Small interfering RNAs that trigger posttranscriptional gene silencing are not required for the histone H3 Lys9 methylation necessary for transgenic tandem repeat stabilization in Neurospora crassa

Molecular and Cellular Biology

Volumn 25, Issue 9, 2005, Pages 3793-3801

  Chicas, Agustin ^a,b   Forrest, Emma C ^a   Sepich, Silvia ^a   Cogoni, Carlo ^a   Macino, Giuseppe ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; LYSINE; SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; DNA MODIFICATION; GENE LOCUS; GENE SILENCING; GENETIC STRAIN; GENETIC TRANSCRIPTION; IMMUNOPRECIPITATION; METHYLATION; MUTANT; NEUROSPORA CRASSA; NONHUMAN; PHENOTYPE; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE; SEQUENCE HOMOLOGY; TANDEM REPEAT; TRANSGENE;

CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; LYSINE; METHYLATION; MUTATION; NEUROSPORA CRASSA; RNA INTERFERENCE; RNA, SMALL INTERFERING; TANDEM REPEAT SEQUENCES; TRANSCRIPTION, GENETIC; TRANSGENES;

NEUROSPORA; NEUROSPORA CRASSA; SCHIZOSACCHAROMYCES POMBE;

EID: 17644380628     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.9.3793-3801.2005     Document Type: Article

References (45)

1. Bernstein, B. E., E. L. Humphrey, R. L. Erlich, R. Schneider, P. Bouman, J. S. Liu, T. Kouzarides, and S. L. Schreiber. 2002. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA 99:8695-8700.
2. Bernstein, E., A. A. Caudy, S. M. Hammond, and G. J. Hannon. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-366.
3. Catalanotto, C., G. Azzalin, G. Macino, and C. Cogoni. 2000. Gene silencing in worms and fungi. Nature 404:245.
4. Catalanotto, C., G. Azzalin, G. Macino, and C. Cogoni. 2002. Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora. Genes Dev. 16:790-795.
5. Catalanotto, C., M. Pallotta, P. ReFalo, M. S. Sachs, L. Vayssie, G. Macino, and C. Cogoni. 2004. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol. Cell. Biol. 24:2536-2545.
6. Chicas, A., and G. Macino. 2001. Characteristics of post-transcriptional gene silencing. EMBO Rep. 2:992-996.
7. Cogoni, C. 2001. Homology-dependent gene silencing mechanisms in fungi. Annu. Rev. Microbiol. 55:381-406.
8. Cogoni, C., J. T. Irelan, M. Schumacher, T. J. Schmidhauser, E. U. Selker, and G. Macino. 1996. 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. 15:3153-3163.
9. Cogoni, C., and G. Macino. 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399:166-169.
10. Cogoni, C., and G. Macino. 1997. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc. Natl. Acad. Sci. USA 94:10233-10238.
11. Cogoni, C., and G. Macino. 1999. Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286:2342-2344.
12. Cogoni, C., N. Romano, and G. Macino. 1994. Suppression of gene expression by homologous transgenes. Antonie Leeuwenhoek 65:205-209.
13. Cowell, I. G., R. Aucott, S. K. Mahadevaiah, P. S. Burgoyne, N. Huskisson, S. Bongiorni, G. Prantera, L. Fanti, S. Pimpinelli, R. Wu, D. M. Gilbert, W. Shi, R. Fundele, H. Morrison, P. Jeppesen, and P. B. Singh. 2002. Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 111:22-36.
14. Dalmay, T., A. Hamilton, S. Rudd, S. Angell, and D. C. Baulcombe. 2000. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101:543-553.
15. Ebbole, D. J., and M. S. Sachs. 1990. A rapid and simple method for isolation of Neurospora crassa homokaryons using microconidia. Neurospora Newslett. 37:17-18.
16. Fire, A. 1999. RNA-triggered gene silencing. Trends Genet. 15:358-363.
17. Freitag, M., D. W. Lee, G. O. Kothe, R. J. Pratt, R. Aramayo, and E. U. Selker. 2004. DNA methylation is independent of RNA interference in Neurospora. Science 304:1939.
18. Gendrel, A. V., Z. Lippman, C. Yordan, V. Colot, and R. A. Martienssen. 2002. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297:1871-1873.
19. Goldoni, M., G. Azzalin, G. Macino, and C. Cogoni. 2004. Efficient gene silencing by expression of double stranded RNA in Neurospora crassa. Fungal Genet. Biol. 41:1016-1024.
20. Hall, I. M., G. D. Shankaranarayana, K. Noma, N. Ayoub, A. Cohen, and S. I. Grewal. 2002. Establishment and maintenance of a heterochromatin domain. Science 297:2232-2237.
21. Hammond, S. M., S. Boettcher, A. A. Caudy, R. Kobayashi, and G. J. Hannon. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293:1146-1150.
22. Henikoff, S. 2000. Heterochromatin function in complex genomes. Biochim. Biophys. Acta 1470:O1-O8.
23. Kondo, Y., and J. P. Issa. 2003. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem. 278:27658-27662.
24. Lehnertz, B., Y. Ueda, A. A. Derijck, U. Braunschweig, L. Perez-Burgos, S. Kubicek, T. Chen, E. Li, T. Jenuwein, and A. H. Peters. 2003. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13:1192-1200.
25. Liu, Y., K. Mochizuki, and M. A. Gorovsky. 2004. Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. Proc. Natl. Acad. Sci. USA 101:1679-1684.
26. Mette, M. F., W. Aufsatz, J. van der Winden, M. A. Matzke, and A. J. Matzke. 2000. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19:5194-5201.
27. Morel, J. B., P. Mourrain, C. Beclin, and H. Vaucheret. 2000. DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis. Curr. Biol. 10:1591-1594.
28. Mourrain, P., C. Beclin, T. Elmayan, F. Feuerbach, C. Godon, J. B. Morel, D. Jouette, A. M. Lacombe, S. Nikic, N. Picault, K. Remoue, M. Sanial, T. A. Vo, and H. Vaucheret. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542.
29. Nakayama, J., J. C. Rice, B. D. Strahl, C. D. Allis, and S. I. Grewal. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110-113.
30. Napoli, C., C. Lemieux, and R. Jorgensen. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279-289.
31. Noma, K., C. D. Allis, and S. I. Grewal. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293:1150-1155.
32. Noma, K., and S. I. Grewal. 2002. Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast. Proc. Natl. Acad. Sci. USA 99(Suppl. 4):16438-16445.
33. Orlando, V., H. Strutt, and R. Paro. 1997. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205-214.
34. Pal-Bhadra, M., B. A. Lisbovitch, S. G. Gandhi, M. Rao, U. Bhadra, J. A. Birchler, and S. C. Elgin. 2004. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303: 669-672.
35. Peters, A. H., S. Kubicek, K. Mechtler, R. J. O'Sullivan, A. A. Derijck, L. Perez-Burgos, A. Kohlmaier, S. Opravil, M. Tachibana, Y. Shinkai, J. H. Martens, and T. Jenuwein. 2003. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12:1577-1589.
36. Peters, A. H., D. O'Carroll, H. Scherthan, K. Mechtler, S. Sauer, C. Schofer, K. Weipoltshammer, M. Pagani, M. Lachner, A. Kohlmaier, S. Opravil, M. Doyle, M. Sibilia, and T. Jenuwein. 2001. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107:323-337.
37. Romano, N., and G. Macino. 1992. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol. Microbiol. 6:3343-3353.
38. Schramke, V., and R. Allshire. 2003. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301:1069-1074.
39. Staben, C., B. C. Jensen, M. J. Singer, J. Pollock, M. Schechtman, J. A. Kinsey, and E. Selker. 1989. Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in Neurospora crassa transformation. Fungal Genet. Newsl. 36:79-81.
40. Tamaru, H., and E. U. Selker. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277-283.
41. Verdel, A., S. Jia, S. Gerber, T. Sugiyama, S. Gygi, S. I. Grewal, and D. Moazed. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672-676.
42. Vollmer, L. J., and C. Yanofsky. 1986. Efficient cloning of genes of Neurospora crassa. Proc. Natl. Acad. Sci. USA 83:4869-4873.
43. Volpe, T. A., C. Kidner, I. M. Hall, G. Teng, S. I. Grewal, and R. A. Martienssen. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837.
44. Wassenegger, M., S. Heimes, L. Riedel, and H. L. Sanger. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567-576.
45. Zilberman, D., X. Cao, and S. E. Jacobsen. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716-719.