RNA polymerase I transcription silences noncoding RNAs at the ribosomal DNA locus in Saccharomyces cerevisiae

Eukaryotic Cell

Volumn 9, Issue 2, 2010, Pages 325-335

  Cesarini, Elisa ^a   Mariotti, Francesca Romana ^a   Cioci, Francesco ^a,c   Camilloni, Giorgio ^a,b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b CNR   (Italy)

^c NONE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; FUNGAL DNA; HISTONE; RIBOSOME DNA; SACCHAROMYCES CEREVISIAE PROTEIN; UNTRANSLATED RNA;

ARTICLE; CHEMISTRY; GENE LOCUS; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE;

DNA, FUNGAL; DNA, RIBOSOMAL; GENE SILENCING; GENETIC LOCI; HISTONES; RNA POLYMERASE I; RNA, UNTRANSLATED; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 75849134166     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.00280-09     Document Type: Article

References (39)

1. Bordi, L., F. Cioci, and G. Camilloni. 2001. In vivo binding and hierarchy of assembly of the yeast RNA polymerase I transcription factors. Mol. Biol. Cell 12:753-760.
2. Bryk, M., M. Banerjee, M. Murphy, K. E. Knudsen, D. J. Garfinkel, and M. J. Curcio. 1997. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11:255-269.
3. Buck, S. W., J. J. Sandmeier, and J. S. Smith. 2002. RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin. Cell 111: 1003-1014.
4. Cioci, F., M. Vogelauer, and G. Camilloni. 2002. Acetylation and accessibility of rDNA chromatin in Saccharomyces cerevisiae in (Delta)top1 and (Delta) sir2 mutants. J. Mol. Biol. 322:41-52.
5. Cioci, F., L. Vu, K. Eliason, M. Oakes, I. N. Siddiqi, and M. Nomura. 2003. Silencing in yeast rDNA chromatin: reciprocal relationship in gene expression between RNA polymerase I and II. Mol. Cell 12:135-145.
6. Conrad-Webb, H., and R. A. Butow. 1995. A polymerase switch in the synthesis of rRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 15:2420-2428.
7. Dammann, R., R. Lucchini, T. Koller, and J. M. Sogo. 1993. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21:2331-2338.
8. Fritze, C. E., K. Verschueren, R. Strich, and R. E. Esposito. 1997. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16:6495-6509.
9. Hontz, R. D., S. L. French, M. L. Oakes, P. Tongaonkar, M. Nomura, A. L. Beyer, and J. S. Smith. 2008. Transcription of multiple yeast ribosomal DNA genes requires targeting of UAF to the promoter by Uaf30. Mol. Cell. Biol. 28:6709-6719.
10. Houseley, J., K. Kotovic, A. E. Hage, and D. Tollervey. 2007. Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J. 26:4996-5006.
11. Hsiang, Y. H., R. Hertzberg, S. Hecht, and L. F. Liu. 1985. Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I. J. Biol. Chem. 260:14873-14878.
12. Imai, S., C. M. Armstrong, M. Kaeberlein, and L. Guarente. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795-800.
13. Keys, D. A., B. S. Lee, J. A. Dodd, T. T. Nguyen, L. Vu, E. Fantino, L. M. Burson, Y. Nogi, and M. Nomura. 1996. Multiprotein transcription factor UAF interacts with the upstream element of the yeast RNA polymerase I promoter and forms a stable preinitiation complex. Genes Dev. 10:887-903.
14. Kim, U. J., M. Han, P. Kayne, and M. Grunstein. 1988. Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO J. 7:2211-2219.
15. Kobayashi, T., and A. R. Ganley. 2005. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309:1581-1584.
16. Kurdistani, S. K., and M. Grunstein. 2003. Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell Biol. 4:276-284.
17. Lalo, D., J. S. Steffan, J. A. Dodd, and M. Nomura. 1996. RRN11 encodes the third subunit of the complex containing Rrn6p and Rrn7p that is essential for the initiation of rDNA transcription by yeast RNA polymerase I. J. Biol. Chem. 271:21062-21067.
