The Application of CRISPR-Cas9 Genome Editing in Caenorhabditis elegans

Suhong Xu

doi:10.1016/j.jgg.2015.06.005

Volume 42 Issue 8

Aug. 2015

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2015 > 42(8): 413-421

PDF( 333 KB)

The Application of CRISPR-Cas9 Genome Editing in Caenorhabditis elegans

doi: 10.1016/j.jgg.2015.06.005

Suhong Xu

Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

More Information

Corresponding author: E-mail address: suhongxu@gmail.com (Suhong Xu)
Received Date: 2015-05-11
Accepted Date: 2015-06-19
Rev Recd Date: 2015-06-15

Available Online: 2015-06-26

Publish Date: 2015-08-20

Abstract

Abstract

Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unparalleled efficacy and facility for modifying genomes in a wide variety of organisms. Caenorhabditis elegans is one of the most convenient multicellular organisms for genetic analysis, and the application of this novel genome editing technique to this organism promises to revolutionize analysis of gene function in the future. CRISPR-Cas9 has been successfully used to generate imprecise insertions and deletions via non-homologous end-joining mechanisms and to create precise mutations by homology-directed repair from donor templates. Key variables are the methods used to deliver the Cas9 endonuclease and the efficiency of the single guide RNAs. CRISPR-Cas9-mediated editing appears to be highly specific in C. elegans, with no reported off-target effects. In this review, I briefly summarize recent progress in CRISPR-Cas9-based genome editing in C. elegans, highlighting technical improvements in mutagenesis and mutation detection, and discuss potential future applications of this technique.
- Genome editing,
- CRISPR,
- Cas9,
- Non-homologous end-joining (NHEJ),
- Homology-directed repair (HDR),
- Somatic mutation

FullText(HTML)

References(79)

