RNA silencing in fungi: Mechanisms and applications

FEBS Letters

Volumn 579, Issue 26, 2005, Pages 5950-5957

  Nakayashiki, Hitoshi ^a  

^a KOBE UNIVERSITY   (Japan)

Author keywords

Dicer; Meiotic silencing by unpaired DNA; Quelling; RNA silencing

Indexed keywords

RNA; RNA DIRECTED RNA POLYMERASE;

DNA DETERMINATION; FUNGAL GENE; FUNGUS; GENE FUNCTION; GENE SILENCING; NEUROSPORA CRASSA; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PRIORITY JOURNAL; SHORT SURVEY;

ANIMALS; DNA; GENE SILENCING; GENETIC TECHNIQUES; GENOME, FUNGAL; GREEN FLUORESCENT PROTEINS; HUMANS; MEIOSIS; MICRORNAS; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; NEUROSPORA; NEUROSPORA CRASSA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RECOMBINATION, GENETIC; RIBONUCLEASE III; RNA INTERFERENCE; RNA REPLICASE; RNA, FUNGAL; RNA, SMALL INTERFERING;

FUNGI; NEUROSPORA CRASSA;

EID: 26944471385     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.08.016     Document Type: Short Survey

References (50)

1. N. Romano, and G. Macino Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences Mol. Microbiol. 6 1992 3343 3353
2. C. Cogoni, J.T. Irelan, M. Schumacher, T.J. Schmidhauser, E.U. Selker, and G. Macino Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation EMBO J. 15 1996 3153 3163
3. C. Cogoni, and G. Macino Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase Nature 399 1999 166 169
4. C. Cogoni, and G. Macino Post-transcriptional gene silencing across kingdoms Curr. Opin. Genet. 10 2000 638 643
5. C. Catalanotto, G. Azzalin, G. Macino, and C. Cogoni Gene silencing in worms and fungi Nature 404 2000 245
6. C. Cogoni, and G. Macino Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase Science 286 1999 2342 2344
7. A. Kato, Y. Akamatsu, Y. Sakuraba, and H. Inoue The Neurospora crassa mus-19 gene is identical to the qde-3 gene, which encodes a RecQ homologue and is involved in recombination repair and postreplication repair Curr Genet. 45 2004 37 44
8. A. Pickford, L. Braccini, G. Macino, and C. Cogoni The QDE-3 homologue RecQ-2 co-operates with QDE-3 in DNA repair in Neurospora crassa Curr Genet. 42 2003 220 227
9. R. Aramayo, and R.L. Metzenberg Meiotic transvection in fungi Cell 86 1996 103 113
10. P.K.T. Shiu, N.B. Raju, D. Zickler, and R.L. Metzenberg Meiotic silencing by unpaired DNA Cell 107 2001 905 916
11. M. Freitag, P.C. Hickey, N.B. Raju, E.U. Selker, and N.D. Read GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa Fung. Genet. Biol. 41 2004 897 910
12. D.W. Lee, R.J. Pratt, M. McLaughlin, and R. Aramayo An argonaute-like protein is required for meiotic silencing Genetics 164 2003 821 828
13. J.E. Galagan The genome sequence of the filamentous fungus Neurospora crassa Nature 422 2003 859 868
14. C. Catalanotto, M. Pallotta, P. ReFalo, M.S. Sachs, L. Vayssie, G. Macino, and C. Cogoni Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa Mol. Cell. Biol. 24 2004 2536 2545
15. H. Kato Pathogenicity, mating ability and DNA restriction fragment length polymorphisms of Pyricularia populations isolated from Gramineae, Bambusideae and Zingiberaceae plants J. Gen. Plant Pathol. 66 2000 30 47
16. N. Kadotani, H. Nakayashiki, Y. Tosa, and S. Mayama One of the two dicer-like proteins in the filamentous fungi Magnaporthe oryzae genome is responsible for hairpin RNA-triggered RNA silencing and related siRNA accumulation J. Biol. Chem. 279 2004 44467 44474
17. J.G. Doench, C.P. Petersen, and P.A. Sharp siRNAs can function as miRNAs Genes Dev. 17 2003 438 442
18. Y.S. Lee, K. Nakahara, J.W. Pham, K. Kim, Z. He, E.J. Sontheimer, and R.W. Carthew Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways Cell 117 2004 69 81
19. K. Okamura, A. Ishizuka, H. Siomi, and M.C. Siomi Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways Genes Dev. 18 2004 1655 1666
20. Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, and J.C. Carrington Genetic and functional diversification of small RNA pathways in plants PLoS Biol. 2 2004 642 652
21. C.J. Bean, C.E. Schaner, and W.G. Kelly Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans Nat. Genet. 36 2004 100 105
22. J.M. Turner, S.K. Mahadevaiah, O. Fernandez-Capetillo, A. Nussenzweig, X. Xu, C.X. Deng, and P.S. Burgoyne Silencing of unsynapsed meiotic chromosomes in the mouse Nat. Genet. 37 2005 41 47
23. M.A. Matzke, and J.A. Birchler RNAi-mediated pathways in the nucleus Nat. Rev. Genet. 6 2005 24 35
24. M. Freitag, D.W. Lee, G.O. Kothe, R.J. Pratt, R. Aramayo, and E.U. Selker DNA methylation is independent of RNA interference in Neurospora Science 304 2004 1939
25. W. Hamada, and P.D. Spanu Co-suppression of the hydrophobin gene HCf-1 is correlated with antisense RNA biosynthesis in Cladosporium fulvum Mol. Gen. Genet. 259 1988 630 638
26. P. van West, S. Kamoun, J.W. van 't Klooster, and F. Govers Internuclear gene silencing in Phytophthora infestans Mol. Cell 3 1999 339 348
27. A. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver, and C.C. Mello Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391 1998 806 811
28. A. Fitzgerald, J.A.L.v. Kan, and K.M. Plummer Simultaneous silencing of multiple genes in the apple scab fungus, Venturia inaequalis, by expression of RNA with chimeric inverted repeats Fung. Genet. Biol. 41 2004 963 971
29. T.M. Hammond, and N.P. Keller RNA silencing in Aspergillus nidulans is independent of RNA-dependent RNA polymerases Genetics 169 2005 607 617
30. N. Kadotani, H. Nakayashiki, Y. Tosa, and S. Mayama RNA silencing in the phytopathogenic fungus Magnaporthe oryzae Mol. Plant Microbe Interact. 16 2003 769 776
31. H. Liu, T.R. Cottrell, L.M. Pierini, W.E. Goldman, and T.L. Doering RNA interference in the pathogenic fungus Cryptococcus neoformans Genetics 160 2002 463 470
32. I. Mouyna, C. Henry, T.L. Doering, and J.P. Latge Gene silencing with RNA interference in the human pathogenic fungus Aspergillus fumigatus FEMS Microbiol. Lett. 237 2004 317 324
33. F.E. Nicolas, S. Torres-Martinez, and R.M. Ruiz-Vazquez Two classes of small antisense RNAs in fungal RNA silencing triggered by non-integrative transgenes EMBO J. 22 2003 3983 3991
34. C.A. Rappleye, J.T. Engle, and W.E. Goldman RNA interference in Histoplasma capsulatum demonstrates a role for alpha-(1,3)-glucan in virulence Mol. Microbiol. 53 2004 153 165
35. M. Latijnhouwers, W. Ligterink, V.G.A.A. Vleeshouwers, P.v. West, and F. Govers A Galpha subunit controls zoospore motility and virulence in the potato late blight pathogen Phytophthora infestans Mol. Microbiol. 51 2004 925 936
36. T.A. Volpe, C. Kidner, I.M. Hall, G. Teng, S.I. Grewal, and R.A. Martienssen Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi Science 297 2002 1833 1837
37. C. Catalanotto, G. Azzalin, G. Macino, and C. Cogoni Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora Genes Dev. 16 2002 790 795
38. K. Mochizuki, and M.A. Gorovsky A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase Genes Dev. 19 2005 77 89
39. A.E. Carpenter, and D.M. Sabatini Systematic genome-wide screens of gene function Nat. Rev. Genet. 5 2004 11 22
40. H. Nakayashiki, S. Hanada, B.Q. Nguyen, N. Kadotani, Y. Tosa, and S. Mayama RNA silencing as a tool for exploring gene function in ascomycete fungi Fung. Genet. Biol. 42 2005 275 283
41. R.S. Allen, A.G. Millgate, J.A. Chitty, J. Thisleton, J.A. Miller, A.J. Fist, W.L. Gerlach, and P.J. Larkin RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy Nat. Biotechnol. 22 2004 1559 1566
42. P. Oberdoerffer, C. Kanellopoulou, V. Heissmeyer, C. Paeper, C. Borowski, I. Aifantis, A. Rao, and K. Rajewsky Efficiency of RNA interference in the mouse hematopoietic system varies between cell types and developmental stages Mol. Cell. Biol. 25 2005 3896 3905
43. A.M. Celotto, and B.R. Graveley Exon-specific RNAi: a tool for dissecting the functional relevance of alternative splicing RNA 8 2002 718 724
44. J. Bai, R.L. Ramos, J.B. Ackman, A.M. Thomas, R.V. Lee, and J.J. LoTurco RNAi reveals doublecortin is required for radial migration in rat neocortex Nat. Neurosci. 6 2003 1277 1283
45. A.L. Jackson Expression profiling reveals off-target gene regulation by RNAi Nat. Biotechnol. 21 2003 635 637
46. D.A. Brummell, P.J. Balint-Kurti, M.H. Harpster, J.M. Palys, P.W. Oeller, and N. Gutterson Inverted repeat of a heterologous 3′-untranslated region for high-efficiency, high-throughput gene silencing Plant J. 33 2003 793 800
47. S.V. Wesley Construct design for efficient, effective and high-throughput gene silencing in plants Plant J. 27 2001 581 590
48. G. Giaever Functional profiling of the Saccharomyces cerevisiae genome Nature 418 2002 387 391
49. Y. Ninomiya, K. Suzuki, C. Ishii, and H. Inoue Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining Proc. Natl. Acad. Sci. USA 101 2004 12248 12253
50. A. Verdel, and D. Moazed RNAi-directed assembly of heterochromatin in fission yeast FEBS Lett. 579 2005 5872 5878