Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Chen, Xiangyang ^a   Xu, Fei ^a   Zhu, Chengming ^a   Ji, Jiaojiao ^a   Zhou, Xufei ^a   Feng, Xuezhu ^a   Guang, Shouhong ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE;

ANIMAL; CAENORHABDITIS ELEGANS; CHROMOSOME; GENE; GENE SILENCING; GENETICS; PROCEDURES;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOMES; DEOXYRIBONUCLEASES; GENE KNOCKDOWN TECHNIQUES; GENES, HELMINTH;

EID: 84923241422     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07581     Document Type: Article

References (58)

1. Geurts, A. M. et al. Knockout rats via embryo microinjection of zinc-finger nucleases. Science 325, 433, doi:10.1126/science.1172447 (2009).
2. Porteus, M. H. & Carroll, D. Gene targeting using zinc finger nucleases. Nat Biotechnol 23, 967-973, doi:10.1038/nbt1125 (2005).
3. Wood, A. J. et al. Targeted genome editing across species using ZFNs and TALENs. Science 333, 307, doi:10.1126/science.1207773 (2011).
4. Bedell, V. M. et al. In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114-118, doi:10.1038/nature11537 (2012).
5. Lo, T. W. et al. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics 195, 331-348, doi:10.1534/genetics.113.155382 (2013).
6. Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29, 143-148, doi:10.1038/nbt.1755 (2011).
7. Bassett, A. R., Tibbit, C., Ponting, C. P. & Liu, J. L. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4, 220-228, doi:10.1016/j.celrep.2013.06.020 (2013).
8. Cong, L. et al.Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823, doi:10.1126/science.1231143 (2013).
9. Feng, Z. et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23, 1229-1232, doi:10.1038/cr.2013.114 (2013).
10. Horii, T. et al. Genome engineering of mammalian haploid embryonic stem cells using the Cas9/RNA system. PeerJ 1, e230, doi:10.7717/peerj.230 (2013).
11. Hsu, P. D., Lander, E. S. & Zhang, F. Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 157, 1262-1278, doi:10.1016/j.cell.2014.05.010 (2014).
12. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31, 233-239, doi:10.1038/nbt.2508 (2013).
13. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826, doi:10.1126/science.1232033 (2013).
14. Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380-1389, doi:10.1016/j.cell.2013.08.021 (2013).
15. Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87, doi:10.1126/science.1247005 (2014).
16. Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67, doi:10.1038/nature13011 (2014).
17. Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910-918, doi:10.1016/j.cell.2013.04.025 (2013).
18. Wang, T.,Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80-84, doi:10.1126/science.1246981 (2014).
19. Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol, doi:10.1038/nbt.2889 (2014).
20. Ren, X. et al. Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci U S A 110, 19012-19017, doi:10.1073/pnas.1318481110 (2013).
21. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997, doi:10.1126/science.1247997 (2014).
22. Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338, doi:10.1038/nature10886 (2012).
23. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821, doi:10.1126/science.1225829 (2012).
24. Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109, E2579-2586, doi:10.1073/pnas.1208507109 (2012).
25. Sander, J. D. & Joung, J. K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32, 347-355, doi:10.1038/nbt.2842 (2014).
26. Chen, C., Fenk, L. A. & de Bono, M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res 41, e193, doi:10.1093/nar/gkt805 (2013).
27. Chiu, H., Schwartz, H. T., Antoshechkin, I. & Sternberg, P. W. Transgene-free genome editing in Caenorhabditis elegans using CRISPR-Cas. Genetics 195, 1167-1171, doi:10.1534/genetics.113.155879 (2013).
28. Cho, S. W., Lee, J., Carroll, D., Kim, J. S. & Lee, J. Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 195, 1177-1180, doi:10.1534/genetics.113.155853 (2013).
29. Dickinson, D. J., Ward, J. D., Reiner, D. J. & Goldstein, B. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods 10, 1028-1034, doi:10.1038/nmeth.2641 (2013).
30. Friedland, A. E. et al. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10, 741-743, doi:10.1038/nmeth.2532 (2013).
