RNA Interference in C. elegans: History, Application, and Perspectives

  • Min, Kyoeng-Woo (Research Center for Functional Cellulomics, Institute of Molecular Biology and Genetics School of Biological Sciences, Seoul National University) ;
  • Lee, Jun-Ho (Research Center for Functional Cellulomics, Institute of Molecular Biology and Genetics School of Biological Sciences, Seoul National University)
  • Published : 2007.12.31

Abstract

RNA interference (RNAi) is the phenomenon of gene silencing by double-stranded RNA (dsRNA) at transcriptional and post-transcriptional levels in a sequence-specific manner. Reverse genetic approaches using RNA interference (RNAi) have become a major tool for biological researches since its discovery in the nematode Caenorhabditis elegans. In this review, we overview how the RNAi phenomenon was discovered and how the underlying mechanism has been elucidated. We also describe and discuss how RNAi experiments can be performed and how RNAi can be used for genetic studies.

Keywords

References

  1. Aoki K, Moriguchi H, Yoshioka T, Okawa K and Tabara H (2007) In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J 26: 5007-5019 https://doi.org/10.1038/sj.emboj.7601910
  2. Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J and Ruvkun G (2003) Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421: 268-272 https://doi.org/10.1038/nature01279
  3. Bastin P, Ellis K, Kohl L and Gull K (2000) Flagellum ontogeny in trypanosomes studied via an inherited and regulated RNA interference system. J Cell Sci 113 (Pt 18): 3321-3328
  4. Bernstein E, Caudy AA, Hammond SM and Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366 https://doi.org/10.1038/35053110
  5. Chuang CF and Meyerowitz EM (2000) Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc Natl Acad Sci USA 97: 4985-4990
  6. Dillin A, Crawford DK and Kenyon C (2002) Timing requirements for insulin/IGF-1 signaling in C. elegans. Science 298: 830-834 https://doi.org/10.1126/science.1074240
  7. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K and Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498 https://doi.org/10.1038/35078107
  8. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811 https://doi.org/10.1038/35888
  9. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M and Ahringer J (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325-330 https://doi.org/10.1038/35042517
  10. Gil J and Esteban M (2000) Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): mechanism of action. Apoptosis 5: 107-114 https://doi.org/10.1023/A:1009664109241
  11. Gottschalk A, Almedom RB, Schedletzky T, Anderson SD, Yates JR 3rd and Schafer WR (2005) Identification and characterization of novel nicotinic receptor-associated proteins in Caenorhabditis elegans. EMBO J 24: 2566-2578 https://doi.org/10.1038/sj.emboj.7600741
  12. Grishok A, Sinskey JL and Sharp PA (2005) Transcriptional silencing of a transgene by RNAi in the soma of C. elegans. Genes Dev 19: 683-696 https://doi.org/10.1101/gad.1247705
  13. Grishok A, Tabara H and Mello CC (2000) Genetic requirements for inheritance of RNAi in C. elegans. Science 287: 2494-2497 https://doi.org/10.1126/science.287.5462.2494
  14. Guo S and Kemphues KJ (1995) par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81: 611-620 https://doi.org/10.1016/0092-8674(95)90082-9
  15. Hannon OJ (2002) RNA interference. Nature 418: 244-251 https://doi.org/10.1038/418244a
  16. Hong M, K won JY, Shim J and Lee J (2004) Differential hypoxia response of hsp-16 genes in the nematode. J Mol Biol 344: 369-381 https://doi.org/10.1016/j.jmb.2004.09.077
  17. Jorgensen R (1990) Altered gene expression in plants due to trans interactions between homologous genes. Trends Biotechnol 8: 340-344 https://doi.org/10.1016/0167-7799(90)90220-R
  18. Kamath RS and Ahringer J (2003) Genome-wide RNAi screening in Caenorhabditis elegans. Methods 30: 313-321 https://doi.org/10.1016/S1046-2023(03)00050-1
  19. Kamath RS, Martinez-Campos M, Zipperlen P, Fraser AG and Ahringer J (2001) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol 2: RESEARCH0002
  20. Kaufinan RJ (1999) Double-stranded RNA-activated protein kinase mediates virus-induced apoptosis: a new role for an old actor. Proc Natl Acad Sci USA 96: 11693-11695
  21. Kennedy S, Wang D and Ruvkun G (2004) A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427: 645-649 https://doi.org/10.1038/nature02302
  22. Kennerdell JR and Carthew RW (1998) Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 95 : 1017-1026 https://doi.org/10.1016/S0092-8674(00)81725-0
  23. Kennerdell JR and Carthew RW (2000) Heritable gene silencing in Drosophila using double-stranded RNA. Nat Biotechnol 18: 896-898 https://doi.org/10.1038/78531
  24. Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J and Ruvkun G (2003) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet 33: 40-48 https://doi.org/10.1038/ng1056
  25. Montgomery MK and Fire A (1998) Double-stranded RNA as a mediator in sequence-specific genetic silencing and cosuppression. Trends Genet 14: 255-258 https://doi.org/10.1016/S0168-9525(98)01510-8
  26. Nakano H, Amemiya S, Shiokawa K and Taira M (2000) RNA interference for the organizer-specific gene Xlim-1 in Xenopus embryos. Biochem Biophys Res Commun 274: 434-439 https://doi.org/10.1006/bbrc.2000.3178
  27. Ngo H, Tschudi C, Gull K and Ullu E (1998) Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA 95: 14687-14692
  28. Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, Jia S, Moazed D and Grewal SI (2004) RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36: 1174-1180 https://doi.org/10.1038/ng1452
  29. Pak J and Fire A (2007) Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315: 241-244 https://doi.org/10.1126/science.1132839
  30. Robert VJ, Sijen T, van Wolfswinkel J and Plasterk RH (2005) Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes Dev 19: 782-787 https://doi.org/10.1101/gad.332305
  31. Romano N and Macino G (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6: 3343-3353 https://doi.org/10.1111/j.1365-2958.1992.tb02202.x
  32. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH and Fire A (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465-476 https://doi.org/10.1016/S0092-8674(01)00576-1
  33. Simmer F, Moorman C, van der Linden AM, Kuijk E, van den Berghe PY, Kamath RS, Fraser AG, Ahringer J and Plasterk RH (2003) Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol 1: E12
  34. Simmer F, Tijsterman M, Parrish S, Koushika SP, Nonet ML, Fire A, Ahringer J and Plasterk RH (2002) Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Curr Biol 12: 1317-1319 https://doi.org/10.1016/S0960-9822(02)01304-0
  35. Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin Nand Maine EM (2000) EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Curr Biol 10: 169-178 https://doi.org/10.1016/S0960-9822(99)00257-2
  36. Tabara H, Grishok A and Mello CC (1998) RNAi in C. elegans: soaking in the genome sequence. Science 282: 430-431 https://doi.org/10.1126/science.282.5388.430
  37. Tavemarakis N, Wang SL, Dorovkov M, Ryazanov A and Driscoll M (2000) Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nat Genet 24: 180-183 https://doi.org/10.1038/72850
  38. Tijstemlan M, Ketting RF, Okihara KL, Sijen T and Plasterk RH (2002) RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Science 295: 694-697 https://doi.org/10.1126/science.1067534
  39. Timmons L and Fire A (1998) Specific interference by ingested dsRNA. Nature 395: 854 https://doi.org/10.1038/27579
  40. Timmons L, Tabara H, Mello CC and Fire AZ (2003) Inducible systemic RNA silencing in Caenorhabditis elegans. Mol Biol Cell 14: 2972-2983 https://doi.org/10.1091/mbc.E03-01-0858
  41. Vaucheret H, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Mourrain P, Palauqui JC and Vemhettes S (1998) Transgene-induced gene silencing in plants. Plant J 16: 651-659 https://doi.org/10.1046/j.1365-313x.1998.00337.x
  42. Wang D, Kennedy S, Conte D Jr, Kim JK, Gabel HW, Kamath RS, Mello CC and Ruvkun G (2005) Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436: 593-597 https://doi.org/10.1038/nature04010
  43. Waterhouse PM, Graham MW and Wang MB (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl A cad Sci USA 95: 13959-13964
  44. Wianny F and Zernicka-Goetz M (2000) Specific interference with gene function by double-stranded RNA in early mouse development. Nat Cell Biol 2: 70-75 https://doi.org/10.1038/35000016
  45. Zamore PD, Tuschl T, Sharp PA and Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101: 25-33 https://doi.org/10.1016/S0092-8674(00)80620-0
  46. Zipperlen P, Fraser AG, Kamath RS, Martinez-Campos M and Ahringer J (2001) Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy. EMBO J 20: 3984-3992 https://doi.org/10.1093/emboj/20.15.3984