Book contents
- Genome Editing and Engineering
- Genome Editing and Engineering
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Biology of Endonucleases (Zinc-Finger Nuclease, TALENs and CRISPRs) and Regulatory Networks
- Part II Genome Editing in Model Organisms
- Part III Technology Development and Screening
- 11 CRISPR Genome Editing in Mice
- 12 Detection of Insertion/Deletion (Indel) Events after Genome Targeting: Pros and Cons of the Available Methods
- 13 Application of TAL Proteins and the CRISPR System to Purification of Specific Genomic Regions for Locus-specific Identification of Chromatin-associated Molecules
- 14 Application of CRISPR for Pooled, Vector-based Functional Genomic Screening in Mammalian Cell Lines
- 15 Generation and Utilization of CRISPR/Cas9 Screening Libraries in Mammalian Cells
- Part IV Genome Editing in Stem Cells and Regenerative Biology
- Part V Genome Editing in Disease Biology
- Part VI Legal (Intellectual Property) and Bioethical Issues of Genome Editing
- Index
- Plate Section (PDF Only)
- References
11 - CRISPR Genome Editing in Mice
from Part III - Technology Development and Screening
Published online by Cambridge University Press: 30 July 2018
Edited by
Foreword by
Book contents
- Genome Editing and Engineering
- Genome Editing and Engineering
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Biology of Endonucleases (Zinc-Finger Nuclease, TALENs and CRISPRs) and Regulatory Networks
- Part II Genome Editing in Model Organisms
- Part III Technology Development and Screening
- 11 CRISPR Genome Editing in Mice
- 12 Detection of Insertion/Deletion (Indel) Events after Genome Targeting: Pros and Cons of the Available Methods
- 13 Application of TAL Proteins and the CRISPR System to Purification of Specific Genomic Regions for Locus-specific Identification of Chromatin-associated Molecules
- 14 Application of CRISPR for Pooled, Vector-based Functional Genomic Screening in Mammalian Cell Lines
- 15 Generation and Utilization of CRISPR/Cas9 Screening Libraries in Mammalian Cells
- Part IV Genome Editing in Stem Cells and Regenerative Biology
- Part V Genome Editing in Disease Biology
- Part VI Legal (Intellectual Property) and Bioethical Issues of Genome Editing
- Index
- Plate Section (PDF Only)
- References
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.
- Type
- Chapter
- Information
- Genome Editing and EngineeringFrom TALENs, ZFNs and CRISPRs to Molecular Surgery, pp. 165 - 180Publisher: Cambridge University PressPrint publication year: 2018
References
Bae, S, Kweon, J, Kim, HS, Kim, J-S. 2014. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods 11: 705–706.CrossRefGoogle ScholarPubMed
Barbaric, I, Miller, G, Dear, TN. 2007. Appearances can be deceiving: phenotypes of knockout mice. Brief Funct Genomic Proteomic 6: 91–103.CrossRefGoogle ScholarPubMed
Bassett, AR, Tibbit, C, Ponting, CP, Liu, J-L. 2013. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4: 220–228.CrossRefGoogle ScholarPubMed
Bétermier, M, Bertrand, P, Lopez, BS. 2014. Is non-homologous end-joining really an inherently error-prone process? PLoS Genet 10(1): e1004086.CrossRefGoogle ScholarPubMed
Bishop, KA, Harrington, A, Kouranova, E, et al. 2016. CRISPR/Cas9-mediated insertion of loxP sites in the mouse dock7 gene provides an effective alternative to use of targeted embryonic stem cells. G3 (Bethesda) 6: 2051–2061.CrossRefGoogle ScholarPubMed
Bolotin, A, Quinquis, B, Sorokin, A, Ehrlich, SD. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551–2561.CrossRefGoogle ScholarPubMed
Brouns, SJJ, Jore, MM, Lundgren, M, et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960–964.CrossRefGoogle ScholarPubMed
Carbery, ID, Ji, D, Harrington, A, et al. 2010. Targeted genome modification in mice using zinc-finger nucleases. Genetics 186: 451–459.CrossRefGoogle ScholarPubMed
Cheng, R, Peng, J, Yan, Y, et al. 2014. Efficient gene editing in adult mouse livers via adenoviral delivery of CRISPR/Cas9. FEBS Lett 588: 3954–3958.CrossRefGoogle ScholarPubMed
Chiruvella, KK, Liang, Z, Wilson, TE. 2013. Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol 5(5): a012757.CrossRefGoogle ScholarPubMed
Chu, VT, Weber, T, Wefers, B, et al. 2015. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33: 543–548.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819–823.CrossRefGoogle ScholarPubMed
Crespan, E, Czabany, T, Maga, G, Hübscher, U. 2012. Microhomology-mediated DNA strand annealing and elongation by human DNA polymerases λ and β on normal and repetitive DNA sequences. Nucleic Acids Res 40(12): 5577–5590.CrossRefGoogle ScholarPubMed
Davies, B, Davies, G, Preece, C, et al. 2013. Site specific mutation of the Zic2 locus by microinjection of TALEN mRNA in mouse CD1, C3H and C57BL/6J oocytes. PLoS One 8: e60216.CrossRefGoogle ScholarPubMed
Davis, AJ, Chen, DJ, 2013. DNA double strand break repair via non-homologous end-joining. Transl Cancer Res 2: 130–143.Google ScholarPubMed
Decottignies, A. 2013. Alternative end-joining mechanisms: a historical perspective. Front Genet 4: 48.CrossRefGoogle ScholarPubMed
Deriano, L, Roth, DB. 2013. Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 47: 433–455.CrossRefGoogle ScholarPubMed
Dianov, GL, Hübscher, U. 2013. Mammalian base excision repair: the forgotten archangel. Nucleic Acids Res 41: 3483–3490.CrossRefGoogle ScholarPubMed
DiCarlo, JE, Norville, JE, Mali, P, et al. 2013. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41: 4336–4343.CrossRefGoogle ScholarPubMed
Dueva, R, Iliakis, G. 2013. Alternative pathways of non-homologous end joining (NHEJ) in genomic instability and cancer. Transl Cancer Res 2: 163–177.Google Scholar
Fujii, W, Kawasaki, K, Sugiura, K, Naito, K. 2013. Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res 41: e187.CrossRefGoogle ScholarPubMed
Gao, P, Yang, H, Rajashankar, KR, Huang, Z, Patel, DJ. 2016. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res 26: 901–913.CrossRefGoogle ScholarPubMed
Griep, AE, John, MC, Ikeda, S, Ikeda, A. 2011. Gene targeting in the mouse. Methods Mol Biol 770: 293–312.CrossRefGoogle ScholarPubMed
Guilinger, JP, Thompson, DB, Liu, DR 2014. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32: 577–582.CrossRefGoogle ScholarPubMed
Haeussler, M, Schönig, K, Eckert, H. 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.CrossRefGoogle ScholarPubMed
Hall, B, Limaye, A, Kulkarni, AB. 2009. Overview: generation of gene knockout mice. Curr Protoc Cell Biol Chapter: Unit-19.1217.CrossRefGoogle Scholar
Hara, S, Tamano, M, Yamashita, S, et al. 2015. Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Sci Rep 5: 11221.CrossRefGoogle ScholarPubMed
Heckl, D, Kowalczyk, MS, Yudovich, D, et al. 2014. Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing. Nat Biotechnol 32: 941–946.CrossRefGoogle ScholarPubMed
Heyer, W-D, Ehmsen, KT, Liu, J. 2010. Regulation of homologous recombination in eukaryotes. Annu Rev Genet 44: 113–139.CrossRefGoogle ScholarPubMed
Hur, JK, Kim, K, Been, KW, et al. 2016. Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins. Nat Biotechnol 34(8): 807–808.CrossRefGoogle ScholarPubMed
Hwang, WY, Fu, Y, Reyon, D, et al. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31: 227–229.CrossRefGoogle ScholarPubMed
Isken, O, Maquat, LE. 2007. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 21: 1833–3856.CrossRefGoogle ScholarPubMed
Jasin, M, Rothstein, R. 2013. Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol 5: a012740.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, Kim, J, Hur, JK, et al. 2016. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol 34: 863–868.CrossRefGoogle ScholarPubMed
Kleinstiver, BP, Pattanayak, V, Prew, MS, et al. 2016. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529: 490–495.CrossRefGoogle ScholarPubMed
Kleinstiver, BP, Prew, MS, Tsai, SQ, et al. 2015. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523: 481–485.CrossRefGoogle ScholarPubMed
Lee, AY-F, Lloyd, KCK. 2014. Conditional targeting of Ispd using paired Cas9 nickase and a single DNA template in mice. FEBS Open Bio 4: 637–642.CrossRefGoogle Scholar
Lee, CM, Cradick, TJ, Bao, G. 2016. The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells. Mol Ther J Am Soc Gene Ther 24: 645–654.CrossRefGoogle ScholarPubMed
Lieber, MR. 1999. The biochemistry and biological significance of nonhomologous DNA end joining: an essential repair process in multicellular eukaryotes. Genes Cells Devoted Mol Cell Mech 4: 77–85.CrossRefGoogle ScholarPubMed
Mali, P, Yang, L, Esvelt, KM, et al. 2013. RNA-guided human genome engineering via Cas9. Science 339: 823–826.CrossRefGoogle ScholarPubMed
Mao, Z, Jiang, Y, Liu, X, Seluanov, A, Gorbunova, V. 2009. DNA repair by homologous recombination, but not by nonhomologous end joining, is elevated in breast cancer cells. Neoplasia N Y N 11: 683–691.CrossRefGoogle Scholar
Maruyama, T, Dougan, SK, Truttmann, MC, et al. 2015. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33: 538–542.CrossRefGoogle ScholarPubMed
Matsuzaki, K, Terasawa, M, Iwasaki, D, Higashide, M, Shinohara, M. 2012. Cyclin-dependent kinase-dependent phosphorylation of Lif1 and Sae2 controls imprecise nonhomologous end joining accompanied by double-strand break resection. Genes Cells Devoted Mol Cell Mech 17: 473–493.CrossRefGoogle ScholarPubMed
McVey, M, Lee, SE. 2008. MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings. Trends Genet 24: 529–538.CrossRefGoogle ScholarPubMed
Mehta, A, Haber, JE. 2014. Sources of DNA double-strand breaks and models of recombinational DNA repair. Cold Spring Harb Perspect Biol 6: a016428.CrossRefGoogle ScholarPubMed
Ménoret, S, De Cian, A, Tesson, L, et al. 2015. Homology-directed repair in rodent zygotes using Cas9 and TALEN engineered proteins. Sci Rep 5: 14410.CrossRefGoogle ScholarPubMed
Müller, M, Lee, CM, Gasiunas, G, et al. 2016. Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome. Mol Ther J Am Soc Gene Ther 24: 636–644.CrossRefGoogle ScholarPubMed
Nakagawa, Y, Sakuma, T, Nishimichi, N, et al. 2016. Ultra-superovulation for the CRISPR-Cas9-mediated production of gene-knockout, single-amino-acid-substituted, and floxed mice. Biol Open 5(8): 1142–1148.CrossRefGoogle ScholarPubMed
Nishimasu, H, Ran, FA, Hsu, PD, et al. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156: 935–949.CrossRefGoogle ScholarPubMed
Niu, Y, Shen, B, Cui, Y, et al. 2014. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156: 836–843.CrossRefGoogle ScholarPubMed
Onuma, A, Fujii, W, Sugiura, K, Naito, K. 2016. Efficient mutagenesis by CRISPR/Cas system during meiotic maturation of porcine oocytes. J Reprod Dev 63(1): 45–50.CrossRefGoogle ScholarPubMed