18. Landry, J., A. Sutton, S. T. Tafrov, R. C. Heller, J. Stebbins, L. Pillus, and R. Sternglanz. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl. Acad. Sci. U. S. A. 97:5807-5811.
19. Li, C., J. E. Mueller, and M. Bryk. 2006. Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer. Mol. Biol. Cell 17:3848-3859.
20. Merz, K., M. Hondele, H. Goetze, K. Gmelch, U. Stoeckl, and J. Griesenbeck. 2008. Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev. 22:1190-1204.
21. Mueller, J. E., C. Li, and M. Bryk. 2007. Isw2 regulates gene silencing at the ribosomal DNA locus in Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 361:1017-1021.
22. Oakes, M., I. Siddiqi, L. Vu, J. Aris, and M. Nomura. 1999. Transcription factor UAF, expansion and contraction of ribosomal DNA (rDNA) repeats, and RNA polymerase switch in transcription of yeast rDNA. Mol. Cell. Biol. 19:8559-8569.
23. Petes, T. D. 1979. Yeast ribosomal DNA genes are located on chromosome XII. Proc. Natl. Acad. Sci. U. S. A. 76:410-414.
24. Robyr, D., Y. Suka, I. Xenarios, S. K. Kurdistani, A. Wang, N. Suka, and M. Grunstein. 2002. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109:437-446.
25. Rundlett, S. E., A. A. Carmen, N. Suka, B. M. Turner, and M. Grunstein. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831-835.
26. Sherman, F., G. R. Fink, and C. Lawrence. 1983. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Smith, J. S., and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241-254.
28. Straight, A. F., W. Shou, G. J. Dowd, C. W. Turck, R. J. Deshaies, A. D. Johnson, and D. Moazed. 1999. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97:245-256.
29. Tanny, J. C., G. J. Dowd, J. Huang, H. Hilz, and D. Moazed. 1999. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99:735-745.
30. Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619-630.
31. Thuriaux, P., S. Mariotte, J. M. Buhler, A. Sentenac, L. Vu, B. S. Lee, and M. Nomura. 1995. Gene RPA43 in Saccharomyces cerevisiae encodes an essential subunit of RNA polymerase I. J. Biol. Chem. 270:24252-24257.
32. Tongaonkar, P., S. L. French, M. L. Oakes, L. Vu, D. A. Schneider, A. L. Beyer, and M. Nomura. 2005. Histones are required for transcription of yeast rRNA genes by RNA polymerase I. Proc. Natl. Acad. Sci. U. S. A. 102: 10129-10134.
33. Vasiljeva, L., M. Kim, N. Terzi, L. M. Soares, and S. Buratowski. 2008. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol. Cell 29:313-323.
34. Venditti, S., and G. Camilloni. 1994. In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae. Mol. Gen. Genet. 242:100-104.
35. Venema, J., and D. Tollervey. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Annu. Rev. Genet. 33:261-311.
36. Verdone, L., G. Camilloni, E. Di Mauro, and M. Caserta. 1996. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16:1978-1988.
37. Vogelauer, M., and G. Camilloni. 1999. Site-specific in vivo cleavages by DNA topoisomerase I in the regulatory regions of the 35 S rRNA in Saccharomyces cerevisiae are transcription independent. J. Mol. Biol. 293:19-28.
38. Vogelauer, M., F. Cioci, and G. Camilloni. 1998. DNA protein-interactions at the Saccharomyces cerevisiae 35 S rRNA promoter and in its surrounding region. J. Mol. Biol. 275:197-209.
39. Vu, L., I. Siddiqi, B. S. Lee, C. A. Josaitis, and M. Nomura. 1999. RNA polymerase switch in transcription of yeast rDNA: role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II. Proc. Natl. Acad. Sci. U. S. A. 96:4390-4395.