Mechanisms and roles of the RNA-based gene silencing

Electronic Journal of Biotechnology

Volumn 7, Issue 3, 2004, Pages 321-332

  Jana, Snehasis ^a   Chakraborty, Chiranjib ^b   Nandi, Shyamsundar ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

^b Glen Mark Laboratories   (India)

Author keywords

Double stranded RNA; Post transcriptional gene silencing; RNA interference; Transcriptional gene silencing

Indexed keywords

BIODEGRADATION; CELLS; FUNGI; METHANOL; PLANTS (BOTANY); RNA; VIRUSES;

DOUBLE-STRANDED RNA (DSRNA); GENE REGULATION; INTERCONNECTED PATHWAYS; METHYLATION;

GENETIC ENGINEERING;

COMPLEMENTARY RNA; DOUBLE STRANDED RNA; HELPER COMPONENT PROTEINASE; MESSENGER RNA; PROTEIN P25; PROTEINASE; RNA; UNCLASSIFIED DRUG; VIRUS ENZYME; VIRUS PROTEIN;

ANIMAL; ANTIVIRAL ACTIVITY; DEGRADATION; DEVELOPMENT; DNA METHYLATION; DNA SEQUENCE; EXPERIMENT; FUNGUS; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE SILENCING; GENE TARGETING; GENETIC TRANSCRIPTION; MOLECULAR MECHANICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PLANT; PLANT DEFENSE; PLANT VIRUS; POSTTRANSCRIPTIONAL GENE SILENCING; PROTEIN TARGETING; REVIEW; RNA DEGRADATION; RNA INTERFERENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

ANIMALIA; FUNGI; POTATO VIRUS X; SOLANUM TUBEROSUM;

EID: 12344300681     PISSN: 07173458     EISSN: None     Source Type: Journal    
DOI: 10.2225/vol7-issue3-fulltext-4     Document Type: Review

References (70)