Qin, W, Dion, SL, Kutny, PM, et al. 2015. Efficient CRISPR/Cas9-mediated genome editing in mice by zygote electroporation of nuclease. Genetics 200: 423–430.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Lin, C-Y, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380–1389.CrossRefGoogle ScholarPubMed
Renaud, J-B, Boix, C, Charpentier, M, et al. 2016. Improved genome editing efficiency and flexibility using modified oligonucleotides with TALEN and CRISPR-Cas9 nucleases. Cell Rep 14: 2263–2272.CrossRefGoogle ScholarPubMed
Roth, DB, Wilson, JH. 1986. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol Cell Biol 6: 4295–4304.Google ScholarPubMed
Shen, B, Zhang, J, Wu, H, et al. 2013. Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23: 720–723.CrossRefGoogle ScholarPubMed
Simsek, D, Jasin, M. 2010. Alternative end-joining is suppressed by the canonical NHEJ component Xrcc4-ligase IV during chromosomal translocation formation. Nat Struct Mol Biol 17: 410–416.CrossRefGoogle ScholarPubMed
Singh, P, Schimenti, JC, Bolcun-Filas, E. 2015. A mouse geneticist’s practical guide to CRISPR applications. Genetics 199: 1–15.CrossRefGoogle ScholarPubMed
Slaymaker, IM, Gao, L, Zetsche, B, et al. 2016. Rationally engineered Cas9 nucleases with improved specificity. Science 351: 84–88.CrossRefGoogle ScholarPubMed
Sorek, R, Lawrence, CM, Wiedenheft, B. 2013. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82: 237–266.CrossRefGoogle ScholarPubMed
Sternberg, SH, Redding, S, Jinek, M, Greene, EC, Doudna, JA. 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507: 62–67.CrossRefGoogle ScholarPubMed
Tesson, L, Usal, C, Ménoret, S, et al. 2011. Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29: 695–696.CrossRefGoogle ScholarPubMed
Vartak, SV, Raghavan, SC. 2015. Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing. FEBS J 282: 4289–4294.CrossRefGoogle ScholarPubMed
Wang, B, Li, K, Wang, A, et al. 2015. Highly efficient CRISPR/HDR-mediated knock-in for mouse embryonic stem cells and zygotes. BioTechniques 59: 201–202, 204, 206–208.CrossRefGoogle ScholarPubMed
Wang, H, Yang, H, Shivalila, CS, et al. 2013. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153: 910–918.CrossRefGoogle ScholarPubMed
Wang, X, Cai, B, Zhou, J, et al. 2016. Disruption of FGF5 in cashmere goats using CRISPR/Cas9 results in more secondary hair follicles and longer fibers. PLoS One 11: e0164640.CrossRefGoogle ScholarPubMed
Xing, H-L, Dong, L, Wang, Z-P, et al. 2014. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14: 327.CrossRefGoogle ScholarPubMed
Yang, H, Wang, H, Jaenisch, R. 2014. Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Nat Protoc 9: 1956–1968.CrossRefGoogle ScholarPubMed
Yang, H, Wang, H, Shivalila, CS, et al. 2013. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas mediated genome engineering. Cell 154: 1370–1379.CrossRefGoogle ScholarPubMed
Yasue, A, Mitsui, SN, Watanabe, T, et al. 2014. Highly efficient targeted mutagenesis in one-cell mouse embryos mediated by the TALEN and CRISPR/Cas systems. Sci Rep 4: 5705.CrossRefGoogle ScholarPubMed
Zetsche, B, Gootenberg, JS, Abudayyeh, OO, et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163: 759–771.CrossRefGoogle ScholarPubMed
Zhang, L, Jia, R, Palange, NJ, et al. 2015. Large genomic fragment deletions and insertions in mouse using CRISPR/Cas9. PLoS One 10: e0120396.CrossRefGoogle ScholarPubMed
Zhu, Z, Verma, N, González, F, Shi, Z-D, Huangfu, D. 2015. A CRISPR/Cas-mediated selection-free knockin strategy in human embryonic stem cells. Stem Cell Rep 4: 1103–1111.CrossRefGoogle ScholarPubMed