Abstract
A specific targeting nuclease is a powerful tool for mediating genome alternative expression with high precision. The RNA sequence-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate genome engineering in cells by using a 20-nt targeting sequence. In this chapter, we describe a set of tools for Cas9-mediated genome editing via non-homologous end joining (NHEJ) or homology-directed repair (HDR) in the generation of modified cell lines for downstream functional studies. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency, and analysis of off-target activity. Beginning with target design, we will cover gene modifications and modified clonal cell lines.
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References
Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157(6):1262–1278
Deveau H, Garneau JE, Moineau S (2010) CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 64:475–493
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170
Garneau JE et al (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71
Makarova KS et al (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9(6):467–477
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322(5909):1843–1845
Brouns SJ et al (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321(5891):960–964
Barrangou R et al (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315(5819):1709–1712
Sapranauskas R et al (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39(21):9275–9282
Magadan AH et al (2012) Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system. PLoS One 7(7):e40913
Gasiunas G et al (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109(39):E2579–E2586
Jinek M et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821
Zhang Y et al (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 50(4):488–503
Cong L et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823
Mali P et al (2013) RNA-guided human genome engineering via Cas9. Science 339(6121):823–826
Jinek M et al (2013) RNA-programmed genome editing in human cells. elife 2:e00471
Hwang WY et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31(3):227–229
Wang H et al (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910–918
Shen B et al (2013) Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23(5):720–723
Ran FA et al (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6):1380–1389
Qi LS et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183
Acknowledgments
National Cancer Institute Core (5P30CA013696), Foundation Fighting Blindness (TA-NMT-0116-0692-COLU), and New York State (C029572).
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Stephen H. Tsang receives grant support from Abeona Therapeutics, Inc and Emendo. He is also the founder of Rejuvitas and is on the scientific and clinical advisory board for Nanoscope Therapeutics and Medical Excellence Capital.
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Chang, YJ., Ryu, J., Cui, X., Tsang, S.H. (2023). CRISPR-Mediated Genome Engineering in Cell Lines. In: Tsang, S.H., Quinn, P.M. (eds) Retinitis Pigmentosa. Methods in Molecular Biology, vol 2560. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2651-1_25
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DOI: https://doi.org/10.1007/978-1-0716-2651-1_25
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