DOT4 Links Silencing and Cell Growth in Saccharomyces cerevisiae

REFERENCES

• Adams, A., D. E. Gottschling, C. A. Kaiser, T. Stearns 1997. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Amerik, A., S. Swaminathan, B. A. Krantz, K. D. Wilkinson, and J. Hochstrasser 1997. In vivo disassembly of free polyubiquitin chains by yeast Ubp14 modulates rates of protein degradation by the proteasome. EMBO J. 16:4826–4838.
   PubMed Web of Science ®Google Scholar
• Aparicio, O. M., B. L. Billington, and J. Gottschling 1991. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66:1279–1287.
   PubMed Web of Science ®Google Scholar
• Aparicio, O. M., and J. Gottschling 1994. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 8:1133–1146.
   PubMed Web of Science ®Google Scholar
• Ausubel F. M., R. Brent, R. E. Kingston, D. O. Moore, J. G. Seidman, J. A. Smith, K. Struhl 1998. Current protocols in molecular biology. John Wiley & Sons, New York, N.Y.
   Google Scholar
• Baker, R. T., J. W. Tobias, and J. Varshavsky 1992. Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J. Biol. Chem. 267:23364–23375.
   PubMed Web of Science ®Google Scholar
• Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and J. Cullin 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329–3330.
   PubMed Web of Science ®Google Scholar
• Boeke, J. D., F. LaCroute, and J. Fink 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197:345–346.
   PubMedGoogle Scholar
• Boscheron, C., L. Maillet, S. Marcand, M. Tsai-Pflugfelder, S. M. Gasser, and J. Gilson 1996. Cooperation at a distance between silencers and proto-silencers at the yeast HML locus. EMBO J. 15:2184–2195.
   PubMed Web of Science ®Google Scholar
• Boulton, S. J., and J. Jackson 1998. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 17:1819–1828.
   PubMed Web of Science ®Google Scholar
• Brachmann, C. B., A. Davies, G. J. Cost, E. Caputo, J. Li, P. Hieter, and J. Boeke 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115–132.
   PubMed Web of Science ®Google Scholar
• Bradbury, E. M. 1992. Reversible histone modifications and the chromosome cell cycle. Bioessays 14:9–16.
   PubMed Web of Science ®Google Scholar
• Bryk, M., M. Banerjee, M. Murphy, K. E. Knudsen, D. J. Garfinkel, and J. Curcio 1997. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11:255–269.
   PubMedGoogle Scholar
• Buck, S. W., and J. Shore 1995. Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes Dev. 9:370–384.
   PubMedGoogle Scholar
• Chalfie, M., Y. Tu, G. Euskirchen, W. W. Ward, and J. Prasher 1994. Green fluorescent protein as a marker for gene expression. Science 263:802–805.
   PubMed Web of Science ®Google Scholar
• Chen, P., and J. Hochstrasser 1995. Biogenesis, structure and function of the yeast 20S proteasome. EMBO J. 14:2620–2630.
   PubMedGoogle Scholar
• Chien, C. T., P. L. Bartel, R. Sternglanz, and J. Fields 1991. The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. USA 88:9578–9582.
   PubMed Web of Science ®Google Scholar
• Chien, C. T., S. Buck, R. Sternglanz, and J. Shore 1993. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell 75:531–541.
   PubMedGoogle Scholar
• Cockell, M., F. Palladino, T. Laroche, G. Kyrion, C. Liu, A. J. Lustig, and J. Gasser 1995. The carboxy termini of Sir4 and Rap1 affect Sir3 localization: evidence for a multicomponent complex required for yeast telomeric silencing. J. Cell Biol. 129:909–924.
   PubMedGoogle Scholar
• Cockell, M., H. Renauld, P. Watt, and J. Gasser 1998. Sif2p interacts with the Sir4p amino-terminal domain and antagonizes telomeric silencing in yeast. Curr. Biol. 8:787–790.
   PubMedGoogle Scholar
• Davie, J. R., and J. Murphy 1990. Level of ubiquitinated histone H2B in chromatin is coupled to ongoing transcription. Biochemistry 29:4752–4757.
   PubMed Web of Science ®Google Scholar
• Freeman, K., M. Gwadz, and J. Shore 1995. Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast. Genetics 141:1253–1262.
   PubMedGoogle Scholar
• Fritze, C. E., K. Verschueren, R. Strich, and J. Easton Esposito 1997. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16:6495–6509.
   PubMedGoogle Scholar
• Gotta, M., T. Laroche, A. Formenton, L. Maillet, H. Scherthan, and J. Gasser 1996. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134:1349–1363.
   PubMedGoogle Scholar
• Gotta, M., S. Strahl-Bolsinger, H. Renauld, T. Laroche, B. K. Kennedy, M. Grunstein, and J. Gasser 1997. Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J. 16:3243–3255.
   PubMedGoogle Scholar
• Gottlieb, S., and J. Esposito 1989. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56:771–776.
   PubMed Web of Science ®Google Scholar
• Gottschling, D. E., O. M. Aparicio, B. L. Billington, and J. Zakian 1990. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751–762.
   PubMed Web of Science ®Google Scholar
• Gottschling Lab Home Page. 27 July 1999, revision date. [Online.] http://www.fhcrc.org/∼gottschling/homepage.html [27 July 1999, last date accessed.]
   Google Scholar
• Gottschling laboratory. Unpublished observations.
   Google Scholar
• Graham, I. R., and J. Chambers 1994. Use of a selection technique to identify the diversity of binding sites for the yeast RAP1 transcription factor. Nucleic Acids Res. 22:124–130.
   PubMedGoogle Scholar
• Gravel, S., M. Larrivee, P. Labrecque, and J. Wellinger 1998. Yeast Ku as a regulator of chromosomal DNA end structure. Science 280:741–744.
   PubMed Web of Science ®Google Scholar
• Grunstein, M. 1990. Histone function in transcription. Annu. Rev. Cell Biol. 6:643–678.
   PubMedGoogle Scholar
• Grunstein, M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9:383–387.
   PubMed Web of Science ®Google Scholar
• Grunstein, M. 1998. Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell 93:325–328.
   PubMedGoogle Scholar
• Guthrie, C., G. R. Fink 1991. Guide to yeast genetics and molecular biology. Academic Press, San Diego, Calif.
   Google Scholar
• Haas, A. L. 1997. Introduction: evolving roles for ubiquitin in cellular regulation. FASEB J. 11:1053–1054.
   PubMedGoogle Scholar
• Haas, A. L., and J. Bright 1985. The immunochemical detection and quantitation of intracellular ubiquitin-protein conjugates. J. Biol. Chem. 260:12464–12473.
   PubMed Web of Science ®Google Scholar
• Hecht, A., T. Laroche, S. Strahl-Bolsinger, S. M. Gasser, and J. Grunstein 1995. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80:583–592.
   PubMed Web of Science ®Google Scholar
• Hecht, A., S. Strahl-Bolsinger, and J. Grunstein 1996. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383:92–96.
   PubMed Web of Science ®Google Scholar
• Hegde, A. N., K. Inokuchi, W. Pei, A. Casadio, M. Ghirardi, D. G. Chain, K. C. Martin, E. R. Kandel, and J. Schwartz 1997. Ubiquitin C-terminal hydrolase is an immediate-early gene essential for long-term facilitation in Aplysia. Cell 89:115–126.
   PubMed Web of Science ®Google Scholar
• Heim, R., A. B. Cubitt, and J. Tsien 1995. Improved green fluorescence. Nature 373:663–664.
   PubMed Web of Science ®Google Scholar
• Henchoz, S., F. De Rubertis, D. Pauli, and J. Spierer 1996. The dose of a putative ubiquitin-specific protease affects position-effect variegation in Drosophila melanogaster. Mol. Cell. Biol. 16:5717–5725.
   PubMedGoogle Scholar
• Henikoff, S., and J. Eghtedarzadeh 1987. Conserved arrangement of nested genes at the Drosophila Gart locus. Genetics 117:711–25.
   PubMedGoogle Scholar
• Hochstrasser, M. 1996. Protein degradation or regulation: Ub the judge. Cell 84:813–815.
   PubMed Web of Science ®Google Scholar
• Hochstrasser, M. 1996. Ubiquitin-dependent protein degradation. Annu. Rev. Genet. 30:405–439.
   PubMed Web of Science ®Google Scholar
• Holmes, S. G., A. B. Rose, K. Steuerle, E. Saez, S. Sayegh, Y. M. Lee, and J. Broach 1997. Hyperactivation of the silencing proteins, Sir2p and Sir3p, causes chromosome loss. Genetics 145:605–614.
   PubMedGoogle Scholar
• Huang, H., A. Kahana, D. E. Gottschling, L. Prakash, and J. Liebman 1997. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:6693–6699.
   PubMedGoogle Scholar
• Huang, Y., R. T. Baker, and J. Fischer-Vize 1995. Control of cell fate by a deubiquitinating enzyme encoded by the fat facets gene. Science 270:1828–1831.
   PubMed Web of Science ®Google Scholar
• Ivy, J. M., A. J. S. Klar, and J. Hicks 1986. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:688–702.
   PubMed Web of Science ®Google Scholar
• James, P., J. Halladay, and J. Craig 1996. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425–1436.
   PubMed Web of Science ®Google Scholar
• Johnson, E. S., and J. Blobel 1997. Ubc9p is the conjugating enzyme for the ubiquitin-like protein Smt3p. J. Biol. Chem. 272:26799–26802.
   PubMed Web of Science ®Google Scholar
• Jones, E. W. 1984. The synthesis and function of proteases in Saccharomyces: genetic approaches. Annu. Rev. Genet. 18:233–270.
   PubMed Web of Science ®Google Scholar
• Kahana, A. 1998 University of Chicago Chicago, Ill.
   Google Scholar
• Kennedy, B. K., M. Gotta, D. A. Sinclair, K. Mills, D. S. McNabb, M. Murthy, S. M. Pak, T. Laroche, S. M. Gasser, and J. Guarente 1997. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae. Cell 89:381–391.
   PubMed Web of Science ®Google Scholar
• Lam, Y. A., W. Xu, G. N. DeMartino, and J. Cohen 1997. Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature 385:737–740.
   PubMed Web of Science ®Google Scholar
• Lammer, D., N. Mathias, J. M. Laplaza, W. Jiang, Y. Liu, J. Callis, M. Goebl, and J. Estelle 1998. Modification of yeast Cdc53p by the ubiquitin-related protein Rub1p affects function of the SCFCdc4 complex. Genes Dev. 12:914–926.
   PubMed Web of Science ®Google Scholar
• Laurenson, P., and J. Rine 1992. Silencers, silencing, and heritable transcriptional states. Microbiol. Rev. 56:543–560.
   PubMedGoogle Scholar
• Li, W., S. Nagaraja, G. P. Delcuve, M. J. Hendzel, and J. Davie 1993. Effects of histone acetylation, ubiquitination and variants on nucleosome stability. Biochem. J. 296:737–744.
   PubMed Web of Science ®Google Scholar
• Liakopoulos, D., G. Doenges, K. Matuschewski, and J. Jentsch 1998. A novel protein modification pathway related to the ubiquitin system. EMBO J. 17:2208–2214.
   PubMed Web of Science ®Google Scholar
• Loayza, D., and J. Michaelis 1998. Role for the ubiquitin-proteasome system in the vacuolar degradation of Ste6p, the a-factor transporter in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:779–789.
   PubMedGoogle Scholar
• Lustig, A. J. 1998. Mechanisms of silencing in Saccharomyces cerevisiae. Curr. Opin. Genet. Dev. 8:233–239.
   PubMedGoogle Scholar
• Lustig, A. J., C. Liu, C. Zhang, and J. Hanish 1996. Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2483–2495.
   PubMedGoogle Scholar
• Marshall, M., D. Mahoney, A. Rose, J. B. Hicks, and J. Broach 1987. Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 7:4441–4452.
   PubMedGoogle Scholar
• Moazed, D., and J. Johnson 1996. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86:667–677.
   PubMedGoogle Scholar
• Moazed, D., A. Kistler, A. Axelrod, J. Rine, and J. Johnson 1997. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc. Natl. Acad. Sci. USA 94:2186–2191.
   PubMedGoogle Scholar
• Moretti, P., K. Freeman, L. Coodly, and J. Shore 1994. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 8:2257–2269.
   PubMed Web of Science ®Google Scholar
• Nash, R., G. Tokiwa, S. Anand, K. Erickson, and J. Futcher 1988. The WHI1+ gene of Saccharomyces cerevisiae tethers cell division to cell size and is a cyclin homolog. EMBO J. 7:4335–4346.
   PubMed Web of Science ®Google Scholar
• Papa, F., and J. Hochstrasser 1993. The yeast DOA4 gene encodes a deubiquitinating enzyme related to a product of the human tre-2 oncogene. Nature 366:313–319.
   PubMed Web of Science ®Google Scholar
• Porter, S. E., P. W. Greenwell, K. B. Ritchie, and J. Petes 1996. The DNA-binding protein Hdf1p (a putative Ku homologue) is required for maintaining normal telomere length in Saccharomyces cerevisiae. Nucleic Acids Res. 24:582–585.
   PubMedGoogle Scholar
• Renauld, H., O. M. Aparicio, P. D. Zierath, B. L. Billington, S. K. Chhablani, and J. Gottschling 1993. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 7:1133–1145.
   PubMed Web of Science ®Google Scholar
• Rine, J., and J. Herskowitz 1987. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9–22.
   PubMed Web of Science ®Google Scholar
• Sambrook, J., E. F. Fritsch, T. Maniatis 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Schmitt, M. E., T. A. Brown, and J. Trumpower 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18:3091–3092.
   PubMed Web of Science ®Google Scholar
• Schwarz, S. E., K. Matuschewski, D. Liakopoulos, M. Scheffner, and J. Jentsch 1998. The ubiquitin-like proteins SMT3 and SUMO-1 are conjugated by the UBC9 E2 enzyme. Proc. Natl. Acad. Sci. USA 95:560–564.
   PubMedGoogle Scholar
• Shore, D. 1994. RAP1: a protean regulator in yeast. Trends Genet. 10:408–412.
   PubMed Web of Science ®Google Scholar
• Sikorski, R. S., and J. Hieter 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Singer, J. D., B. M. Manning, and J. Formosa 1996. Coordinating DNA replication to produce one copy of the genome requires genes that act in ubiquitin metabolism. Mol. Cell. Biol. 16:1356–1366.
   PubMedGoogle Scholar
• Singer, M. S., and J. Gottschling 1994. TLC1: template RNA component of Saccharomyces cerevisiae telomerase. Science 266:404–409.
   PubMed Web of Science ®Google Scholar
• Singer, M. S., A. Kahana, A. J. Wolf, L. L. Meisinger, S. E. Peterson, C. Goggin, M. Mahowald, and J. Gottschling 1998. Identification of high copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150:613–632.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., and J. Boeke 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241–254.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., C. B. Brachmann, L. Pillus, and J. Boeke 1998. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. Genetics 149:1205–1219.
   PubMedGoogle Scholar
• Stevenson, J., and J. Gottschling 1999. Telomeric chromatin modulates replication timing near chromosome ends. Genes Dev. 13:146–151.
   PubMedGoogle Scholar
• Strahl-Bolsinger, S., A. Hecht, K. Luo, and J. Grunstein 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83–93.
   PubMed Web of Science ®Google Scholar
• Sussel, L., D. Vannier, and J. Shore 1993. Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:3919–3928.
   PubMed Web of Science ®Google Scholar
• Taya, S., T. Yamamoto, K. Kano, Y. Kawano, A. Iwamatsu, T. Tsuchiya, K. Tanaka, M. Kanai-Azuma, S. A. Wood, J. S. Mattick, and J. Kaibuchi 1998. The Ras target AF-6 is a substrate of the fam deubiquitinating enzyme. J. Cell Biol. 142:1053–1062.
   PubMedGoogle Scholar
• Triolo, T., and J. Sternglanz 1996. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381:251–253.
   PubMed Web of Science ®Google Scholar
• Tsukamoto, Y., J. Kato, and J. Ikeda 1997. Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388:900–903.
   PubMed Web of Science ®Google Scholar
• van Holde, K. E. 1988. Chromatin. Springer-Verlag, New York, N.Y.
   Google Scholar
• Varshavsky, A. 1996. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93:12142–12149.
   PubMed Web of Science ®Google Scholar
• Wach, A., A. Brachat, C. Alberti-Segui, C. Rebischung, and J. Philippsen 1997. Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae. Yeast 13:1065–1075.
   PubMed Web of Science ®Google Scholar
• Wilkinson, K. D. 1997. Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. FASEB J. 11:1245–1256.
   PubMed Web of Science ®Google Scholar
• Wilkinson, K. D., V. L. Tashayev, L. B. O’Connor, C. N. Larsen, E. Kasperek, and J. Pickart 1995. Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T. Biochemistry 34:14535–14546.
   PubMed Web of Science ®Google Scholar
• Zhang, Z., and J. Buchman 1997. Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Mol. Cell. Biol. 17:5461–5472.
   PubMedGoogle Scholar