Gene silencing in flatworms using RNA interference

Parasitic Flatworms: Molecular Biology, Biochemistry, Immunology and Physiology

Volumn , Issue , 2006, Pages 423-434

  Skelly, P J ^a  

^a TUFTS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

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EID: 33947119480     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (81)

1. Allshire, R. (2002) RNAi and heterochromatin-a hushed-up affair. Science 297, 1818-1819.
2. Ambros, V., Lee, R.C., Lavanway, A., Williams, P.T. and Jewell, D. (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Current Biology 13, 807-818.
3. Baulcombe, D.C. (1999) Gene silencing: RNA makes no protein. Currrent Biology 9, R599-R601.
4. Boyle, J.P., Wu, X.J., Shoemaker, C.B. and Yoshino, T.P. (2003) Using RNA interference to manipulate endogenous gene expression in Schistosoma mansoni sporocysts. Molecular and Biochemical Parasitology 128, 205-215.
5. Caplen, N., Zheng, Z., Falgout, B. and Morgan, R. (2002) Inhibition of viral gene expression and replication in mosquito cells by dsRNA-triggered RNA interference. Molecular Therapy 6, 243.
6. Carpenter, A.E. and Sabatini, D.M. (2004) Systematic genome-wide screens of gene function. Nature Reviews Genetics 5, 11-22.
7. Carthew, R.W. (2001) Gene silencing by double-stranded RNA. Current Opinion in Cell Biology 13, 244-248.
8. Cebria, F., Kobayashi, C., Umesono, Y., Nakazawa, M., Mineta, K., Ikeo, K., Gojobori, T., Itoh, M., Taira, M., Sanchez Alvarado, A. and Agata, K. (2002) FGFR-related gene nou-darake restricts brain tissues to the head region of planarians. Nature 419, 620-624.
9. Charrier-Ferrara, S., Caillol, D. and Goudot-Crozel, V. (1992) Complete sequence of the Schistosoma mansoni glyceraldehyde-3-phosphate dehydrogenase gene encoding a major surface antigen. Molecular and Biochemical Parasitology 56, 339-343.
10. DaRocha, W.D., Otsu, K., Teixeira, S.M. and Donelson, J.E. (2004) Tests of cytoplasmic RNA interference (RNAi) and construction of a tetracycline-inducible T7 promoter system in Trypanosoma cruzi. Molecular and Biochemical Parasitology 133, 175-186.
11. Davis, R.E., Parra, A., LoVerde, P.T., Ribeiro, E., Glorioso, G. and Hodgson, S. (1999) Transient expression of DNA and RNA in parasitic helminths by using particle bombardment. Proceedings of the National Academy of Sciences USA 96, 8687-8692.
12. Djikeng, A., Shi, H., Tschudi, C. and Ullu, E. (2001) RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs. RNA 7, 1522-1530.
13. Dykxhoorn, D.M., Novina, C.D. and Sharp, P.A. (2003) Killing the messenger: short RNAs that silence gene expression. Nature Reviews Molecular Cell Biology 4, 457-467.
14. Elbashir, S.M., 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.
15. Feinberg, E.H. and Hunter, C.P. (2003) Transport of dsRNA into cells by the transmembrane protein SID-1.
16. Science 301, 1545-1547.
17. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E. and Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
18. Fjose, A., Ellingsen, S., Wargelius, A. and Seo, H.C. (2001) RNA interference: mechanisms and applications. Biotechnology Annual Review 7, 31-57.
19. Gotz, B. and Klinkert, M.Q. (1993) Expression and partial characterization of a cathepsin B-like enzyme (Sm31) and a proposed 'haemoglobinase' (Sm32) from Schistosoma mansoni. Biochemical Journal 290, 801-806.
20. Grishok, A. and Mello, C.C. (2002) RNAi (Nematodes: Caenorhabditis elegans). Advances in Genetics 46, 339-360.
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. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23-34.
22. Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R. and Hannon, G.J. (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150.
23. Hannon, G.J. (2002) RNA interference. Nature 418, 244-251.
24. Hommel, J.D., Sears, R.M., Georgescu, D., Simmons, D.L. and DiLeone, R.J. (2003) Local gene knockdown in the brain using viral-mediated RNA interference. Nature Medicine 9, 1539-1544.
25. Hu, W., Myers, C., Kilzer, J., Pfaff, S. and Bushman, F. (2002) Inhibition of retroviral pathogenesis by RNA interference. Current Biology 12, 1301.
26. Hu, W., Yan, Q., Shen, D.K., Liu, F., Zhu, Z.D., Song, H.D., Xu, X.R., Wang, Z.J., Rong, Y.P., Zeng, L.C., Wu, J., Zhang, X., Wang, J.J., Xu, X.N., Wang, S.Y., Fu, G., Zhang, X.L., Wang, Z.Q., Brindley, P.J., McManus, D.P., Xue, C.L., Feng, Z., Chen, Z. and Han, Z.G. (2003) Evolutionary and biomedical implications of a Schistosoma japonicum complementary DNA resource. Nature Genetics 35, 139-147.
27. Hunter, C.P. (1999) Genetics: a touch of elegance with RNAi. Current Biology 9, R440-R442.
28. Hutvagner, G. and Zamore, P.D. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056-2060.
29. Hutvagner, G. and Zamore, P.D. (2002) RNAi: nature abhors a double-strand. Current Opinion in Genetics and Development 12, 225-232.
30. Klink, V.P. and Wolniak, S.M. (2000) The efficacy of RNAi in the study of the plant cytoskeleton. Journal of Plant Growth Regulation 19, 371-384.
31. Knight, S.W. and Bass, B.L. (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269-2271.
32. Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W. and Tuschl, T. (2002) Identification of tissue-specific microRNAs from mouse. Current Biology 12, 735-739.
33. Lai, E.C., Tomancak, P., Williams, R.W. and Rubin, G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biology 4, R42.
34. Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
35. Lingel, A., Simon, B., Izaurralde, E. and Sattler, M. (2003) Structure and nucleic acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465-469.
36. Lipardi, C., Wei, Q. and Paterson, B.M. (2001) RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell 107, 297-307.
37. Maine, E.M. (2001) RNAi as a tool for understanding germline development in Caenorhabditis elegans: uses and cautions. Developmental Biology 239, 177-189.
38. Malhotra, P., Dasaradhi, P.V., Kumar, A., Mohmmed, A., Agrawal, N., Bhatnagar, R.K. and Chauhan, V.S. (2002) Double-stranded RNA-mediated gene silencing of cysteine proteases (falcipain-1 and -2) of Plasmodium falciparum. Molecular Microbiology 45, 1245-1254.
39. Martens, H., Novotny, J., Oberstrass, J., Steck, T.L., Postlethwait, P. and Nellen, W. (2002) RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase. Molecular Biology of the Cell 13, 445-453.
40. McCaffrey, A.P., Nakai, H., Pandey, K., Huang, Z., Salazar, F.H., Xu, H., Wieland, S.F., Marion, P.L. and Kay, M.A. (2003) Inhibition of hepatitis B virus in mice by RNA interference. Nature Biotechnology 21, 639-644.
41. McRobert, L. and McConkey, G.A. (2002) RNA interference (RNAi) inhibits growth of Plasmodium falciparum. Molecular and Biochemical Parasitology 119, 273-278.
42. Morris, J.C., Wang, Z., Drew, M.E. and Englund, P.T. (2002) Glycolysis modulates trypanosome glycoprotein expression as revealed by an RNAi library. EMBO Journal 21, 4429-4438.
43. Newmark, P.A., Reddien, P.W., Cebria, F. and Sanchez Alvarado, A. (2003) Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians. Proceedings of the National Academy of Sciences USA 100(Suppl. 1), 11861-11865.
