Several factors make genome-wide screening in Drosophila a good entry-point into learning about human biology, including study of infection, genetic diseases, and cancer. Here we describe ways that screens initiated in fly cells can be used to identify mammalian genes involved in specific processes or pathways.

Why screen in fly cells?

Several features make RNAi in flies a powerful tool for exploring human gene function, including:

• Relatively small genome (~15,000 genes)
  • Rapid and low-cost genome-wide screening as compared with an equivalent screen in mammalian cells
  • Low redundancy increases the chance a given function will be identified
• Extremely well-annotated genome
  • Wealth of computational and experimental data to draw from for post-analysis
  • Protein-coding and non-coding RNAs well annotated and included in the screening set
  • Higher chance a gene identified in the screen is associated with a function
• Significant similarity to the human genome (search for orthologs)
  • Fly homologs exist for a significant fraction of human disease genes
  • Numerous examples of conserved pathways in flies and humans

Has the approach proven successful?

The answer is "Yes!"

At the bottom of this page is a list of reference citations in which a fly screen was done at the DRSC and the data were quickly carried on to follow-up studies in mammalian systems.

Most researchers take the approach to perform a screen in fly cells first and then follow-up on mammalian homologs in subsequent analyses. An alternative approach would be to perform screens in fly and mammalian cells concurrently, followed by data integration to identify gene hits common to both screens versus those identified in one system but not the other.

Additionally, what you learn about assay design; high-throughput screening and imaging; data and image analysis; and hit verification and validation in fly cells will give you an excellent foundation for performing mammalian cell screens in the future.

What services are available?

Help with Assay Design

The appropriate assay will depend on the interests of your lab group and on available reagents such as cloned genes, markers, and antibodies. Our expert staff can help with fly-specific decisions, such as what cell types and expression vectors would be appropriate for your assay.

State-of-the-Art Screening Facility

Our staff and state-of-the-art automated equipment make it possible for one person from your lab group to perform a genome-wide screen (about 8 weeks) or sub-library screen (about two weeks) on-site at the DRSC.

Please browse the website or contact us for more information about assay design, reagents and screening at the DRSC.

Help with Screen Post-Analysis, Verification and Validation

After the screen, we will assist with data and image analysis so that you can appropriately identify hits in your screen (expert advice and on-line tools provided).

A number of steps post-screening can help narrow a list of hits to a verified list of candidates, including testing with an independent amplicon against the same gene and testing for rescue. Our staff can help you to plan post-screening verification and validation steps (protocols, reagents and on-line tools provided).

We will also help you to identify mammalian homologs of verified gene hits from your fly screen to help you plan next steps. If you take the approach to perform fly and mammalian screens concurrently, we can help you to identify genes that hit in both screens (expert advice, bioinformatics analysis and on-line tools provided).

References

Zhang S, Binari R, Zhou R, Perrimon N. A Genome-wide RNAi Screen for Modifiers of Aggregates Formation by Mutant Huntingtin in Drosophila. Genetics. 2010 Jan 25. [Epub ahead of print]

Sessions OM, Barrows NJ, Souza-Neto JA, Robinson TJ, Hershey CL, Rodgers MA, Ramirez JL, Dimopoulos G, Yang PL, Pearson JL, Garcia-Blanco MA. Discovery of insect and human dengue virus host factors. Nature 2009 Apr 23; 485; 1047-50.

Kwon M, Godinho SA, Chandhok NS, Ganem NJ, Azioune A, Thery M, Pellman D. Mechanisms to suppress multipolar divisions in cancer cells with extra centrosomes. Genes Dev. 2008 Aug 15;22(16):2189-203. Epub 2008 Jul 28.

Sepp KJ, Hong P, Lizarraga SB, Liu JS, Mejia LA, Walsh CA, Perrimon N. Identification of neural outgrowth genes using genome-wide RNAi. PLoS Genet 2008 Jul 4;4(7):e1000111.

Gandre-Babbe S and van der Bliek AM. The Novel Tail-anchored Membrane Protein Mff Controls Mitochondrial and Peroxisomal Fission in Mammalian Cells. Mol Biol Cell 10.1091/mbc.E07-12-1287. epub. ahead of print March 19, 2008.

Farny NG, Hurt JA, Silver PA. Definition of global and transcript-specific mRNA export pathways in metazoans. Genes Dev. 2008 Jan 1;22(1):66-78.

Lu J, Ruhf ML, Perrimon N, Leder P. A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression. Proc Natl Acad Sci U S A. 2007 May 29;104(22):9381-6.

Yi CH, Sogah DK, Boyce M, Degterev A, Christofferson DE, Yuan J. A genome-wide RNAi screen reveals multiple regulators of caspase activation. J Cell Biol. 2007 Nov 19;179(4):619-26.

Gwack Y, Srikanth S, Feske S, Cruz-Guilloty F, Oh-hora M, Neems DS, Hogan PG, Rao A. Biochemical and functional characterization of Orai proteins. J Biol Chem. 2007 Jun 1;282(22):16232-43. Epub 2007 Feb 9.

Gwack Y, Sharma S, Nardone J, Tanasa B, Iuga A, Srikanth S, Okamura H, Bolton D, Feske S, Hogan PG, Rao A. A genome-wide Drosophila RNAi screen identifies DYRK-family kinases as regulators of NFAT. Nature. 2006 Jun 1;441(7093):646-50.

Vig M, Peinelt C, Beck A, Koomoa DL, Rabah D, Koblan-Huberson M, Kraft S, Turner H, Fleig A, Penner R, Kinet JP. CRACM1 is a plasma membrane protein essential for store-operated Ca2+ entry. Science. 2006 May 26;312(5777):1220-3.

Feske S, Gwack Y, Prakriya M, Srikanth S, Puppel SH, Tanasa B, Hogan PG, Lewis RS, Daly M, Rao A. A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function. Nature. 2006 May 11;441(7090):179-85