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Genome-Editing Technology in CRISPR/Cas System: How to Increase Knock-In Efficiency in Mouse Zygotes

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Genome Editing
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Abstract

The use of clustered regularly interspaced short palindromic repeats (CRISPR) and RNA-guided Cas9 nucleases, known as the CRISPR/Cas system, represents a major technological advance in mammalian gene disruption. CRISPR/Cas enables genome editing by inducing targeted DNA double-strand breaks (DSBs) that are repaired by error-prone, nonhomologous end-joining (NHEJ), or homology-directed repair (HDR). This system has emerged as an effective tool for gene knockout via NHEJ; however, it remains inefficient for precise editing of genome sequences depending on HDR. Nevertheless, HDR-mediated gene editing is essential for conditional knockout, introduction of reporter genes, and precise point mutation in mice. Many studies have examined, for example, conditions of Cas9 and guide RNA (gRNA), methods of their introduction, and molecules to increase efficiency. In this review, we describe various methods for increasing the efficiency of editing in mouse zygotes.

Author Contributions

T. Horii and I. Hatada wrote the manuscript.

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Abbreviations

amiRNA:

Artificial microRNA

CRISPR:

Clustered regularly interspaced short palindromic repeats

crRNA:

CRISPR RNA

DSB:

Double-strand breaks

dsDNA:

Double-stranded DNA

ESC:

Embryonic stem cell

gRNA:

Guide RNA

HDR:

Homology-directed repair

indels:

Insertions or deletions

iPSC:

Induced pluripotent stem cells

NHEJ:

Nonhomologous end-joining

ssODN:

Single-stranded oligo-DNA

TALEN:

Transcription activator-like effector nucleases

tracrRNA:

Trans-activating crRNA

ZFN:

Zinc-finger nucleases

References

  1. Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A. 1996;93(3):1156–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol. 2011;29(2):143–8. doi:10.1038/nbt.1755.

    Article  CAS  PubMed  Google Scholar 

  3. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–21. doi:10.1126/science.1225829.

    Article  CAS  PubMed  Google Scholar 

  4. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471(7340):602–7. doi:10.1038/nature09886.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Barnes DE. Non-homologous end joining as a mechanism of DNA repair. Curr Biol. 2001;11(12):R455–7.

    Article  CAS  PubMed  Google Scholar 

  6. Lieber MR. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem. 2010;79:181–211. doi:10.1146/annurev.biochem.052308.093131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. van den Bosch M, Lohman PH, Pastink A. DNA double-strand break repair by homologous recombination. Biol Chem. 2002;383(6):873–92. doi:10.1515/bc.2002.095.

    Article  PubMed  Google Scholar 

  8. Wyman C, Kanaar R. DNA double-strand break repair: all’s well that ends well. Annu Rev Genet. 2006;40:363–83. doi:10.1146/annurev.genet.40.110405.090451.

    Article  CAS  PubMed  Google Scholar 

  9. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013;153(4):910–8. doi:10.1016/j.cell.2013.04.025.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell. 2013;154(6):1370–9. doi:10.1016/j.cell.2013.08.022.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823–6. doi:10.1126/science.1232033.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mashiko D, Young SA, Muto M, Kato H, Nozawa K, Ogawa M, Noda T, Kim YJ, Satouh Y, Fujihara Y, Ikawa M. Feasibility for a large scale mouse mutagenesis by injecting CRISPR/Cas plasmid into zygotes. Dev Growth Differ. 2014;56(1):122–9. doi:10.1111/dgd.12113.

    Article  CAS  PubMed  Google Scholar 

  13. Mashiko D, Fujihara Y, Satouh Y, Miyata H, Isotani A, Ikawa M. Generation of mutant mice by pronuclear injection of circular plasmid expressing Cas9 and single guided RNA. Sci Rep. 2013;3:3355. doi:10.1038/srep03355.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Horii T, Arai Y, Yamazaki M, Morita S, Kimura M, Itoh M, Abe Y, Hatada I. Validation of microinjection methods for generating knockout mice by CRISPR/Cas-mediated genome engineering. Sci Rep. 2014;4:4513. doi:10.1038/srep04513.

    Article  PubMed  Google Scholar 

  15. Lee AY, Lloyd KC. Conditional targeting of Ispd using paired Cas9 nickase and a single DNA template in mice. FEBS Open Bio. 2014;4:637–42. doi:10.1016/j.fob.2014.06.007. eCollection 2014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Miura H, Gurumurthy CB, Sato T, Sato M, Ohtsuka M. CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA. Sci Rep. 2015;5:12799. doi:10.1038/srep12799.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Sakurai T, Watanabe S, Kamiyoshi A, Sato M, Shindo T. A single blastocyst assay optimized for detecting CRISPR/Cas9 system-induced indel mutations in mice. BMC Biotechnol. 2014;14:69. doi:10.1186/1472-6750-14-69.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Singh P, Schimenti JC, Bolcun-Filas E. A mouse geneticist’s practical guide to CRISPR applications. Genetics. 2015;199(1):1–15. doi:10.1534/genetics.114.169771.

    Article  CAS  PubMed  Google Scholar 

  19. Sung YH, Kim JM, Kim HT, Lee J, Jeon J, Jin Y, Choi JH, Ban YH, Ha SJ, Kim CH, Lee HW, Kim JS. Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases. Genome Res. 2014;24(1):125–31. doi:10.1101/gr.163394.113.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Aida T, Chiyo K, Usami T, Ishikubo H, Imahashi R, Wada Y, Tanaka KF, Sakuma T, Yamamoto T, Tanaka K. Cloning-free CRISPR/Cas system facilitates functional cassette knock-in in mice. Genome Biol. 2015;16:87. doi:10.1186/s13059-015-0653-x.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Fujii W, Kawasaki K, Sugiura K, Naito K. Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res. 2013;41(20), e187. doi:10.1093/nar/gkt772.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Shen B, Zhang J, Wu H, Wang J, Ma K, Li Z, Zhang X, Zhang P, Huang X. Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res. 2013;23(5):720–3. doi:10.1038/cr.2013.46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hashimoto M, Takemoto T. Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing. Sci Rep. 2015;5:11315. doi:10.1038/srep11315.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kaneko T, Sakuma T, Yamamoto T, Mashimo T. Simple knockout by electroporation of engineered endonucleases into intact rat embryos. Sci Rep. 2014;4:6382. doi:10.1038/srep06382.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yang H, Wang H, Jaenisch R. Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Nat Protoc. 2014;9(8):1956–68. doi:10.1038/nprot.2014.134.

    Article  CAS  PubMed  Google Scholar 

  26. Fujii W, Onuma A, Sugiura K, Naito K. Efficient generation of genome-modified mice via offset-nicking by CRISPR/Cas system. Biochem Biophys Res Commun. 2014;445(4):791–4. doi:10.1016/j.bbrc.2014.01.141.

    Article  CAS  PubMed  Google Scholar 

  27. Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol. 2015;33(5):538–42. doi:10.1038/nbt.3190.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wu Y, Liang D, Wang Y, Bai M, Tang W, Bao S, Yan Z, Li D, Li J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. 2013;13(6):659–62. doi:10.1016/j.stem.2013.10.016.

    Article  CAS  PubMed  Google Scholar 

  29. Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, Kühn R. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol. 2015;33(5):543–8. doi:10.1038/nbt.3198.

    Article  CAS  PubMed  Google Scholar 

  30. Srivastava M, Nambiar M, Sharma S, Karki SS, Goldsmith G, Hegde M, Kumar S, Pandey M, Singh RK, Ray P, Natarajan R, Kelkar M, De A, Choudhary B, Raghavan SC. An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression. Cell. 2012;151(7):1474–87. doi:10.1016/j.cell.2012.11.054.

    Article  CAS  PubMed  Google Scholar 

  31. Bétermier M, Bertrand P, Lopez BS. Is non-homologous end-joining really an inherently error-prone process? PLoS Genet. 2014;10(1), e1004086. doi:10.1371/journal.pgen.1004086.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Yu C, Liu Y, Ma T, Liu K, Xu S, Zhang Y, Liu H, La Russa M, Xie M, Ding S, Qi LS. Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell. 2015;16(2):142–7. doi:10.1016/j.stem.2015.01.003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hollick JJ, Golding BT, Hardcastle IR, Martin N, Richardson C, Rigoreau LJ, Smith GC, Griffin RJ. 2,6-Disubstituted pyran-4-one and thiopyran-4-one inhibitors of DNA-dependent protein kinase (DNA-PK). Bioorg Med Chem Lett. 2003;13(18):3083–6.