44. Nykanen, A., Haley, B. and Zamore, P.D. (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321.
45. Orii, H., Mochii, M. and Watanabe, K. (2003) A simple "soaking method" for RNA interference in the planarian Dugesia japonica. Developmental Genes and Evolution 213, 138-141.
46. Park, W.S., Hayafune, M., Miyano-Kurosaki, N. and Takaku, H. (2003) Specific HIV-1 env gene silencing by small interfering RNAs in human peripheral blood mononuclear cells. Gene Therapy 10, 2046-2050.
47. Pham, J.W., Pellino, J.L., Lee, Y.S., Carthew, R.W. and Sontheimer, E.J. (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83-94.
48. Pineda, D., Gonzalez, J., Callaerts, P., Ikeo, K., Gehring, W.J. and Salo, E. (2000) Searching for the prototypic eye genetic network: sine oculis is essential for eye regeneration in planarians. Proceedings of the National Academy of Sciences USA 97, 4525-4529.
49. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes and Development 16, 1616-1626.
50. Robinson, K.A. and Beverley, S.M. (2003) Improvements in transfection efficiency and tests of RNA interference (RNAi) approaches in the protozoan parasite Leishmania. Molecular and Biochemical Parasitology 128, 217-228.
51. Salo, E. and Baguna, J. (2002) Regeneration in planarians and other worms: new findings, new tools, and new perspectives. Journal of Experimental Zoology 292, 528-539.
52. Sanchez Alvarado, A. (2003) The freshwater planarian Schmidtea mediterranea: embryogenesis, stem cells and regeneration. Current Opinion in Genetics and Development 13, 438-444.
53. Sanchez Alvarado, A. and Newmark, P.A. (1999) Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proceedings of the National Academy of Sciences USA 96, 5049-5054.
54. Schmid, A., Schindelholz, B. and Zinn, K. (2002) Combinatorial RNAi: a method for evaluating the functions of gene families in Drosophila. Trends in Neuroscience 25, 71-74.
55. Schoppmeier, M. and Damen, W.G. (2001) Double-stranded RNA interference in the spider Cupiennius salei: the role of Distal-less is evolutionarily conserved in arthropod appendage formation. Developmental Genes and Evolution 211, 76-82.
56. Schwarz, D.S., Hutvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208.
57. Shi, H., Djikeng, A., Tschudi, C. and Ullu, E. (2004) Argonaute protein in the early divergent eukaryote Trypanosoma brucei: control of small interfering RNA accumulation and retroposon transcript abundance. Molecular and Cellular Biology 24, 420-427.
58. Silhavy, D., Molnar, A., Lucioli, A., Szittya, G., Hornyik, C., Tavazza, M. and Burgyan, J. (2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO Journal 21, 3070-3080.
59. Skelly, P.J., Kim, J.W., Cunningham, J. and Shoemaker, C.B. (1994) Cloning, characterization, and functional expression of cDNAs encoding glucose transporter proteins from the human parasite Schistosoma mansoni. Journal of Biological Chemistry 269, 4247-4253.
60. Skelly, P.J., Da'dara, A. and Harn, D.A. (2003) Suppression of cathepsin B expression in Schistosoma mansoni by RNA interference. International Journal for Parasitology 33, 363-369.
61. Smardon, A., Spoerke, J.M., Stacey, S.C., Klein, M.E., Mackin, N. and Maine, E.M. (2000) EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Current Biology 10, 169-178.
62. Song, E., Lee, S.K., Wang, J., Ince, N., Ouyang, N., Min, J., Chen, J., Shankar, P. and Lieberman, J. (2003) RNA interference targeting Fas protects mice from fulminant hepatitis. Nature Medicine 9, 347-351.
63. Sui, G., Soohoo, C., Affar el, B., Gay, F., Shi, Y. and Forrester, W.C. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proceedings of the National Academy of Sciences USA 99, 5515-5520.
