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2 - Unbiased Detection of Off-target Cleavage by CRISPR/Cas9 and TALENs Using Integration-defective Lentiviral Vectors

from Part I - Biology of Endonucleases (Zinc-Finger Nuclease, TALENs and CRISPRs) and Regulatory Networks

Published online by Cambridge University Press:  30 July 2018

By
Youjun Wu  and
Jiing-Kuan Yee
Edited by
Krishnarao Appasani
Foreword by
George M. Church
Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
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Chapter
Information
Genome Editing and Engineering
From TALENs, ZFNs and CRISPRs to Molecular Surgery
 , pp. 22 - 36
Publisher: Cambridge University Press
Print publication year: 2018

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References

Chen, B, Gilbert, LA, Cimini, BA, et al. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155: 1479–1491.CrossRefGoogle ScholarPubMed
Choulika, A, Perrin, A, Dujon, B, Nicolas, JF. 1995. Induction of homologous recombination in mammalian chromosomes by using the I-Scei system of Saccharomyces cerevisiae. Mol Cell Biol 15: 1968–1973.CrossRefGoogle ScholarPubMed
Christian, M, Cermak, T, Doyle, EL, et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757–761.CrossRefGoogle ScholarPubMed
Crosetto, N, Mitra, A, Silva, MJ, et al. 2013. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods 10: 361–365.CrossRefGoogle ScholarPubMed
Frock, RL, Hu, J, Meyers, RM, et al. 2015. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol 33: 179–186.CrossRefGoogle ScholarPubMed
Fu, Y, Foden, JA, Khayter, C, et al. 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31: 822–826.CrossRefGoogle ScholarPubMed
Fu, Y, Sander, JD, Reyon, D, et al. 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32: 279–284.CrossRefGoogle ScholarPubMed
Gabriel, R, Lombardo, A, Arens, A, et al. 2011. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29: 816–823.CrossRefGoogle ScholarPubMed
Gaj, T, Gersbach, CA, Barbas, CF III. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31: 397–405.CrossRefGoogle ScholarPubMed
Gao, F, Shen, XZ, Jiang, F, Wu, Y, Han, C. 2016. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nat Biotechnol 34: 768–773.CrossRefGoogle ScholarPubMed
Guilinger, JP, Pattanayak, V, Reyon, D, et al. 2014a. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Methods 11: 429–435.CrossRefGoogle ScholarPubMed
Guilinger, JP, Thompson, DB, Liu, DR. 2014b. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32: 577–582.CrossRefGoogle ScholarPubMed
Guschin, DY, Waite, AJ, Katibah, GE, et al. 2010. A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649: 247–256.CrossRefGoogle ScholarPubMed
Hacein-Bey-Abina, S, Von Kalle, C, Schmidt, M, et al. 2003. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N Engl J Med 348: 255–256.CrossRefGoogle ScholarPubMed
Honma, M, Sakuraba, M, Koizumi, T, et al. 2007. Non-homologous end-joining for repairing I-SceI-induced DNA double strand breaks in human cells. DNA Repair (Amst) 6: 781–788.CrossRefGoogle ScholarPubMed
Hsu, PD, Scott, DA, Weinstein, JA, et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827–832.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–821.CrossRefGoogle ScholarPubMed
Kim, D, Bae, S, Park, J, et al. 2015. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods 12: 237–243, 1 p following 243.CrossRefGoogle ScholarPubMed
Kim, YG, Cha, J, Chandrasegaran, S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 93: 1156–1160.CrossRefGoogle ScholarPubMed
Komor, AC, Kim, YB, Packer, MS, Zuris, JA, Liu, DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533: 420–424.CrossRefGoogle ScholarPubMed
Lieber, MR. 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79: 181–211.CrossRefGoogle ScholarPubMed
Lin, YN, Cradick, TJ, Brown, MT, et al. 2014. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 42: 7473–7485.CrossRefGoogle ScholarPubMed
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J, Almendros, C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155: 733–740.CrossRefGoogle ScholarPubMed
Nelles, DA, Fang, MY, O’Connell, MR, et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165: 488–496.CrossRefGoogle ScholarPubMed
Osborn, MJ, Starker, CG, McElroy, AN, et al. 2013. TALEN-based gene correction for epidermolysis bullosa. Mol Ther 21: 1151–1159.CrossRefGoogle ScholarPubMed
Paruzynski, A, Arens, A, Gabriel, R, et al. 2010. Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat Protoc 5: 1379–1395.CrossRefGoogle ScholarPubMed
Pierson, TC, Kieffer, TL, Ruff, CT, et al. 2002. Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication. J Virol 76: 4138–4144.CrossRefGoogle ScholarPubMed
Ran, FA, Cong, L, Yan, WX, et al. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520: 186–191.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Lin, CY, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380–1389.CrossRefGoogle ScholarPubMed
Saenz, DT, Loewen, N, Peretz, M, et al. 2004. Unintegrated lentivirus DNA persistence and accessibility to expression in nondividing cells: analysis with class I integrase mutants. J Virol 78: 2906–2920.CrossRefGoogle ScholarPubMed
Shah, SA, Erdmann, S, Mojica, FJ, Garrett, RA. 2013. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 10: 891–899.CrossRefGoogle ScholarPubMed
Shen, B, Zhang, W, Zhang, J, et al. 2014. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11: 399–402.CrossRefGoogle ScholarPubMed
Shrivastav, M, De Haro, LP, Nickoloff, JA. 2008. Regulation of DNA double-strand break repair pathway choice. Cell Res 18: 134–147.CrossRefGoogle ScholarPubMed
Silva, G, Poirot, L, Galetto, R, et al. 2011. Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr Gene Ther 11: 11–27.CrossRefGoogle ScholarPubMed
Smith, C, Gore, A, Yan, W, et al. 2014. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15: 12–13.CrossRefGoogle ScholarPubMed
Tsai, SQ, Zheng, Z, Nguyen, NT, et al. 2015. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33: 187–197.CrossRefGoogle ScholarPubMed
Veres, A, Gosis, BS, Ding, Q, et al. 2014. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15: 27–30.CrossRefGoogle ScholarPubMed
Vigna, E, Naldini, L. 2000. Lentiviral vectors: excellent tools for experimental gene transfer and promising candidates for gene therapy. J Gene Med 2: 308–316.3.0.CO;2-3>CrossRefGoogle ScholarPubMed
Wang, X, Wang, Y, Wu, X, et al. 2015. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 33: 175–178.CrossRefGoogle ScholarPubMed
Wanisch, K, Yanez-Munoz, RJ. 2009. Integration-deficient lentiviral vectors: a slow coming of age. Mol Ther 17: 1316–1332.CrossRefGoogle ScholarPubMed
Weinstock, DM, Jasin, M. 2006. Alternative pathways for the repair of RAG-induced DNA breaks. Mol Cell Biol 26: 131–139.CrossRefGoogle ScholarPubMed
Wu, X, Scott, DA, Kriz, AJ, et al. 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32: 670–676.CrossRefGoogle ScholarPubMed
Wyman, C, Kanaar, R. 2006. DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40: 363–383.CrossRefGoogle ScholarPubMed
Zhou, Y, Zhu, S, Cai, C, et al. 2014. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509: 487–491.CrossRefGoogle ScholarPubMed

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