References

[1]	Arribere, J.A., Bell, R.T., Fu, B.X. et al. Genetics, 198 (2014),pp. 837-846
[2]	Bacman, S.R., Williams, S.L., Pinto, M. et al. Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs Nat. Med., 19 (2013),pp. 1111-1113
[3]	Barstead, R.J., Moerman, D.G. Methods Mol. Biol., 351 (2006),pp. 51-58
[4]	Bassett, A.R., Tibbit, C., Ponting, C.P. et al. Cell Rep., 4 (2013),pp. 220-228
[5]	Bassett, A.R., Liu, J.L. J. Genet. Genomics, 41 (2014),pp. 7-19
[6]	Belhaj, K., Chaparro-Garcia, A., Kamoun, S. et al. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system Plant Methods, 9 (2013),p. 39
[7]	Carroll, D. Genome engineering with zinc-finger nucleases Genetics, 188 (2011),pp. 773-782
[8]	Chang, N., Sun, C., Gao, L. et al. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos Cell Res., 23 (2013),pp. 465-472
[9]	Chen, B., Gilbert, L.A., Cimini, B.A. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system Cell, 155 (2013),pp. 1479-1491
[10]	Chen, C., Fenk, L.A., de Bono, M. Nucleic Acids Res., 41 (2013),p. e193
[11]	Chen, X., Xu, F., Zhu, C. et al. Sci. Rep., 4 (2014),p. 7581
[12]	Cheng, Z., Yi, P., Wang, X. et al. Nat. Biotechnol., 31 (2013),pp. 934-937
[13]	Chiu, H., Schwartz, H.T., Antoshechkin, I. et al. Genetics, 195 (2013),pp. 1167-1171
[14]	Cho, S.W., Lee, J., Carroll, D. et al. Genetics, 195 (2013),pp. 1177-1180
[15]	Choudhary, E., Thakur, P., Pareek, M. et al. Gene silencing by CRISPR interference in mycobacteria Nat. Commun., 6 (2015),p. 6267
[16]	Cong, L., Ran, F.A., Cox, D. et al. Multiplex genome engineering using CRISPR/Cas systems Science, 339 (2013),pp. 819-823
[17]	Dianov, G.L., Hubscher, U. Mammalian base excision repair: the forgotten archangel Nucleic Acids Res., 41 (2013),pp. 3483-3490
[18]	DiCarlo, J.E., Norville, J.E., Mali, P. et al. Nucleic Acids Res., 41 (2013),pp. 4336-4343
[19]	Dickinson, D.J., Ward, J.D., Reiner, D.J. et al. Nat. Methods, 10 (2013),pp. 1028-1034
[20]	Dickinson, D.J., Pani, A.M., Heppert, J.K. et al. Streamlined genome engineering with a self-excising drug selection cassette Genetics, 200 (2015),pp. 1035-1049
[21]	Doudna, J.A., Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9 Science, 346 (2014),p. 1258096
[22]	Edgley, M., D'Souza, A., Moulder, G. et al. Improved detection of small deletions in complex pools of DNA Nucleic Acids Res., 30 (2002),p. e52
[23]	Farboud, B., Meyer, B.J. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design Genetics, 199 (2015),pp. 959-971
[24]	Flavell, S.W., Pokala, N., Macosko, E.Z. et al. Cell, 154 (2013),pp. 1023-1035
[25]	Friedland, A.E., Tzur, Y.B., Esvelt, K.M. et al. Nat. Methods, 10 (2013),pp. 741-743
[26]	Frokjaer-Jensen, C. Genetics, 195 (2013),pp. 635-642
[27]	Frokjaer-Jensen, C., Davis, M.W., Ailion, M. et al. Nat. Methods, 9 (2012),pp. 117-118
[28]	Frokjaer-Jensen, C., Davis, M.W., Hollopeter, G. et al. Nat. Methods, 7 (2010),pp. 451-453
[29]	Frokjaer-Jensen, C., Davis, M.W., Hopkins, C.E. et al. Nat. Genet., 40 (2008),pp. 1375-1383
[30]	Fu, Y., Foden, J.A., Khayter, C. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells Nat. Biotechnol., 31 (2013),pp. 822-826
[31]	Gammage, P.A., Rorbach, J., Vincent, A.I. et al. Mitochondrially targeted ZFNs for selective degradation of pathogenic mitochondrial genomes bearing large-scale deletions or point mutations EMBO Mol. Med., 6 (2014),pp. 458-466
[32]	Gengyo-Ando, K., Mitani, S. Biochem. Biophys. Res. Commun., 269 (2000),pp. 64-69
[33]	Gilbert, L.A., Larson, M.H., Morsut, L. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes Cell, 154 (2013),pp. 442-451
[34]	Gratz, S.J., Cummings, A.M., Nguyen, J.N. et al. Genetics, 194 (2013),pp. 1029-1035
[35]	Hannon, G.J. RNA interference Nature, 418 (2002),pp. 244-251
[36]	Hsu, P.D., Lander, E.S., Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering Cell, 157 (2014),pp. 1262-1278
[37]	Hsu, P.D., Scott, D.A., Weinstein, J.A. et al. DNA targeting specificity of RNA-guided Cas9 nucleases Nat. Biotechnol., 31 (2013),pp. 827-832
[38]	Hwang, W.Y., Fu, Y., Reyon, D. et al. Heritable and precise zebrafish genome editing using a CRISPR-Cas system PLoS One, 8 (2013),p. e68708
[39]	Ji, W., Lee, D., Wong, E. et al. Specific gene repression by CRISPRi system transferred through bacterial conjugation ACS Synth. Biol., 3 (2014),pp. 929-931
[40]	Jinek, M., Chylinski, K., Fonfara, I. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science, 337 (2012),pp. 816-821
[41]	Katic, I., Grosshans, H. Genetics, 195 (2013),pp. 1173-1176
[42]	Kim, H., Ishidate, T., Ghanta, K.S. et al. Genetics, 197 (2014),pp. 1069-1080
[43]	Larson, M.H., Gilbert, L.A., Wang, X. et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression Nat. Protoc., 8 (2013),pp. 2180-2196
[44]	Lemire, B. Mitochondrial genetics WormBook (2005),pp. 1-10
[45]	Li, W., Teng, F., Li, T. et al. Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems Nat. Biotechnol., 31 (2013),pp. 684-686
[46]	Li, W., Yi, P., Ou, G. J. Cell Biol., 208 (2015),pp. 683-692
[47]	Liu, P., Long, L., Xiong, K. et al. Cell Res., 24 (2014),pp. 886-889
[48]	Lo, T.W., Pickle, C.S., Lin, S. et al. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions Genetics, 195 (2013),pp. 331-348
[49]	Ma, Y., Zhang, X., Shen, B. et al. Generating rats with conditional alleles using CRISPR/Cas9 Cell Res., 24 (2014),pp. 122-125
[50]	Maggio, I., Goncalves, M.A. Genome editing at the crossroads of delivery, specificity, and fidelity Trends Biotechnol., 33 (2015),pp. 280-291
[51]	Mali, P., Aach, J., Stranges, P.B. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Nat. Biotechnol., 31 (2013),pp. 833-838
[52]	Mali, P., Esvelt, K.M., Church, G.M. Cas9 as a versatile tool for engineering biology Nat. Methods, 10 (2013),pp. 957-963
[53]	Mali, P., Yang, L., Esvelt, K.M. et al. Science, 339 (2013),pp. 823-826
[54]	Paix, A., Wang, Y., Smith, H.E. et al. Genetics, 198 (2014),pp. 1347-1356
[55]	Plasterk, R.H., Groenen, J.T. Embo J., 11 (1992),pp. 287-290
[56]	Port, F., Chen, H.M., Lee, T. et al. Proc. Natl. Acad. Sci. USA, 111 (2014),pp. E2967-E2976
[57]	Qi, L.S., Larson, M.H., Gilbert, L.A. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell, 152 (2013),pp. 1173-1183
[58]	Ran, F.A., Hsu, P.D., Lin, C.Y. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity Cell, 154 (2013),pp. 1380-1389
[59]	Reddy, P., Ocampo, A., Suzuki, K. et al. Selective elimination of mitochondrial mutations in the germline by genome editing Cell, 161 (2015),pp. 459-469
[60]	Robert, V., Bessereau, J.L. Embo J., 26 (2007),pp. 170-183
[61]	Segal, D.J., Meckler, J.F. Genome engineering at the dawn of the golden age Annu. Rev. Genomics Hum. Genet., 14 (2013),pp. 135-158
[62]	Shen, Z., Zhang, X., Chai, Y. et al. Dev. Cell, 30 (2014),pp. 625-636
[63]	Singh, P., Schimenti, J.C., Bolcun-Filas, E. A mouse geneticist's practical guide to CRISPR applications Genetics, 199 (2015),pp. 1-15
[64]	Smith, C., Gore, A., Yan, W. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs Cell Stem Cell, 15 (2014),pp. 12-13
[65]	Tian, D., Diao, M., Jiang, Y. et al. Anillin regulates neuronal migration and neurite growth by linking RhoG to the actin cytoskeleton Curr. Biol., 25 (2015),pp. 1135-1145
[66]	Tzur, Y.B., Friedland, A.E., Nadarajan, S. et al. Genetics, 195 (2013),pp. 1181-1185
[67]	Veres, A., Gosis, B.S., Ding, Q. et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing Cell Stem Cell, 15 (2014),pp. 27-30
[68]	Voutev, R., Hubbard, E.J. Genetics, 180 (2008),pp. 103-119
[69]	Waaijers, S., Boxem, M. Methods, 68 (2014),pp. 381-388
[70]	Waaijers, S., Portegijs, V., Kerver, J. et al. Genetics, 195 (2013),pp. 1187-1191
[71]	Wang, H., Yang, H., Shivalila, C.S. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering Cell, 153 (2013),pp. 910-918
[72]	Wang, Y., Li, Z., Xu, J. et al. Cell Res., 23 (2013),pp. 1414-1416
[73]	Ward, J.D. Genetics, 199 (2015),pp. 363-377
[74]	Wei, C., Liu, J., Yu, Z. et al. TALEN or Cas9-rapid, efficient and specific choices for genome modifications J. Genet. Genomics, 40 (2013),pp. 281-289
[75]	Wood, A.J., Lo, T.W., Zeitler, B. et al. Targeted genome editing across species using ZFNs and TALENs Science, 333 (2011),p. 307
[76]	Xu, S., Chisholm, A.D. Dev. Cell, 31 (2014),pp. 48-60
[77]	Yang, H., Wang, H., Shivalila, C.S. et al. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering Cell, 154 (2013),pp. 1370-1379
[78]	Yu, Z., Ren, M., Wang, Z. et al. Genetics, 195 (2013),pp. 289-291
[79]	Zhao, P., Zhang, Z., Ke, H. et al. Cell Res., 24 (2014),pp. 247-250