31. Tzur, Y. B. et al. Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics 195, 1181-1185, doi:10.1534/genetics.113.156075 (2013).
32. Katic, I. & Grosshans, H. Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans. Genetics 195, 1173-1176, doi:10.1534/genetics.113.155754 (2013).
33. Waaijers, S. & Boxem, M. Engineering the Caenorhabditis elegans genome with CRISPR/Cas9. Methods, doi:10.1016/j.ymeth.2014.03.024 (2014).
34. Waaijers, S. et al. CRISPR/Cas9-targeted mutagenesis in Caenorhabditis elegans. Genetics 195, 1187-1191, doi:10.1534/genetics.113.156299 (2013).
35. Zhao, P., Zhang, Z., Ke, H., Yue, Y. & Xue, D. Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system. Cell Res 24, 247-250, doi:10.1038/cr.2014.9 (2014).
36. Kim, H. et al. A Co-CRISPR Strategy for Efficient Genome Editing in Caenorhabditis elegans. Genetics, doi:10.1534/genetics.114.166389 (2014).
37. Paix, A. et al. Scalable and Versatile Genome Editing Using Linear DNAs with Micro-Homology to Cas9 Sites in Caenorhabditis elegans. Genetics, doi:10.1534/genetics.114.170423 (2014).
38. Arribere, J. A. et al. Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans. Genetics, doi:10.1534/genetics.114.169730 (2014).
39. Shen, B. et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11, 399-402, doi:10.1038/nmeth.2857(2014).
40. Choi, P. S. & Meyerson, M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun 5, 3728, doi:10.1038/ncomms4728 (2014).
41. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71-94 (1974).
42. Zhou, X. et al. Nuclear RNAi contributes to the silencing of off-target genes and repetitive sequences in Caenorhabditis elegans. Genetics 197, 121-132, doi:10.1534/genetics.113.159780 (2014).
43. Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237, doi:10.1038/nature01278 (2003).
44. Shirayama, M., Stanney, W., 3rd, Gu, W., Seth, M. & Mello, C. C. The Vasa Homolog RDE-12 engages target mRNA and multiple argonaute proteins to promote RNAi in C. elegans. Curr Biol 24, 845-851, doi:10.1016/j.cub.2014.03.008 (2014).
45. Yang, H. et al. The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans. Curr Biol 24, 832-838, doi:10.1016/j.cub.2014.01.008 (2014).
46. Kennedy, S., Wang, D. & Ruvkun, G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427, 645-649, doi:10.1038/nature02302 (2004).
47. Feng, X. & Guang, S. Non-coding RNAs mediate the rearrangements of genomic DNA in ciliates. Sci China Life Sci 56, 937-943, doi:10.1007/s11427-013-4539-4 (2013).
48. Edgley, M. et al. Improved detection of small deletions in complex pools of DNA. Nucleic Acids Res 30, e52 (2002).
49. Jansen, G., Hazendonk, E., Thijssen, K. L. & Plasterk, R. H. Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat Genet 17, 119-121, doi:10.1038/ng0997-119 (1997).
50. Ahringer, J. Reverse Genetics, The C. elegans Research Community, WormBook WormBook, doi/10.1895/wormbook.1.47.1, http://www.wormbook.org (Apr 6, 2006) (2006).
51. Frokjaer-Jensen, C. et al. Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat Methods 11, 529-534, doi:10.1038/nmeth.2889 (2014).
52. Frokjaer-Jensen, C., Davis, M. W., Ailion, M. & Jorgensen, E. M. Improved Mos1-mediated transgenesis in C. elegans. Nat Methods 9, 117-118, doi:10.1038/nmeth.1865 (2012).
53. Frokjaer-Jensen, C. et al. Targeted gene deletions in C. elegans using transposon excision. Nat Methods 7, 451-453, doi:10.1038/nmeth.1454 (2010).
54. Nam, J. W. & Bartel, D. P. Long noncoding RNAs in C. elegans. Genome Res 22, 2529-2540, doi:10.1101/gr.140475.112 (2012).
55. Canver, M. C. et al. Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells. J Biol Chem 289, 21312-21324, doi:10.1074/jbc.M114.564625 (2014).
56. Sakuma, T., Nishikawa, A., Kume, S., Chayama, K. & Yamamoto, T. Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system. Sci Rep 4, 5400, doi:10.1038/srep05400 (2014).
57. Zhou, J. et al. Dual sgRNAs facilitate CRISPR/Cas9-mediated mouse genome targeting. FEBS J 281, 1717-1725, doi:10.1111/febs.12735 (2014).
58. Zhou, J. et al. One-step generation of different immunodeficient mice with multiple gene modifications by CRISPR/Cas9 mediated genome engineering. Int J Biochem Cell Biol 46, 49-55, doi:10.1016/j.biocel.2013.10.010 (2014).