Skip to main content

Identifying MicroRNA Regulators of Cell Death in Drosophila

  • Protocol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 342))

Abstract

Animal genomes contain on the order of at least hundreds of microRNAs (miRNAs). Although most remain uncharacterized, it is already clear that miRNAs regulate many bio-logical processes. A number of Drosophila miRNAs have been identified as likely cell death regulators, but functions for most have simply not been explored. Here we describe a protocol for identifying miRNAs that can act as cell death regulators. We also describe a simple protocol for testing roles for mRNAs identified as candidate miRNA targets using computational or other approaches.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Hay, B. A., Huh, J. R., and Guo M. (2004) The genetics of cell death: approaches, insights and opportunities in Drosophila. Nat. Rev. Genet. 5, 911–922.

    Article  CAS  PubMed  Google Scholar 

  2. Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.

    Article  CAS  PubMed  Google Scholar 

  3. Berezikov, E. Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H., and Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24.

    Article  CAS  PubMed  Google Scholar 

  4. Ambros, V. (2001) MicroRNAs: tiny regulators with great potential. Cell 107, 823–826.

    Article  CAS  PubMed  Google Scholar 

  5. Tomari, Y. and Zamore, P. D. (2005) Perspective: machines for RNAi. Genes Dev. 19, 517–529.

    Article  CAS  PubMed  Google Scholar 

  6. Ambros, V. (2004) The functions of animal microRNAs. Nature 431, 350–355.

    Article  CAS  PubMed  Google Scholar 

  7. Xu, P., Vernooy, S. Y., Guo, M., and Hay, B. A. (2003) The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790–795.

    Article  CAS  PubMed  Google Scholar 

  8. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., and Cohen, S. M. (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regu-lates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.

    Article  CAS  PubMed  Google Scholar 

  9. Stark, A., Brennecke, J., Russell, R. B., and Cohen, S. M. (2003) Identification of Droso-phila microRNA targets. PLOS Biol. 1, 397–409.

    Article  CAS  Google Scholar 

  10. Xu, P., Guo, M., and Hay, B. A. (2004) MicroRNAs and the regulation of cell death. Trends Genet. 20, 617–624.

    Article  CAS  PubMed  Google Scholar 

  11. Vernooy, S. Y., Copeland, J., Ghaboosi, N., Griffen, E. E., Yoo, S. J., and Hay, B. A. (2000) Cell death regulation in Drosophila: conservation of mechanism and unique insights. J. Cell Biol. 150, F69–F76.

    Article  CAS  PubMed  Google Scholar 

  12. Lu, J., Get, G., Miska, E. A., et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435, 834–838.

    Article  CAS  PubMed  Google Scholar 

  13. Green, D. R. and Evan, G. I. (2002) A matter of life and death. Cancer Cell 1, 19–30.

    Article  CAS  PubMed  Google Scholar 

  14. Bonini, N. M. and Fortini, M. E. (2003) Human neurodegenerative disease modeling using Drosophila. Annu. Rev. Neurosci. 26, 627–656.

    Article  CAS  PubMed  Google Scholar 

  15. Khorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216.

    Article  Google Scholar 

  16. Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208.

    Article  CAS  PubMed  Google Scholar 

  17. Doench, J. G. and Sharp, P. A. (2004) Specificity of microRNA target selection in trans-lational repression. Genes Dev. 18, 504–511.

    Article  CAS  PubMed  Google Scholar 

  18. Kiriakidou, M., Nelson, P. T. Kouranov, A., et al. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165–1178.

    Article  CAS  PubMed  Google Scholar 

  19. Haley, B. and Zamore, P. D. (2004) Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11, 599–606.

    Article  CAS  PubMed  Google Scholar 

  20. Brennecke, J., Stark, A., Russell, R. B., and Cohen, S. M. (2005) Principles of microRNA-target recognition. PloS Biol. 3, 404–418.

    Article  CAS  Google Scholar 

  21. Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D. S. (2003) MicroRNA targets in Drosophila. Genome Biol. 5, R1.

    Article  PubMed  Google Scholar 

  22. Lewis, B. P., Shih, L.-H., Jones-Rhoades, M. W., Bartel, D. P., and Burge, C. B. (2003) Prediction of mammalian microRNA targets. Cell 115, 787–798.

    Article  CAS  PubMed  Google Scholar 

  23. Jones-Rhoades, M. W. and Bartel, D. P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787–799.

    Article  CAS  PubMed  Google Scholar 

  24. John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004) Human microRNA targets. PLoS Biol. 2, 1862–1879.

    Article  CAS  Google Scholar 

  25. Krek, A., Grun, D., Poy, M. N., et al. (2005) Combinatorial microRNA target predictions. Nat. Genet. 37, 495–500.

    Article  CAS  PubMed  Google Scholar 

  26. Robins, H., Li, Y., and Padgett, R. W. (2005) Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA 102, 4006–4009.

    Article  CAS  PubMed  Google Scholar 

  27. Burgler, C. and Macdonald, P. M. (2005) Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction program. BMC Genomics 6, http://www.biomedcentral.com/1471-2164/6/88. Last accessed Dec. 22, 2005.

  28. Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20.

    Article  CAS  PubMed  Google Scholar 

  29. McGuire, S. E., Roman, G., and Davis, R. L. (2004) Gene expression systems in Droso-phila: a synthesis of time and space. Trends Genet. 20, 384–391.

    Article  CAS  PubMed  Google Scholar 

  30. Hay, B. A., Wolff, T., and Rubin, G. M. (1994) Expression of baculovirus P35 prevents cell death in Drosophila. Development 120, 2121–2129.

    CAS  PubMed  Google Scholar 

  31. Brand, A. H. and Perrimon, N. (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415.

    CAS  PubMed  Google Scholar 

  32. Rorth, P. (1998) Gal4 in the Drosophila female germline. Mech. Dev. 78, 113–118.

    Article  CAS  PubMed  Google Scholar 

  33. Bernards, A. and Hariharan, I. K. (2001) Of flies and men-studying human disease in Drosophila. Curr. Opin. Genet. Dev. 11, 274–278.

    Article  CAS  Google Scholar 

  34. Giordano, E., Rendina, R., Peluso, I., and Furia, M. (2002) RNAi triggered by symmetri-cally transcribed transgenes in Drosophila melanogaster. Genetics 160, 637–648.

    CAS  PubMed  Google Scholar 

  35. Lee, Y. S. and Carthew, R. W. (2003) Making a better RNAi vector for Drosophila: use of intron spacers. Methods 30, 322–329.

    Article  CAS  PubMed  Google Scholar 

  36. Kimura, K.-I., Kodama, A., Hayasaka, Y., and Ohta, T. (2004) Activation of the cAMP/ PKA signaling pathway is required for post-ecdysial cell death in wing epidermal cells of Drosophila. Development 131, 1597–1606.

    Article  CAS  PubMed  Google Scholar 

  37. Nagata, S., Nagase, H., Kawane, K., Mukae, N., and Fukuyama, H. (2003) Degradation of chromosomal DNA during apoptosis. Cell Death Differ. 10, 108–116.

    Article  CAS  PubMed  Google Scholar 

  38. Wang, S. L., Hawkins, C. J., Yoo, S. J., Muller, H. A., and Hay, B. A. (1999) The Droso-phila caspase inhibitor DIAP1 is essential for cell survival and is negatively regulated by HID. Cell 98, 453–463.

    Article  CAS  PubMed  Google Scholar 

  39. Yoo, S. J., et al. (2002) Apoptosis inducers Hid, Rpr and Grim negatively regulate levels of the caspase inhibitor DIAP1 by distinct mechanisms. Nat. Cell Biol. 4, 416–424.

    Article  CAS  PubMed  Google Scholar 

  40. McCall, K., Baum, J. S., Cullen, K., and Peterson, J. S. (2004) Visualizing apoptosis. In: Methods in Molecular Biology, vol. 247, Drosophila Cytogenetic Protocols Visualizing Apoptosis (Henderson, D. S., ed.), Humana Totowa, NJ, pp. 431–442.

    Google Scholar 

  41. Wolff, T. and Ready, D. F. (1991) Cell death in normal and rough eye mutants of Droso-phila. Development 113, 825–839.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Humana Press Inc.

About this protocol

Cite this protocol

Chen, CH., Guo, M., Hay, B.A. (2006). Identifying MicroRNA Regulators of Cell Death in Drosophila . In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology™, vol 342. Humana Press. https://doi.org/10.1385/1-59745-123-1:229

Download citation

  • DOI: https://doi.org/10.1385/1-59745-123-1:229

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-581-1

  • Online ISBN: 978-1-59745-123-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics