Nsi1 plays a significant role in the silencing of ribosomal DNA in Saccharomyces cerevisiae

Nucleic Acids Research

Volumn 40, Issue 11, 2012, Pages 4892-4903

  Ha, Cheol Woong ^a   Sung, Min Kyung ^a   Huh, Won Ki ^a  

^a Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; NTS1 SILENCING 1 PROTEIN; NUCLEAR PROTEIN; RIBOSOME DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOB1; TRANSCRIPTION FACTOR NET1; TRANSCRIPTION FACTOR SIR2; UNCLASSIFIED DRUG;

ARTICLE; CELL STRUCTURE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DEACETYLATION; DNA REPLICATION; GENE SILENCING; HISTONE ACETYLATION; LIFE EXTENSION; LONGEVITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SACCHAROMYCES CEREVISIAE; YEAST CELL;

CELL CYCLE PROTEINS; CELL NUCLEOLUS; DNA REPLICATION; DNA, RIBOSOMAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENE SILENCING; NUCLEAR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; SIRTUIN 2;

EID: 84862180715     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks188     Document Type: Article

References (51)

1. Johnston, M., Hillier, L., Riles, L., Albermann, K., Andre, B., Ansorge, W., Benes, V., Bruckner, M., Delius, H., Dubois, E. et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature, 387, 87-90. (Pubitemid 27334673)
2. Sinclair, D.A. and Guarente, L. (1997) Extrachromosomal rDNA circles-a cause of aging in yeast. Cell, 91, 1033-1042. (Pubitemid 28027835)
3. Huang, J. and Moazed, D. (2003) Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev., 17, 2162-2176. (Pubitemid 37052295)
4. Imai, S., Armstrong, C.M., Kaeberlein, M. and Guarente, L. (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature, 403, 795-800. (Pubitemid 30111843)
5. Landry, J., Sutton, A., Tafrov, S.T., Heller, R.C., Stebbins, J., Pillus, L. and Sternglanz, R. (2000) The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl Acad. Sci. USA, 97, 5807-5811. (Pubitemid 30367480)
6. Smith, J.S., Brachmann, C.B., Celic, I., Kenna, M.A., Muhammad, S., Starai, V.J., Avalos, J.L., Escalante-Semerena, J.C., Grubmeyer, C., Wolberger, C. et al. (2000) A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl Acad. Sci. USA, 97, 6658-6663. (Pubitemid 30412770)
7. Hoppe, G.J., Tanny, J.C., Rudner, A.D., Gerber, S.A., Danaie, S., Gygi, S.P. and Moazed, D. (2002) Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol., 22, 4167-4180. (Pubitemid 34556587)
8. Luo, K., Vega-Palas, M.A. and Grunstein, M. (2002) Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev., 16, 1528-1539. (Pubitemid 34686334)
9. Rusche, L.N., Kirchmaier, A.L. and Rine, J. (2002) Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell, 13, 2207-2222. (Pubitemid 34831327)
10. Kaeberlein, M., McVey, M. and Guarente, L. (1999) The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev., 13, 2570-2580. (Pubitemid 29489648)
11. Fritze, C.E., Verschueren, K., Strich, R. and Easton Esposito, R. (1997) Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J., 16, 6495-6509. (Pubitemid 27483275)
12. Straight, A.F., Shou, W., Dowd, G.J., Turck, C.W., Deshaies, R.J., Johnson, A.D. and Moazed, D. (1999) Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell, 97, 245-256. (Pubitemid 29194275)
13. Huang, J., Brito, I.L., Villen, J., Gygi, S.P., Amon, A. and Moazed, D. (2006) Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes Dev., 20, 2887-2901. (Pubitemid 44771749)
14. Mekhail, K., Seebacher, J., Gygi, S.P. and Moazed, D. (2008) Role for perinuclear chromosome tethering in maintenance of genome stability. Nature, 456, 667-670.
15. Rabitsch, K.P., Petronczki, M., Javerzat, J.P., Genier, S., Chwalla, B., Schleiffer, A., Tanaka, T.U. and Nasmyth, K. (2003) Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I. Dev. Cell, 4, 535-548. (Pubitemid 36437560)
16. Guarente, L. (1997) Link between aging and the nucleolus. Genes Dev., 11, 2449-2455. (Pubitemid 27438827)
17. Olson, M.O. (2004) Sensing cellular stress: another new function for the nucleolus? Sci. STKE, 2004, pe10.
18. Sherr, C.J. and Weber, J.D. (2000) The ARF/p53 pathway. Curr. Opin. Genet. Dev., 10, 94-99. (Pubitemid 30113711)
19. Visintin, R. and Amon, A. (2000) The nucleolus: the magician's hat for cell cycle tricks. Curr. Opin. Cell Biol., 12, 752.
20. Pederson, T. and Tsai, R.Y. (2009) In search of nonribosomal nucleolar protein function and regulation. J. Cell. Biol., 184, 771-776.
21. Warner, J.R. and McIntosh, K.B. (2009) How common are extraribosomal functions of ribosomal proteins? Mol. Cell, 34, 3-11.
22. Andersen, J.S., Lam, Y.W., Leung, A.K., Ong, S.E., Lyon, C.E., Lamond, A.I. and Mann, M. (2005) Nucleolar proteome dynamics. Nature, 433, 77-83. (Pubitemid 40101146)
23. Andersen, J.S., Lyon, C.E., Fox, A.H., Leung, A.K., Lam, Y.W., Steen, H., Mann, M. and Lamond, A.I. (2002) Directed proteomic analysis of the human nucleolus. Curr. Biol., 12, 1-11.
24. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S. and O'Shea, E.K. (2003) Global analysis of protein localization in budding yeast. Nature, 425, 686-691. (Pubitemid 37314307)
25. Longtine, M.S., McKenzie, A. 3rd, Demarini, D.J., Shah, N.G., Wach, A., Brachat, A., Philippsen, P. and Pringle, J.R. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast, 14, 953-961. (Pubitemid 28328001)
26. Sung, M.K. and Huh, W.K. (2007) Bimolecular fluorescence complementation analysis system for in vivo detection of protein-protein interaction in Saccharomyces cerevisiae. Yeast, 24, 767-775.
27. Gietz, R.D., Schiestl, R.H., Willems, A.R. and Woods, R.A. (1995) Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast, 11, 355-360.
28. Sherman, F. (2002) Getting started with yeast. Methods Enzymol., 350, 3-41. (Pubitemid 34619482)
29. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D. and Brown, P.O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
30. Ha, C.W. and Huh, W.K. (2011) Rapamycin increases rDNA stability by enhancing association of Sir2 with rDNA in Saccharomyces cerevisiae. Nucleic Acids Res., 39, 1336-1350.
31. Ray, A., Hector, R.E., Roy, N., Song, J.H., Berkner, K.L. and Runge, K.W. (2003) Sir3p phosphorylation by the Slt2p pathway effects redistribution of silencing function and shortened lifespan. Nat. Genet., 33, 522-526. (Pubitemid 36390017)
32. Tsang, C.K., Li, H. and Zheng, X.S. (2007) Nutrient starvation promotes condensin loading to maintain rDNA stability. EMBO J., 26, 448-458. (Pubitemid 46160945)
33. Park, P.U., McVey, M. and Guarente, L. (2002) Separation of mother and daughter cells. Methods Enzymol., 351, 468-477. (Pubitemid 34615006)
34. Tsang, C.K., Bertram, P.G., Ai, W., Drenan, R. and Zheng, X.F. (2003) Chromatin-mediated regulation of nucleolar structure and RNA Pol I localization by TOR. EMBO J., 22, 6045-6056. (Pubitemid 37463248)
35. Stegmeier, F., Huang, J., Rahal, R., Zmolik, J., Moazed, D. and Amon, A. (2004) The replication fork block protein Fob1 functions as a negative regulator of the FEAR network. Curr. Biol., 14, 467-480. (Pubitemid 38431281)
36. Hall, D.B., Wade, J.T. and Struhl, K. (2006) An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol. Cell. Biol., 26, 3672-3679.
37. Kasahara, K., Ohtsuki, K., Ki, S., Aoyama, K., Takahashi, H., Kobayashi, T., Shirahige, K. and Kokubo, T. (2007) Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae. Mol. Cell. Biol., 27, 6686-6705. (Pubitemid 47483622)
38. Siddiqi, I.N., Dodd, J.A., Vu, L., Eliason, K., Oakes, M.L., Keener, J., Moore, R., Young, M.K. and Nomura, M. (2001) Transcription of chromosomal rRNA genes by both RNA polymerase I and II in yeast uaf30 mutants lacking the 30 kDa subunit of transcription factor UAF. EMBO J., 20, 4512-4521. (Pubitemid 32772045)
39. Keys, D.A., Vu, L., Steffan, J.S., Dodd, J.A., Yamamoto, R.T., Nogi, Y. and Nomura, M. (1994) RRN6 and RRN7 encode subunits of a multiprotein complex essential for the initiation of rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae. Genes Dev., 8, 2349-2362. (Pubitemid 24314296)
40. Lalo, D., Steffan, J.S., Dodd, J.A. and Nomura, M. (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. (Pubitemid 26292954)
41. Fleischer, T.C., Weaver, C.M., McAfee, K.J., Jennings, J.L. and Link, A.J. (2006) Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev., 20, 1294-1307. (Pubitemid 43727590)
42. Mohanty, B.K. and Bastia, D. (2004) Binding of the replication terminator protein Fob1p to the Ter sites of yeast causes polar fork arrest. J. Biol. Chem., 279, 1932-1941. (Pubitemid 38084464)
43. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627. (Pubitemid 30103994)
44. Li, C., Mueller, J.E. and Bryk, M. (2006) Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer. Mol. Biol. Cell, 17, 3848-3859. (Pubitemid 44330870)
45. Wohlschlegel, J.A., Johnson, E.S., Reed, S.I. and Yates, J.R. 3rd (2004) Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem., 279, 45662-45668. (Pubitemid 39491554)
46. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
47. Wong, J., Nakajima, Y., Westermann, S., Shang, C., Kang, J.S., Goodner, C., Houshmand, P., Fields, S., Chan, C.S., Drubin, D. et al. (2007) A protein interaction map of the mitotic spindle. Mol. Biol. Cell, 18, 3800-3809. (Pubitemid 47519474)
48. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574. (Pubitemid 32295017)
49. Scheer, U. and Hock, R. (1999) Structure and function of the nucleolus. Curr. Opin. Cell. Biol., 11, 385-390. (Pubitemid 29273811)
50. Boisvert, F.M. and Lamond, A.I. (2010) p53-Dependent subcellular proteome localization following DNA damage. Proteomics, 10, 4087-4097.
51. Lam, Y.W., Evans, V.C., Heesom, K.J., Lamond, A.I. and Matthews, D.A. (2010) Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol. Cell Proteomics, 9, 117-130.