Skip to main content

Using CRISPR-Cas9 to Study ERK Signaling in Drosophila

  • Protocol
  • First Online:
Book cover ERK Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1487))

Abstract

Genome engineering using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated nuclease 9 (Cas9) technology is revolutionizing biomedical research. CRISPR-Cas9 enables precise editing of genes in a wide variety of cells and organisms, thereby accelerating molecular studies via targeted mutagenesis, epitope tagging, and other custom genetic modifications. Here, we illustrate the CRISPR-Cas9 methodology by focusing on Capicua (Cic), a nuclear transcriptional repressor directly phosphorylated and inactivated by ERK/MAPK. Specifically, we use CRISPR-Cas9 for targeting an ERK docking site of Drosophila Cic, thus generating ERK-insensitive mutants of this important signaling sensor.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Moynahan ME, Jasin M (2010) Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 11:196–207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Jackson SP, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461:1071–1078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mojica FJM, Díez-Villaseñor C, García-Martínez J et al (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174–182

    Article  CAS  PubMed  Google Scholar 

  5. Deltcheva E, Chylinski K, Sharma CM et al (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821

    Article  CAS  PubMed  Google Scholar 

  7. Gasiunas G, Barrangou R, Horvath P et al (2012) Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109:E2579–E2586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Jinek M, East A, Cheng A et al (2013) RNA-programmed genome editing in human cells. eLife 2:e00471

    Article  PubMed  PubMed Central  Google Scholar 

  11. Cho SW, Kim S, Kim JM et al (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232

    Article  CAS  PubMed  Google Scholar 

  12. Hwang WY, Fu Y, Reyon D et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Anders C, Niewoehner O, Duerst A et al (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:569–573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157: 1262–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wright AV, Nuñez JK, Doudna JA (2016) Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering. Cell 164:29–44

    Article  CAS  PubMed  Google Scholar 

  16. Yang L, Güell M, Niu D et al (2015) Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350:1101–1104

    Article  CAS  PubMed  Google Scholar 

  17. Gantz VM, Bier E (2015) The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 348:442–444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wang Y, Cheng X, Shan Q et al (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32:947–951

    Article  CAS  PubMed  Google Scholar 

  19. Gratz SJ, Cummings AM, Nguyen JN et al (2013) Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194:1029–1035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bassett AR, Tibbit C, Ponting CP et al (2013) Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4:220–228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kondo S, Ueda R (2013) Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics 195:715–721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Yu Z, Ren M, Wang Z et al (2013) Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics 195: 289–291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Ren X, Sun J, Housden BE et al (2013) Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci U S A 110:19012–19017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gratz SJ, Ukken FP, Rubinstein CD et al (2014) Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics 196:961–971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Port F, Chen HM, Lee T et al (2014) Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc Natl Acad Sci U S A 111:E2967–E2976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jiménez G, Shvartsman SY, Paroush Z (2012) The Capicua repressor – a general sensor of RTK signaling in development and disease. J Cell Sci 125:1383–1391

    Article  PubMed  PubMed Central  Google Scholar 

  27. Astigarraga S, Grossman R, Díaz‐Delfín J et al (2007) A MAPK docking site is critical for downregulation of Capicua by Torso and EGFR RTK signaling. EMBO J 26:668–677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Andreu MJ, Ajuria L, Samper N et al (2012) EGFR-dependent downregulation of Capicua and the establishment of Drosophila dorsoventral polarity. Fly 6:234–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Jiménez G, Guichet A, Ephrussi A et al (2000) Relief of gene repression by Torso RTK signaling: role of capicua in Drosophila terminal and dorsoventral patterning. Genes Dev 14:224–231

    PubMed  PubMed Central  Google Scholar 

  30. Goff DJ, Nilson LA, Morisato D (2001) Establishment of dorsal-ventral polarity of the Drosophila egg requires capicua action in ovarian follicle cells. Development 128:4553–4562

    CAS  PubMed  Google Scholar 

  31. Roch F, Jiménez G, Casanova J (2002) EGFR signalling inhibits Capicua-dependent repression during specification of Drosophila wing veins. Development 129:993–1002

