Skip to main content

Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs

  • Protocol
  • First Online:
PIWI-Interacting RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1093))

  • 2547 Accesses

Abstract

Gene knockdown using double-stranded RNA (dsRNA) is a powerful tool to characterize gene function in Drosophila. The Drosophila germline provides an elegant model to study the regulation of numerous processes, such as stem cell fate, gametogenesis, piRNA, and piRNA-related gene functions. However, for unknown reasons, traditional dsRNA gene knockdown has not been successful in the germline. Here, we establish a simple gene silencing method for the Drosophila germline by the generation of artificial miRNA-mimicking siRNAs. This method, which is different from that of classical dsRNA, mimics natural miRNA biogenesis and enables the analysis of gene functions specifically in the Drosophila germline.

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 119.00
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. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811

    Article  CAS  PubMed  Google Scholar 

  2. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404(6775):293–296

    Article  CAS  PubMed  Google Scholar 

  3. Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101(1):25–33

    Article  CAS  PubMed  Google Scholar 

  4. Elbashir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21-and 22-nucleotide RNAs. Gene Dev 15(2):188–200

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ, Lowe SW (2005) Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 37(11):1289–1295

    CAS  PubMed  Google Scholar 

  6. Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G, Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ (2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 37(11):1281–1288

    CAS  PubMed  Google Scholar 

  7. Alonso AGD, Gutierrez L, Fritsch C, Papp B, Beuchle D, Muller J (2007) A genetic screen identifies novel polycomb group genes in Drosophila. Genetics 176(4):2099–2108

    Article  Google Scholar 

  8. Bokel C (2008) EMS screens: from mutagenesis to screening and mapping. Methods Mol Biol 420:119–138

    Article  PubMed  Google Scholar 

  9. Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM (1999) The Berkeley Drosophila Genome Project gene disruption project: single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153(1):135–177

    CAS  PubMed Central  PubMed  Google Scholar 

  10. Oh SW, Kingsley T, Shin HH, Zheng Z, Chen HW, Chen X, Wang H, Ruan P, Moody M, Hou SX (2003) A P-element insertion screen identified mutations in 455 novel essential genes in Drosophila. Genetics 163(1):195–201

    CAS  PubMed Central  PubMed  Google Scholar 

  11. Mathey-Prevot B, Perrimon N (2006) Drosophila genome-wide RNAi screens: are they delivering the promise? Cold Spring Harb Symp 71:141–148

    Article  CAS  Google Scholar 

  12. Friedman A, Perrimon N (2004) Genome-wide high-throughput screens in functional genomics. Curr Opin Genet Dev 14(5):470–476

    Article  CAS  PubMed  Google Scholar 

  13. Juliano C, Wang J, Lin H (2011) Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Ann Rev Genet 45:447–469

    Article  CAS  PubMed  Google Scholar 

  14. Siomi MC, Sato K, Pezic D, Aravin AA (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258

    Article  CAS  PubMed  Google Scholar 

  15. Haley B, Hendrix D, Trang V, Levine M (2008) A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol 321(2):482–490

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Okamura K, Ishizuka A, Siomi H, Siomi MC (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 18(14):1655–1666

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10(2):126–139

    Article  CAS  PubMed  Google Scholar 

  18. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10(2):94–108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Tomari Y, Du T, Zamore PD (2007) Sorting of Drosophila small silencing RNAs. Cell 130(2):299–308

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods 8(5):405–407

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Rorth P (1998) Gal4 in the Drosophila female germline. Mech Dev 78(1–2):113–118

    Article  CAS  PubMed  Google Scholar 

  22. Spradling AC, Rubin GM (1982) Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218(4570):341–347

    Article  CAS  PubMed  Google Scholar 

  23. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125(5):887–901

    Article  CAS  PubMed  Google Scholar 

  24. McKearin DM, Spradling AC (1990) bag-of-marbles: a Drosophila gene required to initiate both male and female gametogenesis. Genes Dev 4:2242–2251

    Article  CAS  PubMed  Google Scholar 

  25. Chen D, McKearin DM (2003) A discrete transcriptional silencer in the bam gene determines asymmetric division of the Drosophila germline stem cell. Development 130:1159–1170

    Article  CAS  PubMed  Google Scholar 

  26. Song X, Wong MD, Kawase E, Xi R, Ding BC, McCarthy JJ, Xie T (2004) Bmp signals from niche cells directly repress transcription of a differentiation-promoting gene, bag of marbles, in germline stem cells in the Drosophila ovary. Development 131(6):1353–1364

    Article  CAS  PubMed  Google Scholar 

  27. Wang H, Mu Y, Chen D (2011) Effective gene silencing in Drosophila ovarian germline by artificial microRNAs. Cell Res 21(4):700–703

    Article  PubMed Central  PubMed  Google Scholar 

  28. Xia L, Jia S, Huang S, Wang H, Zhu Y, Mu Y, Kan L, Zheng W, Wu D, Li X, Sun Q, Meng A, Chen D (2010) The Fused/Smurf complex controls the fate of Drosophila germline stem cells by generating a gradient BMP response. Cell 143(6):978–990

    Article  CAS  PubMed  Google Scholar 

  29. Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N, Hannon GJ (2009) Hierarchical rules for Argonaute loading in Drosophila. Mol Cell 36(3):445–456

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD (2010) Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16(1):43–56

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Wang, H., Huang, H., Chen, D. (2014). Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs. In: Siomi, M. (eds) PIWI-Interacting RNAs. Methods in Molecular Biology, vol 1093. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-694-8_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-694-8_18

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-693-1

  • Online ISBN: 978-1-62703-694-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics