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RNAi screening: tips and techniques

Nature Immunology volume 10, pages 799–804 (2009)Cite this article

By identifying gene products whose knockdown is associated with phenotypic changes, large-scale RNA-mediated interference screens have demonstrated previously unknown components of biological pathways. This commentary provides general guidelines for using such screens to answer questions of immunological interest.

The biological question

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Figure 1: Steps involved in RNAi screening.
Figure 2: Various types of RNAi chemistry.
Figure 3: Z-factor calculation and ranking of screen 'hits'.

References

  1. Echeverri, C.J. & Perrimon, N. Nat. Rev. Genet. 7, 373–384 (2006).

    Article  CAS  Google Scholar 

  2. Perrimon, N. & Mathey-Prevot, B. Genetics 175, 7–16 (2007).

    Article  CAS  Google Scholar 

  3. Moffat, J. & Sabatini, D.M. Nat. Rev. Mol. Cell Biol. 7, 177–187 (2006).

    Article  CAS  Google Scholar 

  4. Brummelkamp, T.R., Nijman, S.M., Dirac, A.M. & Bernards, R. Nature 424, 797–801 (2003).

    Article  CAS  Google Scholar 

  5. Oberdoerffer, S. et al. Science 321, 686–691 (2008).

    Article  CAS  Google Scholar 

  6. Wu, Z. et al. Immunity 29, 839–841 (2008).

    Article  Google Scholar 

  7. Feske, S. et al. Nature 441, 179–185 (2006).

    Article  CAS  Google Scholar 

  8. Vig, M. et al. Science 312, 1220–1223 (2006).

    Article  CAS  Google Scholar 

  9. Zhang, S.L. et al. Proc. Natl. Acad. Sci. USA 103, 9357–9362 (2006).

    Article  CAS  Google Scholar 

  10. Gwack, Y. et al. Nature 441, 646–650 (2006).

    Article  CAS  Google Scholar 

  11. Chen, Z., Stockton, J., Mathis, D. & Benoist, C. Proc. Natl. Acad. Sci. USA 103, 16400–16405 (2006).

    Article  CAS  Google Scholar 

  12. Hannon, G.J. & Rossi, J.J. Nature 431, 371–378 (2004).

    Article  CAS  Google Scholar 

  13. Sledz, C.A. & Williams, B.R. Biochem. Soc. Trans. 32, 952–956 (2004).

    Article  CAS  Google Scholar 

  14. Kittler, R. et al. Nature 432, 1036–1040 (2004).

    Article  CAS  Google Scholar 

  15. Liou, J. et al. Curr. Biol. 15, 1235–1241 (2005).

    Article  CAS  Google Scholar 

  16. Elbashir, S.M., Lendeckel, W. & Tuschl, T. Genes Dev. 15, 188–200 (2001).

    Article  CAS  Google Scholar 

  17. Bramsen, J.B., et al. Nucleic Acids Res. 10, 2867–2881 (2009).

    Article  Google Scholar 

  18. McManus, M.T. et al. J. Immunol. 169, 5754–5760 (2002).

    Article  CAS  Google Scholar 

  19. Laderach, D., Compagno, D., Danos, O., Vainchenker, W. & Galy, A. J. Immunol. 171, 1750–1757 (2003).

    Article  CAS  Google Scholar 

  20. Brummelkamp, T.R., Bernards, R. & Agami, R. Science 296, 550–553 (2002).

    Article  CAS  Google Scholar 

  21. Stewart, S.A. et al. RNA 9, 493–501 (2003).

    Article  CAS  Google Scholar 

  22. Silva, J.M. et al. Nat. Genet. 37, 1281–1288 (2005).

    Article  CAS  Google Scholar 

  23. Yamamoto, T. et al. Blood 108, 3305–3312 (2006).

    Article  CAS  Google Scholar 

  24. Wein, M.N., Jones, D.C. & Glimcher, L.H. Methods Mol. Biol. 455, 149–155 (2008).

    Article  CAS  Google Scholar 

  25. Ziauddin, J. & Sabatini, D.M. Nature 411, 107–110 (2001).

    Article  CAS  Google Scholar 

  26. Neumann, B. et al. Nat. Methods 3, 385–390 (2006).

    Article  CAS  Google Scholar 

  27. Simpson, K.J. et al. Nat. Cell Biol. 10, 1027–1038 (2008).

    Article  CAS  Google Scholar 

  28. Zhang, J.H., Chung, T.D. & Oldenburg, K.R. J. Biomol. Screen. 4, 67–73 (1999).

    Article  CAS  Google Scholar 

  29. Ngo, V.N. et al. Nature 441, 106–110 (2006).

    Article  CAS  Google Scholar 

  30. Luo, B. et al. Proc. Natl. Acad. Sci. USA 105, 20380–20385 (2008).

    Article  CAS  Google Scholar 

  31. Schlabach, M.R. et al. Science 319, 620–624 (2008).

    Article  CAS  Google Scholar 

  32. Echeverri, C.J. et al. Nat. Methods 3, 777–779 (2006).

    Article  CAS  Google Scholar 

  33. Judge, A.D. et al. Nat. Biotechnol. 23, 457–462 (2005).

    Article  CAS  Google Scholar 

  34. Brass, A.L. et al. Science 319, 921–926 (2008).

    Article  CAS  Google Scholar 

  35. Zhou, H. et al. Cell Host Microbe 4, 495–504 (2008).

    Article  CAS  Google Scholar 

  36. König, R. et al. Cell 135, 49–60 (2008).

    Article  Google Scholar 

  37. Goff, S.P. Cell 135, 417–420 (2008).

    Article  CAS  Google Scholar 

  38. Bidère, N. et al. Nature 458, 92–96 (2009).

    Article  Google Scholar 

  39. Shaffer, A.L. et al. Nature 454, 226–231 (2008).

    Article  CAS  Google Scholar 

  40. Kaelin, W.G. Jr. Nat. Rev. Cancer 5, 689–698 (2005).

    Article  CAS  Google Scholar 

  41. Whitehurst, A.W. et al. Nature 446, 815–819 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Supported by the US National Institutes of Health (A.R.), the Juvenile Diabetes Research Foundation (A.R.), the Canadian Institutes for Health Research (S.S.) and the Leukemia and Lymphoma Society (S.S.).

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Authors and Affiliations

  1. Sonia Sharma and Anjana Rao are in the Department of Pathology, Harvard Medical School, Immune Disease Institute and the Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts, USA.,

    Sonia Sharma & Anjana Rao

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  1. Sonia Sharma
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  2. Anjana Rao
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Correspondence to Anjana Rao.

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Competing interests

A.R. is a shareholder of and scientific advisor to CaliMedica and receives laboratory support from Glaxo-Smith-Kline.

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Sharma, S., Rao, A. RNAi screening: tips and techniques. Nat Immunol 10, 799–804 (2009). https://doi.org/10.1038/ni0809-799

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