Analysing the outcome of CRISPR-aided genome editing in embryos: Screening, genotyping and quality control

Methods

Volumn 121-122, Issue , 2017, Pages 68-76

  Mianné, Joffrey ^a   Codner, Gemma F ^a   Caulder, Adam ^a   Fell, Rachel ^a   Hutchison, Marie ^a   King, Ruairidh ^a   Stewart, Michelle E ^a   Wells, Sara ^a   Teboul, Lydia ^a  

^a Medical Research Council Harwell Institute   (United Kingdom)

Author keywords

Cas9; CRISPR; Genome editing; Genotyping; Mouse; Mutant; QC; Screening

Indexed keywords

ALLELE; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; CRISPR-CAS9 SYSTEM; EMBRYO; FEMALE; GENE DELETION; GENE EDITING; GENE MUTATION; GENETIC SCREENING; GENOTYPE; IN VIVO STUDY; MOLECULAR GENETICS; MOSAICISM; MOUSE; MUTAGENESIS; MUTANT; NONHUMAN; OUTCOME ASSESSMENT; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; ANIMAL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; CYTOLOGY; DNA END JOINING REPAIR; DOUBLE STRANDED DNA BREAK; GENE KNOCKOUT; GENE TARGETING; GENE TRANSFER; GENETICS; GENOME; GENOTYPING TECHNIQUE; INDEL MUTATION; MAMMALIAN EMBRYO; METABOLISM; MICROINJECTION; NEWBORN; POINT MUTATION; PROCEDURES; RECOMBINATION REPAIR; TRANSGENIC MOUSE; ZYGOTE;

BACTERIAL PROTEIN; CAS9 ENDONUCLEASE STREPTOCOCCUS PYOGENES; ENDONUCLEASE; GUIDE RNA;

ALLELES; ANIMALS; ANIMALS, NEWBORN; BACTERIAL PROTEINS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DNA BREAKS, DOUBLE-STRANDED; DNA END-JOINING REPAIR; EMBRYO, MAMMALIAN; ENDONUCLEASES; GENE EDITING; GENE KNOCKOUT TECHNIQUES; GENE TARGETING; GENE TRANSFER TECHNIQUES; GENOME; GENOTYPING TECHNIQUES; INDEL MUTATION; MICE; MICE, TRANSGENIC; MICROINJECTIONS; POINT MUTATION; QUALITY CONTROL; RECOMBINATIONAL DNA REPAIR; RNA, GUIDE; ZYGOTE;

EID: 85020873454     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2017.03.016     Document Type: Review

References (22)

1. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier, E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:6096 (2012), 816–821.
2. Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., Zhang, F., Multiplex genome engineering using CRISPR/Cas systems. Science 339:6121 (2013), 819–823.
3. Wang, H., Yang, H., Shivalila, C.S., Dawlaty, M.M., Cheng, A.W., Zhang, F., Jaenisch, R., One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:4 (2013), 910–918.
4. Yang, H., Wang, H., Shivalila, C.S., Cheng, A.W., Shi, L., Jaenisch, R., One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154:6 (2013), 1370–1379.
5. Chu, V.T., Weber, T., Graf, R., Sommermann, T., Petsch, K., Sack, U., Volchkov, P., Rajewsky, K., Kuhn, R., Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol., 16, 2016, 4.
6. Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C., Doudna, J.A., DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507:7490 (2014), 62–67.
7. Richardson, C.D., Ray, G.J., DeWitt, M.A., Curie, G.L., Corn, J.E., Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34:3 (2016), 339–344.
8. Mianne, J., Chessum, L., Kumar, S., Aguilar, C., Codner, G., Hutchison, M., Parker, A., Mallon, A.M., Wells, S., Simon, M.M., Teboul, L., Brown, S.D., Bowl, M.R., Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair. Genome Med., 8(1), 2016, 16.
9. Yang, Z., Steentoft, C., Hauge, C., Hansen, L., Thomsen, A.L., Niola, F., Vester-Christensen, M.B., Frodin, M., Clausen, H., Wandall, H.H., Bennett, E.P., Fast and sensitive detection of indels induced by precise gene targeting. Nucleic Acids Res., 43(9), 2015, e59.
10. Shen, B., Zhang, W., Zhang, J., Zhou, J., Wang, J., Chen, L., Wang, L., Hodgkins, A., Iyer, V., Huang, X., Skarnes, W.C., Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods 11:4 (2014), 399–402.
11. Bassett, A.R., Tibbit, C., Ponting, C.P., Liu, J.L., Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9. Biol. Open 3:1 (2014), 42–49.
12. Ousterout, D.G., Kabadi, A.M., Thakore, P.I., Majoros, W.H., Reddy, T.E., Gersbach, C.A., Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nat. Commun., 6, 2015, 6244.
13. Brown, S.D., Moore, M.W., The international mouse phenotyping consortium: past and future perspectives on mouse phenotyping. Mamm. Genome 23:9–10 (2012), 632–640.
14. Haeussler, M., Schonig, K., Eckert, H., Eschstruth, A., Mianne, J., Renaud, J.B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J., Joly, J.S., Concordet, J.P., Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol., 17(1), 2016, 148.
15. Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., Cradick, T.J., Marraffini, L.A., Bao, G., Zhang, F., DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31:9 (2013), 827–832.
16. Hodgkins, A., Farne, A., Perera, S., Grego, T., Parry-Smith, D.J., Skarnes, W.C., Iyer, V., WGE: a CRISPR database for genome engineering. Bioinformatics 31:18 (2015), 3078–3080.
17. Renaud, J.B., Boix, C., Charpentier, M., De Cian, A., Cochennec, J., Duvernois-Berthet, E., Perrouault, L., Tesson, L., Edouard, J., Thinard, R., Cherifi, Y., Menoret, S., Fontaniere, S., de Croze, N., Fraichard, A., Sohm, F., Anegon, I., Concordet, J.P., Giovannangeli, C., Improved genome editing efficiency and flexibility using modified oligonucleotides with TALEN and CRISPR-Cas9 nucleases. Cell Rep. 14:9 (2016), 2263–2272.
18. Gardiner, W.J., Teboul, L., Overexpression transgenesis in mouse: pronuclear injection. Methods Mol. Biol. 561 (2009), 111–126.
19. Fu, Y., Foden, J.A., Khayter, C., Maeder, M.L., Reyon, D., Joung, J.K., Sander, J.D., High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31:9 (2013), 822–826.
20. Iyer, V., Shen, B., Zhang, W., Hodgkins, A., Keane, T., Huang, X., Skarnes, W.C., Off-target mutations are rare in Cas9-modified mice. Nat. Methods, 12(6), 2015, 479.
21. Low, B.E., Krebs, M.P., Joung, J.K., Tsai, S.Q., Nishina, P.M., Wiles, M.V., Correction of the Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair. Invest. Ophthalmol. Vis. Sci. 55:1 (2014), 387–395.
22. Codner, G.F., Lindner, L., Caulder, A., Wattenhofer-Donze, M., Radage, A., Mertz, A., Eisenmann, B., Mianne, J., Evans, E.P., Beechey, C.V., Fray, M.D., Birling, M.C., Herault, Y., Pavlovic, G., Teboul, L., Aneuploidy screening of embryonic stem cell clones by metaphase karyotyping and droplet digital polymerase chain reaction. BMC Cell Biol., 17(1), 2016, 30.