    Article  CAS  PubMed  Google Scholar 

  34. Rahman SH, Bobis-Wozowicz S, Chatterjee D, Gellhaus K, Pars K, Heilbronn R, Jacobs R, Cathomen T. The nontoxic cell cycle modulator indirubin augments transduction of adeno-associated viral vectors and zinc-finger nuclease-mediated gene targeting. Hum Gene Ther. 2013;24(1):67–77. doi:10.1089/hum.2012.168. Epub 2012 Dec 10.

    Article  CAS  PubMed  Google Scholar 

  35. Hatada S, Subramanian A, Mandefro B, Ren S, Kim HW, Tang J, Funari V, Baloh RH, Sareen D, Arumugaswami V, Svendsen CN. Low-dose irradiation enhances gene targeting in human pluripotent stem cells. Stem Cells Transl Med. 2015;4(9):998–1010. doi:10.5966/sctm.2015-0050.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Heyer WD, Ehmsen KT, Liu J. Regulation of homologous recombination in eukaryotes. Annu Rev Genet. 2010;44:113–39. doi:10.1146/annurev-genet-051710-150955.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lin S, Staahl BT, Alla RK, Doudna JA. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. elife. 2014;3:e04766. doi:10.7554/eLife.04766.

  38. Adenot PG, Mercier Y, Renard JP, Thompson EM. Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos. Development. 1997;124(22):4615–25.

    CAS  PubMed  Google Scholar 

  39. Yoshimi K, Kaneko T, Voigt B, Mashimo T. Allele-specific genome editing and correction of disease-associated phenotypes in rats using the CRISPR-Cas platform. Nat Commun. 2014;5:4240. doi:10.1038/ncomms5240.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Huang X, Wang Y, Yan W, Smith C, Ye Z, Wang J, Gao Y, Mendelsohn L, Cheng L. Production of gene-corrected adult beta globin protein in human erythrocytes differentiated from patient iPSCs after genome editing of the sickle point mutation. Stem Cells. 2015;33(5):1470–9. doi:10.1002/stem.1969.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Li HL, Fujimoto N, Sasakawa N, Shirai S, Ohkame T, Sakuma T, Tanaka M, Amano N, Watanabe A, Sakurai H, Yamamoto T, Yamanaka S, Hotta A. Precise correction of the dystrophin gene in Duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Rep. 2015;4(1):143–54. doi:10.1016/j.stemcr.2014.10.013.

    Article  CAS  Google Scholar 

  42. Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA. Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nat Commun. 2015;6:6244. doi:10.1038/ncomms7244.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Song B, Fan Y, He W, Zhu D, Niu X, Wang D, Ou Z, Luo M, Sun X. Improved hematopoietic differentiation efficiency of gene-corrected beta-thalassemia induced pluripotent stem cells by CRISPR/Cas9 system. Stem Cells Dev. 2015;24(9):1053–65. doi:10.1089/scd.2014.0347.

    Article  CAS  PubMed  Google Scholar 

  44. Xie F, Ye L, Chang JC, Beyer AI, Wang J, Muench MO, Kan YW. Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac. Genome Res. 2014;24(9):1526–33. doi:10.1101/gr.173427.114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Liang P, Xu Y, Zhang X, Ding C, Huang R, Zhang Z, Lv J, Xie X, Chen Y, Li Y, Sun Y, Bai Y, Songyang Z, Ma W, Zhou C, Huang J. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 2015;6(5):363–72. doi:10.1007/s13238-015-0153-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported in part by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan; the Ministry of Health, Labor, and Welfare of Japan; the National Institute of Biomedical Innovation; and the Takeda Science Foundation.

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The authors declare no conflicts of interest.

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Correspondence to Izuho Hatada .

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Horii, T., Hatada, I. (2016). Genome-Editing Technology in CRISPR/Cas System: How to Increase Knock-In Efficiency in Mouse Zygotes. In: Turksen, K. (eds) Genome Editing. Springer, Cham. https://doi.org/10.1007/978-3-319-34148-4_5

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