell, M. (2019). CRISPR-gRNA Design. In: Luo, Y. (eds) CRISPR Gene Editing. Methods in Molecular Biology, vol 1961. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9170-9_1
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DOI: https://doi.org/10.1007/978-1-4939-9170-9_1
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