High-throughput, liquid-based genome-wide RNAi screening in C. Elegans

Methods in Molecular Biology

Volumn 1470, Issue , 2016, Pages 151-162

  O’Reilly, Linda P ^a   Knoerdel, Ryan R ^a   Silverman, Gary A ^a   Pak, Stephen C ^a  

^a NONE

Author keywords

Arrayscan; C. elegans; Genome wide; High throughput screening; RNAi

Indexed keywords

AMPICILLIN; FLOXURIDINE; GLYCEROL; RED FLUORESCENT PROTEIN;

ADULT; ASSAY; CAENORHABDITIS ELEGANS; CENTRIFUGE; DATA ANALYSIS SOFTWARE; ESCHERICHIA COLI; GENETIC SCREENING; HIGH THROUGHPUT SCREENING; HUMAN; LIQUID BASED GENOME WIDE METHOD; MOLECULAR CLONING; NONHUMAN; ORTHOLOGY; PHENOTYPE; PREDICTION; RNA INTERFERENCE; TRANSGENIC ANIMAL; WORM SORTER; ANIMAL; GENETICS; GENOME; IMAGE PROCESSING; PROCEDURES;

ANIMALS; CAENORHABDITIS ELEGANS; GENOME, HELMINTH; HIGH-THROUGHPUT SCREENING ASSAYS; IMAGE PROCESSING, COMPUTER-ASSISTED; RNA INTERFERENCE;

EID: 84984996523     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6337-9_12     Document Type: Chapter

References (21)

1. Fraser AG, Kamath RS, Zipperlen P et al (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408(6810):325–330. doi: 10.1038/35042517
2. Kamath RS, Fraser AG, Dong Y et al (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421(6920):231–237. doi: 10.1038/nature01278
3. Rual JF, Ceron J, Koreth J et al (2004) Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14(10B):2162–2168. doi: 10.1101/gr.2505604
4. Hamilton B, Dong Y, Shindo M et al (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev 19(13):1544–1555. doi: 10.1101/gad.1308205
5. Lehner B, Tischler J, Fraser AG (2006) RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat Protoc 1(3):1617–1620. doi: 10.1038/nprot.2006.245
6. Lejeune FX, Mesrob L, Parmentier F et al (2012) Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons. BMC Genomics 13:91. doi: 10.1186/1471-2164-13-91
7. O’Rourke EJ, Conery AL, Moy TI (2009) Whole-animal high-throughput screens: the C. elegans model. Methods Mol Biol 486:57–75. doi: 10.1007/978-1-60327-545-3_5
8. Swierczek NA, Giles AC, Rankin CH et al (2011) High-throughput behavioral analysis in C. elegans. Nat Methods 8(7):592–598. doi: 10.1038/nmeth.1625
9. Buckingham SD, Sattelle DB (2009) Fast, automated measurement of nematode swimming (thrashing) without morphometry. BMC Neurosci 10:84. doi: 10.1186/1471-2202-10-84
10. O’Reilly LP, Luke CJ, Perlmutter DH et al (2014) C. elegans in high-throughput drug discovery. Adv Drug Deliv Rev 69–70:247–253. doi: 10.1016/j.addr.2013.12.001
11. Gosai SJ, Kwak JH, Luke CJ et al (2010) Automated high-content live animal drug screening using C. elegans expressing the aggregation prone serpin α1-antitrypsin Z. PLoS One 5(11):e15460. doi: 10.1371/journal.pone.0015460
12. Long OS, Gosai SJ, Kwak JH et al (2011) Using Caenorhabditis elegans to study serpinopathies. Methods Enzymol 499:259–281. doi: 10.1016/B978-0-12-386471-0.00013-4
13. O’Reilly LP, Long OS, Cobanoglu MC et al (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of alpha1-antitrypsin deficiency. Hum Mol Genet 23(19):5123–5132. doi: 10.1093/hmg/ddu236
14. Benson JA, Cummings EE, O’Reilly LP et al (2014) A high-content assay for identifying small molecules that reprogram C. elegans germ cell fate. Methods 68(3):529–535. doi: 10.1016/j.ymeth.2014.05.011
15. Leung CK, Deonarine A, Strange K et al. High-throughput screening and biosensing with fluorescent C. elegans strains. J Vis Exp. 2011;(51). doi: 10.3791/2745
16. Hamamichi S, Rivas RN, Knight AL et al (2008) Hypothesis-based RNAi screening identifies neuroprotective genes in a Parkinson’s disease model. Proc Natl Acad Sci U S A 105(2):728–733. doi: 10.1073/pnas.0711018105
17. Morley JF, Brignull HR, Weyers JJ et al (2002) The threshold for polyglutamine-expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in Caenorhabditis elegans. Proc Natl Acad Sci U S A 99(16):10417–10422. doi: 10.1073/pnas.152161099
18. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77(1):71–94
19. Birmingham A, Selfors LM, Forster T et al (2009) Statistical methods for analysis of highthroughput RNA interference screens. Nat Methods 6(8):569–575, doi:nmeth.1351[pii] 10.1038/nmeth.1351
20. Shaye DD, Greenwald I (2011) OrthoList: a compendium of C. elegans genes with human orthologs. PLoS One 6(5):e20085. doi: 10.1371/journal.pone.0020085
21. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. doi: 10.1038/nprot.2008.211