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Creating Genome Modifications in C. elegans Using the CRISPR/Cas9 System

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C. elegans

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1327))

Abstract

The clustered, regularly interspaced, short, palindromic repeat (CRISPR)-associated (CAS) nuclease Cas9 has been used in many organisms to generate specific mutations and transgene insertions. Here we describe a method using the S. pyogenes Cas9 in C. elegans that provides a convenient and effective approach for making heritable changes to the worm genome.

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References

  1. Mali P et al (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10:957–963

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Frokjaer-Jensen C (2013) Exciting prospects for precise engineering of Caenorhabditis elegans genomes with CRISPR/Cas9. Genetics 195:635–642

    Article  PubMed Central  PubMed  Google Scholar 

  3. Waaijers S, Boxem M (2014) Engineering the Caenorhabditis elegans genome with CRISPR/Cas9. Methods 68(3):381–388

    Article  CAS  PubMed  Google Scholar 

  4. Chen C et al (2013) Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res 41, e193

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Chiu H et al (2013) Transgene-free genome editing in Caenorhabditis elegans using CRISPR-Cas. Genetics 195:1167–1171

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Dickinson DJ et al (2013) Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods 10:1028–1034

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Friedland AE et al (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10:741–743

    Article  CAS  PubMed  Google Scholar 

  8. Katic I, Grosshans H (2013) Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans. Genetics 195:1173–1176

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Lo TW et al (2013) Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics 195:331–348

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Tzur YB et al (2013) Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics 195:1181–1185

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Waaijers S et al (2013) CRISPR/Cas9-targeted mutagenesis in Caenorhabditis elegans. Genetics 195:1187–1191

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Zhao P et al (2014) Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system. Cell Res 24:247–250

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Cho SW et al (2013) Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 195:1177–1180

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77:71–94

    PubMed Central  CAS  PubMed  Google Scholar 

  15. Kadandale P et al (2009) Germline transformation of Caenorhabditis elegans by injection. Methods Mol Biol 518:123–133

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Farboud B, Meyer BJ (2015) Dramatic enhancement of genome editing by CRISPR/ Cas9 through improved guide RNA design. Genetics 199:959–971

    Article  CAS  PubMed  Google Scholar 

  17. Hwang WY et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227–229

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Sugi T et al (2014) Versatile strategy for isolating transcription activator-like effector nuclease-mediated knockout mutants in Caenorhabditis elegans. Dev Growth Differ 56:78–85

    Article  CAS  PubMed  Google Scholar 

  19. Arribere JA et al (2014) Efficient marker-free recovery of custom genetic modifications with CRISPR/Cas9 in Caenorhabditis elegans. Genetics 198(3):837–846

    Article  CAS  PubMed  Google Scholar 

  20. Paix A et al (2014) Scalable and versatile genome editing using linear DNAs with micro-homology to cas9 sites in Caenorhabditis elegans. Genetics 198(4):1347–1356

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Kim H et al (2014) A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans. Genetics 197:1069–1080

    Article  PubMed Central  PubMed  Google Scholar 

  22. Ward JD (2015) Rapid and precise engineering of the Caenorhabditis elegans genome with lethal mutation co-conversion and inactivation of NHEJ repair. Genetics 199:363–3377

    Article  PubMed Central  PubMed  Google Scholar 

  23. Giordano-Santini R et al (2010) An antibiotic selection marker for nematode transgenesis. Nat Methods 7:721–723

    Article  CAS  PubMed  Google Scholar 

  24. Frokjaer-Jensen C et al (2014) Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat Methods 11:529–534

    Article  PubMed Central  PubMed  Google Scholar 

  25. Frokjaer-Jensen C et al (2012) Improved Mos1-mediated transgenesis in C. elegans. Nat Methods 9:117–118

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Gibson DG (2011) Enzymatic assembly of overlapping DNA fragments. Methods Enzymol 498:349–361

    Article  CAS  PubMed  Google Scholar 

  27. Gibson DG et al (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345

    Article  CAS  PubMed  Google Scholar 

  28. Shirayama M et al (2012) piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150:65–77

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Semple JI et al (2012) Generating transgenic nematodes by bombardment and antibiotic selection. Nat Methods 9:118–119

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank the many investigators who have contributed to the recent developments in genome editing and transgenesis techniques in C. elegans. These studies have been referenced throughout our manuscript and should be consulted for additional advice and tips for genome editing. In particular, we thank the Jorgensen, Dupuy, and Goldstein laboratories for the development of highly useful selectable markers and strategies that are effective for both Mos- and CRISPR/Cas9-based editing approaches. Many of the approaches and reagents described by these groups have been helpful in establishing the current methodology described here. We have also greatly appreciated excellent collaborations with Yonatan Tzur, Monica Colaiacovo, Kevin Esvelt, and George Church which led to the original protocol that the current approach is based upon. We also thank Heesun Kim, Masaki Shirayama, and Craig Mello for continued stimulating discussions regarding improvements in this exciting technology. Our work has been supported by US National Institutes of Health Early Independence Award (1DP5OD009153) and additional support from Harvard University to J.A.C. and a Ralph Ellison/American Federation for Aging Research postdoctoral fellowship to A.E.F.

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Correspondence to John A. Calarco .

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Calarco, J.A., Friedland, A.E. (2015). Creating Genome Modifications in C. elegans Using the CRISPR/Cas9 System. In: Biron, D., Haspel, G. (eds) C. elegans. Methods in Molecular Biology, vol 1327. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-4939-2842-2_6

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  • DOI: https://doi.org/10.1007/978-1-4939-2842-2_6

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-4939-2841-5

  • Online ISBN: 978-1-4939-2842-2

  • eBook Packages: Springer Protocols

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