1. ALVARADO, A.S. and NEWMARK, P.A. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proceedings of the National Academy of Sciences of the United States of America, 1999, vol. 96, no. 9, p. 5049-5054.
2. ANGELL, S.M. and BAULCOMBE, B. Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. European Molecular Biology Organization Journal, 1997, vol. 16, no. 12, p. 3675-3684.
3. BAULCOMBE, D. RNA as a target and an initiator of posttranscriptional gene silencing in transgenic plants. Plant Molecular Biology, 1996, vol. 32, p. 79-88.
4. BECLIN, C.; BOUTE, S.; WATERHOUSE, P. and VAUCHERET, H. A branched pathway for transgeneinduced RNA silencing in plants. Current Biology, 2002, vol. 12, no. 8, p. 684-688.
5. BOSHER, J.M.; DUFOURCQ, P.; SOOKHAREEA, S. and LABOUESSE, M. RNA interference can target pre-mRNA: consequences for gene expression in a Caenorhabditis elegans operon. Genetics, 1999, vol. 153, no. 3, p. 1245-1256.
6. BRANTL, S. Antisense-RNA regulation and RNA interference. Biochemical Biophysical Acta, 2002, vol. 1575, no. 1-3, p. 15-25.
7. CAO, X.; WERNER, A.; DANIEL, Z.M.; FLORIAN, M.; MICHAEL, S.; HUANG, M. and STEVEN, E.J. Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation. Current Biology, 2003, vol. 13, no. 24, p. 2212-2217.
8. CARMELL, M.A.; XUAN, Z.; ZHANG, M.Q. and HANNON, G.J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes and Development, 2002, vol. 16, no. 21, p. 2733-2742.
9. CARTHEW, R.W. Gene silencing by double-stranded RNA. Current Opinion in Genetics and Development, 2001, vol. 13, no. 2, p. 244-248.
10. COGONI, C. and MACINO, G. Post-transcriptional gene silencing across kingdoms. Current Opinion in Genetics and Development, 2000, vol. 10, no. 6, p. 638-643.
11. COGONI, C. and MACINO, G. Post-transcriptional gene silencing in Neurospora by a RecQ DNA helicase. Science, 1999, vol. 286, no. 5448, p. 2342-2344.
12. COUZIN, J. Breakthrough of the year. Small RNAs make big splash. Science, 2002, vol. 298, p. 2296-2297.
13. COX, D.N.; CHAO, A.; BAKER, J.; CHANG, L.; QIAO, D. and LIN, H. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell selfrenewal. Genes and Development, 1998, vol. 12, no. 23, p. 3715-3727.
14. DALMAY, T.; HAMILTON, A.; RADD, S.; ANGELL, S. and BAULCOMBE, D.C. An RNA-dependent RNA polymerase gene in Arabidopsis is required for post transcriptional gene silencing mediated by a transgene but not by a virus. Cell, 2000, vol. 101, p. 543-553.
15. DOENCH, J.G.; PETERSEN, C.P. and SHARP, P.A. siRNAs can function as miRNAs. Genes and Development, 2003, vol. 17, no. 4, p. 438-442.
16. ELBASHIR, S.M.; LENDECKEL, W. and TUSCHL, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes and Development, 2001, vol. 15, no. 2, p. 188-200.
17. FAGARD, M.; BOUTET, S.; MOREL, J.B.; BELLINI, C. and VAUCHERET, H. AGO1, QDE-2, and RDE-1 are related proteins required for posttranscriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proceedings of the National Academy of Sciences in the United States of America, 2000, vol. 97, no. 21, p. 11650-11654.
18. FINNEGAN, E.J.; MARGIS, R. and WATERHOUSE, P.M. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from Drosophila. Current Biology, 2003, vol. 13, no. 3, p. 236-240.
19. FIRE, A. RNA-triggered gene silencing. Trends in Genetics, 1999, vol. 15, no. 9, p. 358-363.
20. FIRE, A.; XU, S.; MONTGOMERY, M.K.; KOSTAS, S.A.; DRIVER, S.E. and MELLO, C.C. Potent and specific genetic interference by double-stranded RNA in C. elegans. Nature, 1998, vol. 391, p. 806-811.
21. GRISHOK, A.; PASQUINELLI, A.E.; CONTE, D.; LI, N.; PARRISH, S.; HA, I.; BAILLIE, D.L.; FIRE, A.; RUVKUN, G. and Mello, C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 2001, vol. 106, no. 1, p. 23-34.
22. GUO, S. and KEMPUES, K.J. par- 1, a gene required for establishing polarity in C. elegans embryos, encodes a putative ser/thr kinase that is asymmetrically distributed. Cell, 1995, vol. 81, no. 4, p. 611-620.
23. HAMILTON, A.; VOINNET, O.; CHAPPELL, L. and BAULCOMBE, D. Two classes of short interfering RNA in RNA silencing. European Molecular Biology Organization journal, 2002, vol. 21, no. 17, p. 4671-4679.
24. HAMILTON, A.J. and BAULCOMBE, D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 1999, vol. 286, no. 5441, p. 950-952.
25. HUNTER, C. A touch of elegance with RNAi. Current Biology, 1999, vol. 9, no. 12, p. R440-R442.
26. HUTVAGNER, G.; MCLACHLAN, J.; PASQUINELLI, A.E.; BALINT, É.; TUSCHL, T. and ZAMORE, P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 2001, vol. 293, no. 5531, p. 834-838.
27. JONES, L.; RATCHIFF, F. and BAULCOMBE, D.C. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met-1 for maintenance. Current Biology, 2001, vol. 11, no. 10, p. 747-757.
28. KASSCHAU, K.D.; XIE, Z.; ALLEN, E.; LLAVE, C.; CHAPMAN, E.J.; KRIZAN, K.A. and CARRINGTON, J.C. P1/HC-Pro, a viral suppressor of RNA silencing,interferes with Arabidopsis development and miRNA function. Development and Cell, 2003, vol. 4, p. 205-217.
29. KETTING, R.F.; FISCHER, S.E.; BERNSTEIN, E.; SIJEN, T.; HANNON, G.J. and PLASTERK, R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes and Development, 2001, vol. 15, no. 20, p. 2654-2659.
30. KETTING, R.F. and PLASTERK, R.H. A genetic link between co-suppression and RNA interference in C. elegans. Nature, 2000, vol. 404, no. 6775, p. 296-298.
31. KETTING, R.F.; HAVERKAMP, T.H.; VAN LUENEN, H.G. and PLASTERK, R.H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell, 1999, vol. 99, no. 2, p. 133-141.
32. LAKATOS, L.; SZITTYA, G.; SILHAVY, D. and BURGYAN, J. Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. European Molecular Biology Organisation Journal, 2004, vol. 23, no. 4, p. 876-884.
33. LI, Y.X.; FARRELL, M.J.; LIU, R.; MOHANTY, N. and KIRBY, M.L. Double-stranded RNA injection produces null phenotypes in zebrafish. Developmental Biology, 2000, vol. 217, no. 2, p. 394-405.
34. LLAVE, C.; KASSCHAU, K.D.; RECTOR, M.A. and CARRINGTON, J.C. Endogenous and silencing-associated small RNAs in plants. Plant Cell, 2002, vol. 14, no. 7, p. 1605-1619.
35. LLAVE, C.; XIE, Z.; KASSCHAU, K.D. and CARRINGTON, J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 2000, vol. 297, p 2053-2056.
36. MALLORY, A.C.; REINHART, B.J.; BARTEL, D.; VANCE, V.B. and BOWMAN, L.H. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco. Proceedings of the National Academy of Sciences in the United States of America, 2002, vol. 99, no. 23, p. 15228-15233.
37. MALLORY, A.; ELY, L.; SMITH, T.; MARATHE, R.; ANANDALAKSHMI,R.; FAGARD, M. et al. HC-Pro suppression of gene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. Plant Cell, 2001, vol. 13, p. 571-583.
38. MARTINEZ, J.; PATKANIOWSKA, A.; URLAUB, H.; LUHRMANN, R. and TUSCHL, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 2002, vol. 110, no. 5, p. 563-574.
39. MATZKE, M.A.; MATZKE, A.J.M. and KOTTER, J.M. RNA: guiding gene silencing. Science, 2001, vol. 293, no. 5532, p. 1080-1083.
40. MATZKE, M.A. and MATZKE, A.J.M. How and why do plants inactivate homologous transgenes? Plant Physiology, 1995, vol. 107, no. 5, p. 679-685.
41. METTE, M.F.; AUFSATZ, K.; VAN DER, W.; MATZKE M.A. and MATZKE, A.J.M. Transcriptional gene silencing and promoter methylation triggered by dsRNA. European Molecular Biology Organisation Journal, 2000, vol. 19, p. 5194-5201
42. MIYAGISHI, M.; HAYASHI, M. and TAIRA, K. Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells. Antisense Nucleic Acid Drug Development, 2003, vol. 13, no. 1, p. 1-7.
43. MONTGOMERY, M.K. and FIRE, A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends in Genetics, 1998, vol. 14, no. 7, p. 255-258.
44. MOREL, J.B.; GODON, C.; MOURRAIN, P.; BECLIN, C.; BOUTET, S.; FEUERBACH, F.; PROUX, F. and VAUCHERET, H. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell, 2002, vol. 14, no. 3, p. 629-639.
45. MOURELATOS, Z.; DOSTIE, J.; PAUSHKIN, S.; SHARMA, A.; CHARROUX, B.; ABEL, L.; RAPPSILBER, J.; MANN, M. and DREYFUSS, G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes and Development, 2002, vol. 16, no. 6, p. 720-728.
46. MOURRAIN, P.; BECLIN, C.; ELMAYAN, T.; FEUERBACH, F.; GODON, C.; MOREL, J.B.; JOUETTE, D.; LACOMBE, A.M.; NIKIC, S. and PICAULT, N. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 2000, vol. 101, p. 533-542.
