Expanding CRISPR/Cas9 genome editing capacity in Zebrafish using SaCas9

G3: Genes, Genomes, Genetics

Volumn 6, Issue 8, 2016, Pages 2517-2521

  Feng, Yan ^a   Chen, Cheng ^a   Han, Yuxiang ^a   Chen, Zelin ^a,b   Lu, Xiaochan ^a   Liang, Fang ^a   Li, Song ^a   Qin, Wei ^a   Lin, Shuo ^a,b  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

CRISPR Cas9; Gene editing; KKH SaCas9 variant; SaCas9; Zebrafish

Indexed keywords

ANIMAL EXPERIMENT; BIOINFORMATICS; BIOLOGY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; MUTATION; NONHUMAN; ORTHOLOGY; SITE DIRECTED MUTAGENESIS; STAPHYLOCOCCUS AUREUS; ZEBRA FISH; ANIMAL; CRISPR CAS SYSTEM; EMBRYOLOGY; GENE EDITING; GENETICS; GENOME; NONMAMMALIAN EMBRYO; TRANSGENIC ANIMAL;

BACTERIAL PROTEIN;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; BACTERIAL PROTEINS; CRISPR-CAS SYSTEMS; EMBRYO, NONMAMMALIAN; GENE EDITING; GENOME; STAPHYLOCOCCUS AUREUS; ZEBRAFISH;

EID: 84983683558     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.116.031914     Document Type: Article

References (37)

1. Bassett, A. R., C. Tibbit, C. P. Ponting, and J. L. Liu, 2013 Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Reports 4: 220-228.
2. Bell, R.T., B.X. Fu, and A.Z. Fire, 2016 Cas9 variants expand the target repertoire in Caenorhabditis elegans. Genetics 202: 381-388.
3. Burger, A., H. Lindsay, A. Felker, C. Hess, C. Anders et al., 2016 Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 143: 2025-2037.
4. Camp, E., and M. Lardelli, 2001 Tyrosinase gene expression in zebrafish embryos. Dev. Genes Evol. 211: 150-153.
5. Chang, N., C. Sun, L. Gao, D. Zhu, X. Xu et al., 2013 Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res. 23: 465-472.
6. Cong, L., F. A. Ran, D. Cox, S. Lin, R. Barretto et al., 2013 Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-823.
7. Dang, Y., G. Jia, J. Choi, H. Ma, E. Anaya et al., 2015 Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency. Genome Biol. 16: 280.
8. Dickinson, D. J., J. D. Ward, D. J. Reiner, and B. Goldstein, 2013 Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat. Methods 10: 1028-1034.
9. Doyon, Y., J. M. McCammon, J. C. Miller, F. Faraji, C. Ngo et al., 2008 Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 26: 702-708.
10. Elliott, B., C. Richardson, J. Winderbaum, J. A. Nickoloff, and M. Jasin, 1998 Gene conversion tracts from double-strand break repair in mammalian cells. Mol. Cell. Biol. 18: 93-101.
11. Findlay, G. M., E. A. Boyle, R. J. Hause, J. C. Klein, and J. Shendure, 2014 Saturation editing of genomic regions by multiplex homologydirected repair. Nature 513: 120-123.
12. Friedland, A. E., Y. B. Tzur, K. M. Esvelt, M. P. Colaiacovo, G. M. Church et al., 2013 Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat. Methods 10: 741-743.
13. Gagnon, J. A., E. Valen, S. B. Thyme, P. Huang, L. Akhmetova et al., 2014 Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9: e98186.
14. Gratz, S. J., A. M. Cummings, J. N. Nguyen, D. C. Hamm, L. K. Donohue et al., 2013 Genome engineering of Drosophila with the CRISPR RNAguided Cas9 nuclease. Genetics 194: 1029-1035.
15. Hou, Z., Y. Zhang, N. E. Propson, S. E. Howden, L. F. Chu et al., 2013 Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl. Acad. Sci. USA 110: 15644-15649.
16. Hsu, P. D., E. S. Lander, and F. Zhang, 2014 Development and applications of CRISPR-Cas9 for genome engineering. Cell 157: 1262-1278.
17. Huang, P., A. Xiao, M. Zhou, Z. Zhu, S. Lin et al., 2011 Heritable gene targeting in zebrafish using customized TALENs. Nat. Biotechnol. 29: 699-700.
18. Hwang, W. Y., Y. Fu, D. Reyon, M. L. Maeder, S. Q. Tsai et al., 2013 Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31: 227-229.
19. Jinek, M., A. East, A. Cheng, S. Lin, E. Ma et al., 2013 RNA-programmed genome editing in human cells. eLife 2: e00471.
20. Karvelis, T., G. Gasiunas, A. Miksys, R. Barrangou, P. Horvath et al., 2013 crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol. 10: 841-851.
21. Kimmel, C. B., W. W. Ballard, S. R. Kimmel, B. Ullmann, and T. F. Schilling, 1995 Stages of embryonic development of the zebrafish. Dev. Dyn. 203: 253-310.
22. Kleinstiver, B. P., M. S. Prew, S. Q. Tsai, N. T. Nguyen, V. V. Topkar et al., 2015a Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat. Biotechnol. 33: 1293-1298.
23. Kleinstiver, B. P., M. S. Prew, S. Q. Tsai, V. V. Topkar, N. T. Nguyen et al., 2015b Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523: 481-485.
24. Liu, D., Z. Wang, A. Xiao, Y. Zhang, W. Li, Y. Zu, S. Yao, S. Lin, and B. Zhang, 2014 Efficient gene targeting in zebrafish mediated by a zebrafish-codonoptimized cas9 and evaluation of off-targeting effect. J. Genet. Genomics 41: 43-46.
25. Makarova, K. S., L. Aravind, Y. I. Wolf, and E. V. Koonin, 2011 Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 6: 38.
26. Makarova, K. S., Y. I. Wolf, O. S. Alkhnbashi, F. Costa, S. A. Shah et al., 2015 An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13: 722-736.
27. Mali, P., L. Yang, K. M. Esvelt, J. Aach, M. Guell et al., 2013 RNA-guided human genome engineering via Cas9. Science 339: 823-826.
28. Meng, X., M. B. Noyes, L. J. Zhu, N. D. Lawson, and S. A. Wolfe, 2008 Targeted gene inactivation in zebrafish using engineered zincfinger nucleases. Nat. Biotechnol. 26: 695-701.
29. Qin, W., F. Liang, Y. Feng, H. Bai, R. Yan et al., 2015 Expansion of CRISPR/Cas9 genome targeting sites in zebrafish by Csy4-based RNA processing. Cell Res. 25: 1074-1077.
30. Ran, F.A., L. Cong, W. X. Yan, D.A. Scott, J. S.Gootenberg et al., 2015 In vivo genome editing using Staphylococcus aureus Cas9. Nature 520: 186-191.
31. Shalem, O., N. E. Sanjana, E. Hartenian, X. Shi, D. A. Scott et al., 2014 Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343: 84-87.
32. Shmakov, S., O. O. Abudayyeh, K. S. Makarova, Y. I. Wolf, J. S. Gootenberg et al., 2015 Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60: 385-397.
33. Sternberg, S. H., and J. A. Doudna, 2015 Expanding the biologist's toolkit with CRISPR-Cas9. Mol. Cell 58: 568-574.
34. Wang, T., J. J. Wei, D. M. Sabatini, and E. S. Lander, 2014 Genetic screens in human cells using the CRISPR-Cas9 system. Science 343: 80-84.
35. Wright, A. V., J. K. Nunez, and J. A. Doudna, 2016 Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164: 29-44.
36. Yang, H., H. Wang, C. S. Shivalila, A. W. Cheng, L. Shi et al., 2013a Onestep generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154: 1370-1379.
37. Yang, L., M. Guell, S. Byrne, J. L. Yang, A. De Los Angeles et al., 2013b Opti mization of scarless human stem cell genome editing. Nucleic Acids Res. 41: 9049-9061.