Genome-wide screening for gene function using RNAi in mammalian cells

Immunology and Cell Biology

Volumn 83, Issue 3, 2005, Pages 217-223

  Cullen, Lara M ^a   Arndt, Greg M ^a  

^a JOHNSON AND JOHNSON   (United States)

Author keywords

Genome wide screening; RNA interference; RNAi library; ShRNA; SiRNA

Indexed keywords

SMALL INTERFERING RNA;

ANIMAL CELL; CAENORHABDITIS ELEGANS; CELL ASSAY; CELL SPECIFICITY; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE SILENCING; GENETIC SCREENING; GENETIC SELECTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MAMMAL CELL; MOLECULAR LIBRARY; NONHUMAN; PHENOTYPE; PREDICTION; RAT; REVIEW; RNA INTERFERENCE; RNA INTERFERENCE LIBRARY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

ANIMALS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOMICS; HUMANS; RETROVIRIDAE; RNA INTERFERENCE; RNA, DOUBLE-STRANDED;

MAMMALIA;

EID: 20444424942     PISSN: 08189641     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1440-1711.2005.01332.x     Document Type: Review

References (44)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391: 806-811.
2. Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000; 404: 293-6.
3. Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD. How cells respond to interferons. Annu. Rev. Biochem. 1998; 67: 227-64.
4. Wang J, Tekle E, Oubrahim H, Mieyal JJ, Stadtman ER, Chock PB. Stable and controllable RNA interference: Investigating the physiological function of glutathionylated actin. Proc. Natl Acad. Sci. USA 2003; 100: 5103-106.
5. Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J, Ruvkun G. A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat. Genet. 2003; 33: 40-48.
6. Kaykas A, Moon RT. A plasmid-based system for expressing small interfering RNA libraries in mammalian cells. BMC Cell Biol. 2004; 5: 16.
7. Tran N, Cairns MJ, Dawes IW, Arndt GM. Expressing functional siRNAs in mammalian cells using convergent transcription. BMC Biotechnol. 2003; 3: 21.
8. Zheng L, Liu J, Batalov S et al. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl Acad. Sci. USA 2004; 101: 135-40.
9. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002; 296: 550-53.
10. Paul CP, Good PD, Winer I, Engelke DR. Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 2002; 20: 505-508.
11. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 2002; 16: 948-58.
12. Paddison PJ, Silva JM, Conklin DS et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004; 428: 427-31.
13. Boutros M, Kiger AA, Armknecht S et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004; 303: 832-5.
14. Berns K, Hijmans EM, Mullenders J et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004; 428: 431-7.
15. Waterhouse PM, Helliwell CA. Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 2003; 4: 29-38.
16. Kamath RS, Fraser AG, Dong Y et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003; 421: 231-7.
17. Poulin G, Nandakumar R, Ahringer J. Genome-wide RNAi screens in Caenorhabditis elegans: impact on cancer research. Oncogene 2004; 23: 8340-45.
18. Dasgupta R, Perrimon N. Using RNAi to catch Drosophila genes in a web of interactions: insights into cancer research. Oncogene 2004; 23: 8359-65.
19. Tabara H, Grishok A, Mello CC. RNAi in C. elegans: soaking in the genome sequence. Science 1998; 282: 430-31.
20. Timmons L, Fire A. Specific interference by ingested dsRNA. Nature 1998; 395: 854.
21. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 2000; 408: 325-30.
22. Kamath RS, Ahringer J. Genome-wide RNAi screening in Caenorhabditis elegans. Methods 2003; 30: 313-21.
23. Pothof J, van Haaften G, Thijssen K et al. Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev. 2003; 17: 443-8.
24. Ashrafi K, Chang FY, Watts JL et al. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 2003; 421: 268-72.
25. Nollen EA, Garcia SM, van Haaften G et al. Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Proc. Natl Acad. Sci. USA 2004; 101: 6403-408.
26. van Haaften G, Plasterk RH, Tijsterman M. Genomic instability and cancer: scanning the Caenorhabditis elegans genome for tumor suppressors. Oncogene 2004; 23: 8366-75.
27. van Haaften G, Vastenhouw NL, Nollen EA, Plasterk RH, Tijsterman M. Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality. Proc. Natl Acad. Sci. USA 2004; 101: 12 992-6.
28. Kiger AA, Baum B, Jones S et al. A functional genomic analysis of cell morphology using RNA interference. J. Biol. 2003; 2: 27.
29. Eggert US, Kiger AA, Richter C et al. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol. 2004; 2: e379.
30. Lum L, Yao S, Mozer B et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 2003; 299: 2039-45.
31. Drosophila RNAi Screening Center [homepage on the Internet]. Department of Genetics, Harvard Medical School, Boston, MA, USA [updated January 2005; cited December 2004]. Available from: http://www.flyrnai.org/.
32. Kim YO, Park SJ, Balaban RS, Nirenberg M, Kim Y. A functional genomic screen for cardiogenic genes using RNA interference in developing Drosophila embryos. Proc. Natl Acad. Sci. USA 2004; 101: 159-64.
33. Ivanov AI, Rovescalli AC, Pozzi P et al. Genes required for Drosophila nervous system development identified by RNA interference. Proc. Natl Acad. Sci. USA 2004; 101: 16 216-21.
34. Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell 2003; 12: 627-37.
35. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-97.
36. Brummelkamp TR, Bernards R. New tools for functional mammalian cancer genetics. Nat. Rev. Cancer 2003; 3: 781-9.
37. Silva J, Chang K, Hannon GJ, Rivas FV. RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age. Oncogene 2004; 23: 8401-409.
38. Shirane D, Sugao K, Namiki S, Tanabe M, Iino M, Hirose K. Enzymatic production of RNAi libraries from cDNAs. Nat. Genet. 2004; 36: 190-96.
39. Sen G, Wehrman TS, Myers JW, Blau HM. Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nat. Genet. 2004; 36: 183-9.
40. Luo B, Heard AD, Lodish HF. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl Acad. Sci. USA 2004; 101: 5494-9.
41. Ziauddin J, Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature 2001; 411: 107-110.
42. Erfle H, Simpson JC, Bastiaens PI, Pepperkok R. siRNA cell arrays for high-content screening microscopy. Biotechniques 2004; 37: 454-62.
43. Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc. Natl Acad. Sci. USA 2004; 101: 6548-52.
44. Tran N, Raponi M, Dawes IW, Arndt GM. Control of specific gene expression in mammalian cells by co-expression of long complementary RNAs. FEBS Lett. 2004; 573: 127-34.