47. NGO, H.; TSCHUDI, C.; GULL, K. and ULLU, E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proceedings of the National Academy of Sciences in the United States of America, 1998, vol. 95, no. 25, p. 14687-14692.
48. PAPP, I.; METTE, M.F.; AUFSATZ, W.; DAXINGER, L.; SCHAUER, S.E.; RAY, A.; WINDEN, J.; MATZKE, M.; and Matzke, A.J. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiology, 2003, vol. 132, no. 3, p. 1382-1390.
49. PLASTERK, R.H.A. and KETTING, R.F. The silence of the genes. Current Opinion in Genetics and Development, 2000, vol. 10, p. 562-567.
50. REINHART, B.J.; SLACK, F.J.; BASSON, M.; PASQUINELLI, A.E.;BETTINGER, J.C.; ROUGVIE, A.E.; HORVITZ, H.R. and RUVKUN, G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 2000, vol. 403, no. 6772, p. 901-906.
51. SEGGERSON, K.; TANG, L. and MOSS, E.G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Developmental Biology, 2002, vol. 243, no. 2, p. 215-225.
52. SHUEY, D.J.; MCCALLUS, D.E. and GIORDANO, T. RNAi: gene-silencing in therapeutic intervention. Drug Discovery Today, 2002, vol. 7, p. 1040-1046.
53. SIJEN, T.; VIJN, I.; REBOCHO, A.; BLOCKLAND, R.V.; ROELOFS, D.; MOL, J.N.M. and KOOTER, J.M. Transcriptional and post-transcriptional gene silencing are mechanistically related. Current Biology, 2001, vol. 11, no. 6, p. 436-440.
54. SILHAVY, D.; MOLNAR, A.; LUCIOLI, A.; SZITTYA, G.; HORNYIK, C.; TAVAZZA, M. and BURGYAN, J. A viral protein suppresses RNA silencing and binds silencinggenerated, 21- to 25-nucleotide doublestranded RNAs. European Molecular Biology Organisation Journal, 2002, vol. 21, no. 12, p. 3070-3080.
55. SILVA, J.M.; HAMMOND, S.M. and HANNON, G.J. RNA interference: a promising approach to antiviral therapy? Trends in Molecular Medicine, 2002, vol. 8, p. 505-508.
56. SIMON W.L.; DANIEL Z.; ZHIXIN, X.; LISA, K.J.; CARRINGTON, J.C. and JACOBSEN, S.E. RNA Silencing Genes Control de Novo DNA Methylation. Science, 2004, vol. 303, p. 1336.
57. SMARDON, A.; SPOERKE, J.M.; STACEY, S.C.; KLIEN, M.E.; MACKEN, N. and MAINE, E.M. EGO-1 is related to RNA-directed RNA polymerase and functions in germline development and RNA interference in C. elegans. Current Biology, 2000, vol. 10, no. 4, p. 169-178.
58. TABARA, H.; SARKISSIAN, M.; KELLY, W.G.; FLEENOR, J.; GRISHOK, A.; TIMMONS, L.; FIRE, A. and MELLO, C.C. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell, 1999, vol. 99, no. 2, p. 123-132.
59. TANG, G.; REINHART, B.J.; BARTEL, D.P. and ZAMORE, P.D. A biochemical framework for RNA silencing in plants. Genes and Development, 2003, vol. 17, no. 1, p. 49-63.
60. TIMMONS, L. and FIRE, A. Specific interference by ingested dsRNA. Nature, 1998, vol. 395, no. 6705, p. 854.
61. VANCE, V. and VAUCHERET,H. RNA silencing in plants-defense and counter defense. Science, 2001, vol. 292, no. 5525, p. 2277-2280.
62. VAUCHERET, H.; BECLIN, C.; ELMAYAN, T.; FEUERBACH, F.; GODON, C.; MOREL, J.B.; MOURRAIN, P.; PALAUQUI, J.C. and VERNHETTES, S. Transgene-induced gene silencing in plants. Plant Journal, 1998, vol. 16, no. 6, p. 651-659.
63. VOINNET, O. RNA silencing: small RNAs as ubiquitous regulators of gene expression. Current Opinion in Plant Biology, 2002, vol. 5, p. 444-451.
64. VOINNET, O.; LEDERER, C. and BAULCOMBE, D.C. A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell, 2000, vol. 103, no. 1, p. 157-167.
65. WALTERS, D.K. and JELINEK, D.F. The effectiveness of double-stranded short inhibitory RNAs (siRNAs) may depend on the method of transfection. Antisense Nucleic Acid Drug Development, 2002, vol. 12, no. 6, p. 411-418.
66. WARGELIUS, A. and ELLINGSEN, S. Double-stranded RNA induces specific developmental defects in zebrafish embryos. Biochemical Biophysical Research Communication, 1999, vol. 263, no. 1, p. 156-161.
67. WASSENEGGER, M.; HEIMES, S.; RIEDEL, L. and SANGER, H.L. RNA-directed de novo methylation of genomic sequences in plants. Cell, 1994, vol. 76, p. 567-576.
68. ZAMORE, P.D. Ancient pathways programmed by small RNAs. Science, 2002, vol. 296, no. 1265, p. 1265-1269.
69. ZAMORE, P.D. RNA interference: listening to the sound of silence. Nature Structural Biology, 2001, vol. 8, no. 9, p. 746-750.
70. ZILBERMAN, D.; CAO, X. and JACOBSEN, S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 2003, vol. 299, no. 5607, p. 716-719.