64. Tabara, H., Grishok, A. and Mello, C.C. (1998) RNAi in C. elegans: soaking in the genome sequence. Science 282, 430-431.
65. Tabara, H., Sarkissian, M., Kelly, W.G., Fleenor, J., Grishok, A., Timmons, L., Fire, A. and Mello, C.C. (1999) The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123-132.
66. Tabara, H., Yigit, E., Siomi, H. and Mello, C.C. (2002) The dsRNA binding protein RDE-4 interacts with RDE- 1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell 109, 861-871.
67. Tahbaz, N., Kolb, F.A., Zhang, H., Jaronczyk, K., Filipowicz, W. and Hobman, T.C. (2004) Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Reports 5, 189-194.
68. Timmons, L., Court, D.L. and Fire, A. (2001) Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103-112.
69. Tort, J., Brindley, P.J., Knox, D., Wolfe, K.H. and Dalton, J.P. (1999) Proteinases and associated genes of parasitic helminths. Advances in Parasitology 43, 161-266.
70. Ullu, E., Tschudi, C. and Chakraborty, T. (2004) RNA interference in protozoan parasites. Cellular Microbiology 6, 509-519.
71. Urwin, P.E., Lilley, C.J. and Atkinson, H.J. (2002) Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Molecular Plant-Microbe Interactions 15, 747-752.
72. Verjovski-Almeida, S., DeMarco, R., Martins, E.A., Guimaraes, P.E., Ojopi, E.P., Paquola, A.C., Piazza, J.P., Nishiyama, M.Y., Kitajima, J.P., Adamson, R.E., Ashton, P.D., Bonaldo, M.F., Coulson, P.S., Dillon, G.P., Farias, L.P., Gregorio, S.P., Ho, P.L., Leite, R.A., Malaquias, L.C., Marques, R.C., Miyasato, P.A., Nascimento, A.L., Ohlweiler, F.P., Reis, E.M., Ribeiro, M.A., Sa, R.G., Stukart, G.C., Soares, M.B., Gargioni, C., Kawano, T., Rodrigues, V., Madeira, A.M., Wilson, R.A., Menck, C.F., Setubal, J.C., Leite, L.C. and Dias-Neto, E. (2003) Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics 35, 148-157.
73. Volpe, T.A., Kidner, C., Hall, I.M., Teng, G., Grewal, S.I. and Martienssen, R.A. (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837.
74. Wianny, F. and Zernicka-Goetz, M. (2000) Specific interference with gene function by double-stranded RNA in early mouse development. Nature Cell Biology 2, 70-75.
75. Winston, W.M., Molodowitch, C. and Hunter, C.P. (2002) Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 295, 2456-2459.
76. Wippersteg, V., Kapp, K., Kunz, W., Jackstadt, W.P., Zahner, H. and Grevelding, C.G. (2002) HSP70-controlled GFP expression in transiently transformed schistosomes. Molecular and Biochemical Parasitology 120, 141-150.
77. Worby, C.A., Simonson-Leff, N. and Dixon, J.E. (2001) RNA interference of gene expression (RNAi) in cultured Drosophila cells. Science STKE 2001, pl1.
78. Yang, D., Buchholz, F., Huang, Z., Goga, A., Chen, C.Y., Brodsky, F.M. and Bishop, J.M. (2002) Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proceedings of the National Academy of Sciences USA 99, 9942-9947.
79. Zamore, P.D. (2001) RNA interference: listening to the sound of silence. Nature Structural Biology 8, 746-750.
80. Zhang, Y., Boado, R.J. and Pardridge, W.M. (2003) In vivo knockdown of gene expression in brain cancer with intravenous RNAi in adult rats. The Journal of Gene Medicine 5, 1039-1045.
81. Zilberman, D., Cao, X. and Jacobsen, S.E. (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716-719.