Quantitative and automated high-throughput genome-wide RNAi screens in C. elegans

Journal of Visualized Experiments

Volumn , Issue 60, 2012, Pages

  Squiban, Barbara ^a   Belougne, Jérôme ^a   Ewbank, Jonathan ^a   Zugasti, Olivier ^a  

^a CENTRE D IMMUNOLOGIE DE MARSEILLE LUMINY   (France)

Author keywords

Biosort; C. elegans; Drechmeria coniospora; Fluorescent reporter; Innate immunity; Issue 60; LIMS; Molecular biology

Indexed keywords

EID: 84857868467     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/3448     Document Type: Article

References (25)

1. Timmons, L. & Fire, A. Specific interference by ingested dsRNA. Nature. 395, 854 (1998).
2. Kamath, R.S. & Ahringer, J. Genome-wide RNAi screening in Caenorhabditis elegans. Methods. 30, 313-321 (2003).
3. Rual, J.F., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14, 2162-2168 (2004).
4. Lee, S.S., et al. A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat. Genet. 33, 40-48 (2003).
5. Hamilton, B., et al. A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 19, 1544-1555 (2005).
6. Frand, A.R., Russel, S., & Ruvkun, G. Functional genomic analysis of C. elegans molting. PLoS Biol. 3, e312 (2005).
7. Parry, D.H., Xu, J., & Ruvkun, G. A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr. Biol. 17, 2013-2022 (2007).
8. O'Rourke, E.J., Conery, A.L. & Moy, T.I. Whole-animal high-throughput screens: the C. elegans model. Methods Mol. Biol. 486, 57-75 (2009).
9. Pujol, N., et al. Distinct innate immune responses to infection and wounding in the C. elegans epidermis. Curr. Biol. 18, 481-489 (2008).
10. Stiernagle, T. Maintenance of C. elegans. In: WormBook. The C. elegans Research Community, eds., e-linkurlhttp://www.wormbook.org/url/e-link. 1551-8507, doi/10.1895/wormbook.1.101.1 (2006).
11. Powell, J.R. & Ausubel, F.M. Models of Caenorhabditis elegans Infection by Bacterial and Fungal Pathogens. In: Methods Mol Biol, Vol. 415, Ewbank, J. & Vivier, E., eds. Humana Press, 403-427 (2008).
12. Cardoso, C., et al. XNP-1/ATR-X acts with RB, HP1 and the NuRD complex during larval development in C. elegans. Dev. Biol. 278, 49-59 (2005).
13. Pujol, N., et al. Anti-fungal innate immunity in C. elegans is enhanced by evolutionary diversification of antimicrobial peptides. PLoS Pathog. 4, e1000105 (2008).
14. Simmer, F., et al. Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions. PLoS Biol. 1, e12 (2003).
15. Couillault, C., et al. TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM. Nat Immunol. 5, 488-494 (2004).
16. Morton, E. & Lamitina, T. A suite of MATLAB-based computational tools for automated analysis of COPAS Biosort data. Biotechniques. 48, xxv-xxx (2010).
17. Rohlfing, A.K., Miteva, Y., Hannenhalli, S., & Lamitina, T. Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. PLoS One. 5, e9010 (2010).
18. Lee, K.Z., Kniazeva, M., Han, M., Pujol, N., & Ewbank, J.J. The fatty acid synthase fasn-1 acts upstream of WNK and Ste20/GCK-VI kinases to modulate antimicrobial peptide expression in C. elegans epidermis. Virulence. 1, 113-122 (2010).
19. Duverger, Y., et al. A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans. Nucleic Acids Res. 35, e11 (2007).
20. Pierce-Shimomura, J.T., et al. Genetic analysis of crawling and swimming locomotory patterns in C. elegans. Proc. Natl. Acad. Sci. U.S.A. 105, 20982-20987 (2008).
21. Ruzanov, P. & Riddle, D.L. Deep SAGE analysis of the Caenorhabditis elegans transcriptome. Nucleic Acids Res. 38, 3252-3262 (2010).
22. Kurz, C.L. & Ewbank, J.J. Infection in a dish: high-throughput analyses of bacterial pathogenesis. Curr. Opin. Microbiol. 10, 10-16 (2007).
23. Okoli, I., et al. Identification of antifungal compounds active against Candida albicans using an improved high-throughput Caenorhabditis elegans assay. PLoS One. 4, e7025 (2009).
24. Moy, T.I., et al. Identification of novel antimicrobials using a live-animal infection model. Proc. Natl. Acad. Sci. U. S. A. 103, 10414-10419 (2006).
25. Ballestriero, F., Thomas, T., Burke, C., Egan, S., & Kjelleberg, S. Identification of compounds with bioactivity against the nematode Caenorhabditis elegans by a screen based on the functional genomics of the marine bacterium Pseudoalteromonas tunicata D2. Appl. Environ. Microbiol. 76, 5710-5717 (2010).