    CAS  PubMed  Google Scholar 

  32. Tseng ASK, Tapon N, Kanda H et al (2007) Capicua regulates cell proliferation downstream of the receptor tyrosine kinase/Ras signaling pathway. Curr Biol 17:728–733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Bischof J, Maeda RK, Hediger M et al (2007) An optimized transgenesis system for Drosophila using germ-line-specific φC31 integrases. Proc Natl Acad Sci U S A 104:3312–3317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Berg CA (2005) The Drosophila shell game: patterning genes and morphological change. Trends Genet 21:346–355

    Article  CAS  PubMed  Google Scholar 

  35. Cheung LS, Schüpbach T, Shvartsman SY (2011) Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis. Curr Opin Genet Dev 21:719–725

    Article  CAS  PubMed  Google Scholar 

  36. Atkey MR, Boisclair Lachance JF, Walczak M et al (2006) Capicua regulates follicle cell fate in the Drosophila ovary through repression of mirror. Development 133:2115–2123

    Article  CAS  PubMed  Google Scholar 

  37. Schüpbach T (1987) Germ line and soma cooperate during oogenesis to establish the dorsoventral pattern of egg shell and embryo in Drosophila melanogaster. Cell 49:699–707

    Article  PubMed  Google Scholar 

  38. Ajuria L, Nieva C, Winkler C et al (2011) Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila. Development 138:915–924

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Garcia M, Stathopoulos A (2011) Lateral gene expression in Drosophila early embryos is supported by Grainyhead-mediated activation and tiers of dorsally-localized repression. PLoS One 6:e29172

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Lim B, Samper N, Lu H et al (2013) Kinetics of gene derepression by ERK signaling. Proc Natl Acad Sci U S A 110:10330–10335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ren X, Yang Z, Xu J et al (2014) Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep 9:1151–1162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Marx V (2014) Gene editing: how to stay on-target with CRISPR. Nat Methods 11:1021–1026

    Article  CAS  Google Scholar 

  43. Lam YC, Bowman AB, Jafar-Nejad P et al (2006) ATAXIN-1 interacts with the repressor Capicua in its native complex to cause SCA1 neuropathology. Cell 127:1335–1347

    Article  CAS  PubMed  Google Scholar 

  44. Forés M, Ajuria L, Samper N et al (2015) Origins of context-dependent gene repression by Capicua. PLoS Genet 11:e1004902

    Article  PubMed  PubMed Central  Google Scholar 

  45. Neuman-Silberberg FS, Schupbach T (1994) Dorsoventral axis formation in Drosophila depends on the correct dosage of the gene gurken. Development 120:2457–2463

    CAS  PubMed  Google Scholar 

  46. Boisclair Lachance JF, Fregoso Lomas M, Eleiche A et al (2009) Graded Egfr activity patterns the Drosophila eggshell independently of autocrine feedback. Development 136: 2893–2902

    Article  PubMed  Google Scholar 

  47. Zartman JJ, Kanodia JS, Cheung LS et al (2009) Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis. Development 136:2903–2911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Jin Y, Ha N, Forés M et al (2015) EGFR/Ras signaling controls Drosophila intestinal stem cell proliferation via Capicua-regulated genes. PLoS Genet 11:e1005634

    Article  PubMed  PubMed Central  Google Scholar 

  49. Stathopoulos A, Levine M (2005) Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo. Dev Biol 280:482–493

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank A. Olza for Drosophila injections, N. Samper for experimental support, and F. Port, S. González-Crespo, Z. Paroush, M. Ruiz-Gómez, and A. Veraksa for discussions. This work was funded by grants from the Spanish Ministry of Science and Innovation (BFU2014-52863-P) and Fundació La Marató de TV3 (20131730). G.J. is an ICREA investigator.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gerardo Jiménez .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Forés, M., Papagianni, A., Rodríguez-Muñoz, L., Jiménez, G. (2017). Using CRISPR-Cas9 to Study ERK Signaling in Drosophila . In: Jimenez, G. (eds) ERK Signaling. Methods in Molecular Biology, vol 1487. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6424-6_26

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6424-6_26

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6422-2

  • Online ISBN: 978-1-4939-6424-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics