Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-78c5997874-fbnjt Total loading time: 0 Render date: 2024-11-11T07:33:21.913Z Has data issue: false hasContentIssue false

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.
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
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

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

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

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×