Skip to main content

Using RNA Interference to Study Protein Function

  • Protocol
Book cover The Nuclear Receptor Superfamily

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 505))

Abstract

RNA interference can be extremely useful in determining the function of an endogenously-expressed protein in its normal cellular environment. In this chapter, we describe a method that uses small interfering RNA (siRNA) to knock down mRNA and protein expression in cultured cells so that the effect of a putative regulatory protein on gene expression can be delineated. Methods of assessing the effectiveness of the siRNA procedure using real time quantitative PCR and Western analysis are also included.

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. Harborth, J., Elbashir, S. M., Bechert, K., Tuschl, T., and Weber, K. (2001) Identification of essential genes in cultured mammalian cells using small interfering RNAs. J Cell Sci 114, 4557–65.

    CAS  PubMed  Google Scholar 

  2. Harborth, J., Elbashir, S. M., Vanden-burgh, K., Manninga, H., Scaringe, S. A., Weber, K., and Tuschl, T. (2003) Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev 13, 83–105.

    Article  CAS  PubMed  Google Scholar 

  3. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis ele-gans. Nature 391, 806–11.

    Article  CAS  PubMed  Google Scholar 

  4. Montgomery, M. K., and Fire, A. (1998) Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 14, 255–8.

    Article  CAS  PubMed  Google Scholar 

  5. Tuschl, T., Zamore, P. D., Lehmann, R., Bar-tel, D. P., and Sharp, P. A. (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13, 3191–7.

    Article  CAS  PubMed  Google Scholar 

  6. Bernstein, E., Caudy, A. A., Hammond, S. M., and Hannon, G. J. (2001) Role for a biden-tate ribonuclease in the initiation step of RNA interference. Nature 409, 363–6.

    Article  CAS  PubMed  Google Scholar 

  7. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–8.

    Article  CAS  PubMed  Google Scholar 

  8. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15, 188–200.

    Article  CAS  PubMed  Google Scholar 

  9. Jackson, A. L., Bartz, S. R., Schelter, J., Koba-yashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., and Linsley, P. S. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21, 635–7.

    Article  CAS  PubMed  Google Scholar 

  10. Schwarz, D. S., Tomari, Y., and Zamore, P. D. (2004) The RNA-induced silencing complex is a Mg2 ; -dependent endonuclease. Curr Biol 14, 787–91.

    Article  CAS  PubMed  Google Scholar 

  11. Curtis, C. D., Likhite, V. S., McLeod, I. X., Yates, J. R., and Nardulli, A. M. (2007) Interaction of nonmetastatic protein 23 homolog H1 and estrogen receptor alpha alters estrogen-responsive gene expression and DNA nicking. Cancer Res 67, 10600–7.

    Article  CAS  PubMed  Google Scholar 

  12. Marzouk, S., Schultz-Norton, J., McLeod, I., Yates, J., and Nardulli, A. (2007) Rho GDP dissociation inhibitor alpha interacts with estrogen receptor alpha and influences estrogen responsiveness. J Mol Endocrinol 39, 249–59.

    Article  PubMed  Google Scholar 

  13. Rao, A. K., Ziegler, Y. S., McLeod, I. S., Yates, J. R., and Nardulli, A. M. (2008) Effects of Cu/Zn Superoxide Dismutase (SOD1) on estrogen responsiveness and oxidative stress in human breast cancer cells. Mol Endocrinol 22, 1113–1124.

    Article  CAS  PubMed  Google Scholar 

  14. Schultz-Norton, J. R., McDonald, W. H., Yates, J. R., and Nardulli, A. M. (2006) Protein disulfide isomerase serves as a molecular chap-erone to maintain estrogen receptor α structure and function. Mol Endocrinol 20, 1982–95.

    Article  Google Scholar 

  15. Schultz-Norton, J. R., Walt, K. A., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Raetz-man, L. T., and Nardulli, A. M. (2007) The DNA repair protein flap endonucle-ase-1 (FEN-1) modulates estrogen-responsive gene expression. Mol Endocrinol 21, 1569–80.

    Article  Google Scholar 

  16. Schultz-Norton, J. R., Gabisi, V. A., Ziegler, Y. S., McLeod, I. X., Yates, J. R., and Nardulli, A. M. (2007) Estrogen receptor alpha interaction with the DNA repair protein proliferating cell nuclear antigen (PCNA). Nucleic Acids Res 35, 5028–38.

    Article  Google Scholar 

  17. Brummelkamp, T. R., Bernards, R., and Agami, R. (2002) Stable suppression of tum-origenicity by virus-mediated RNA interference. Cancer Cell 2, 243–7.

    Article  CAS  PubMed  Google Scholar 

  18. Brummelkamp, T. R., Bernards, R., and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550–3.

    Article  CAS  PubMed  Google Scholar 

  19. Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J., and Conklin, D. S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16, 948–58.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We are grateful to J. Bonéy Montoya, A. Rao, D. Thorngren, and Y. Ziegler for assistance in the preparation of this manuscript. This work was supported by NIH grant R01 DK 53884 (to AMN).

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Curtis, C.D., Nardulli, A.M. (2009). Using RNA Interference to Study Protein Function. In: McEwan, I.J. (eds) The Nuclear Receptor Superfamily. Methods in Molecular Biology™, vol 505. Humana Press. https://doi.org/10.1007/978-1-60327-575-0_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-575-0_11

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-574-3

  • Online ISBN: 978-1-60327-575-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics