Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age

Abstract

Sequencing of complete genomes has provided researchers with a wealth of information to study genome organization, genetic instability, and polymorphisms, as well as a knowledge of all potentially expressed genes. The identification of all genes encoded in the human genome opens the door for large-scale systematic gene silencing using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs). With the recent development of siRNA and shRNA expression libraries, the application of RNAi technology to assign function to cancer genes and to delineate molecular pathways in which these genes affect in normal and transformed cells, will contribute significantly to the knowledge necessary to develop new and also improve existing cancer therapy.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1
Figure 2
Figure 3

References

  • Aravind L, Dixit VM and Koonin EV . (2001). Science, 291, 1279–1284.

  • Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL and Cooke MP . (2003). Mol. Cell, 12, 627–637.

  • Basson ME, Moore RL, O'Rear J and Rine J . (1987). Genetics, 117, 645–655.

  • Bender A and Pringle JR . (1991). Mol. Cell Biol., 11, 1295–1305.

  • Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL and Bernards R . (2004). Nature, 428, 431–437.

  • Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Consortium HF, Paro R and Perrimon N . (2004). Science, 303, 832–835.

  • Brummelkamp TR, Nijman SM, Dirac AM and Bernards R . (2003). Nature, 424, 797–801.

  • Celera Genomics Project (2001). Science, 291, 1304–1351.

  • Chen Z and Han M . (2000). Bioessays, 22, 503–506.

  • Chuaqui RF, Bonner RF, Best CJ, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V and Emmert-Buck MR . (2002). Nat. Genet., 32 (Suppl), 509–514.

  • Churchill GA . (2002). Nat. Genet., 32 (Suppl), 490–495.

  • Clemens JC, Worby CA, Simonson-Leff N, Muda M, Maehama T, Hemmings BA and Dixon JE . (2000). Proc. Natl. Acad. Sci., 97, 6499–6503.

  • Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P and Souciet JL . (2004). Nature, 430, 35–44.

  • Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K and Tuschl T . (2001). Nature, 411, 494–498.

  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC . (1998). Nature, 391, 806–811.

  • Forsburg SL . (2001). Nat. Rev. Genet., 2, 659–668.

  • Forster T, Roy D and Ghazal P . (2003). J. Endocrinol., 178, 195–204.

  • Glass B . (1954). Adv. Genet., 6, 95–139.

  • Hannon GJ . (2002). Nature, 418, 244–251.

  • Harborth J, Elbashir SM, Bechert K, Tuschl T and Weber K . (2001). J. Cell Sci., 114, 4557–4565.

  • Hsieh AC, Bo R, Manola J, Vazquez F, Bare O, Khvorova A, Scaringe S and Sellers WR . (2004). Nucleic Acids Res., 32, 893–901.

  • Huang Q, Raya A, DeJesus P, Chao SH, Quon KC, Caldwell JS, Chanda SK, Izpisua-Belmonte JC and Schultz PG . (2004). Proc. Natl. Acad. Sci., 101, 3456–3461.

  • International Human Genome Sequencing Consortium (2001). Nature, 409, 860–921.

  • Jorgensen EM and Mango SE . (2002). Nat. Rev. Genet., 3, 356–369.

  • Kumar R, Conklin DS and Mittal V . (2003). Genome Res., 13, 2333–2340.

  • Manche L, Green SR, Schmedt C and Mathews MB . (1992). Mol. Cell Biol., 12, 5238–5248.

  • Michiels F, van Es H, van Rompaey L, Merchiers P, Francken B, Pittois K, van der Schueren J, Brys R, Vandersmissen J, Beirinckx F, Herman S, Dokic K, Klaassen H, Narinx E, Hagers A, Laenen W, Piest I, Pavliska H, Rombout Y, Langemeijer E, Ma L, Schipper C, Raeymaeker MD, Schweicher S, Jans M, van Beeck K, Tsang IR, van de Stolpe O, Tomme P, Arts GJ and Donker J . (2002). Nat. Biotechnol., 20, 1154–1157.

  • Mikkers H and Berns A . (2003). Adv. Cancer Res., 88, 53–99.

  • Minks MA, West DK, Benvin S and Baglioni C . (1979). J. Biol. Chem., 254, 10180–10183.

  • Montgomery MK . (2004). Methods Mol. Biol., 265, 3–21.

  • Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hautaniemi S, Elkahloun AG, Lotufo RA, Choudary A, Dougherty ER, Suh E and Kallioniemi O . (2003). Genome Res., 13, 2341–2347.

  • Paddison PJ and Hannon GJ . (2002). Cancer Cell, 2, 17–23 . RNA interference: the new somatic cell genetics?.

  • Paddison PJ and Hannon GJ . (2003). Curr. Opin. Mol. Ther., 5, 217–224.

  • Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ and Hannon GJ . (2004). Nature, 428, 427–431.

  • Shoemaker DD, Lashkari DA, Morris D, Mittmann M and Davis RW . (1996). Nat. Genet., 14, 450–456.

  • Shuman HA and Silhavy TJ . (2003). Nat. Rev. Genet., 4, 419–431.

  • Silva JM, Mizuno H, Brady A, Lucito R and Hannon GJ . (2004). Proc. Natl. Acad. Sci., 101, 6548–6552.

  • Somma MP, Fasulo B, Cenci G, Cundari E and Gatti M . (2002). Mol. Biol. Cell, 13, 2448–2460.

  • St Johnston D . (2002). Nat. Rev. Genet., 3, 176–188.

  • Tabara H, Grishok A and Mello CC . (1998). Science, 282, 430–431.

  • Timmons L and Fire A . (1998). Nature, 395, 854.

  • Ziauddin J and Sabatini DM . (2001). Nature, 411, 107–110.

Download references

Acknowledgements

We thank JP O'Keefe for critical reading and suggestions. JS is supported by a postdoctoral fellowship from the US Army Prostate Cancer Research Program. FVR is a Jane Coffin Childs Memorial Cancer Research Fund fellow. GJH is supported by an Innovator Award from the US Army Breast Cancer Research Program and by grants from the National Institutes of Health.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gregory J Hannon.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Silva, J., Chang, K., Hannon, G. et al. RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age. Oncogene 23, 8401–8409 (2004). https://doi.org/10.1038/sj.onc.1208176

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/sj.onc.1208176

Keywords

  • RNAi
  • high throughput screening
  • functional genomics
  • cancer
  • apoptosis
  • synthetic lethality

Further reading

Search

Quick links