A Methyltransferase Targeting Assay Reveals Silencer-Telomere Interactions in Budding Yeast

REFERENCES

• Abraham, J., K. A. Nasmyth, J. N. Srathern, A. J. Klar, and J. B. Hicks. 1984. Regulation of mating-type information in yeast. Negative control requiring sequences both 5′ and 3′ to the regulated region. J. Mol. Biol. 176: 307–331.
   PubMedGoogle Scholar
• Andrulis, E. D., A. M. Neiman, D. C. Zappulla, and R. Sternglanz. 1998. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394: 592–595.
   PubMed Web of Science ®Google Scholar
• Aragon-Alcaide, L., and A. V. Strunnikov. 2000. Functional dissection of in vivo interchromosome association in Saccharomyces cerevisiae. Nat. Cell Biol. 2: 812–818.
   PubMedGoogle Scholar
• Bonneaud, N., O. Ozier-Kalogeropoulos, G. Y. Li, M. Labouesse, L. Minvielle-Sebastia, and F. Lacroute. 1991. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7: 609–615.
   PubMed Web of Science ®Google Scholar
• Boscheron, C., L. Maillet, S. Marcand, M. Tsai-Pflugfelder, S. M. Gasser, and E. 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
• Boyle, S., S. Gilchrist, J. M. Bridger, N. L. Mahy, J. A. Ellis, and W. A. Bickmore. 2001. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum. Mol. Genet. 10: 211–219.
   PubMed Web of Science ®Google Scholar
• Buck, S. W., and D. 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
• Burgess, S. M., and N. Kleckner. 1999. Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. Genes Dev. 13: 1871–1873.
   PubMedGoogle Scholar
• Croft, J. A., J. M. Bridger, S. Boyle, P. Perry, P. Teague, and W. A. Bickmore. 1999. Differences in the localization and morphology of chromosomes in the human nucleus. J. Cell Biol. 145: 1119–1131.
   PubMed Web of Science ®Google Scholar
• Csink, A. K., and S. Henikoff. 1996. Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381: 529–531.
   PubMedGoogle Scholar
• de Bruin, D., S. M. Kantrow, R. A. Liberatore, and V. A. Zakian. 2000. Telomere folding is required for the stable maintenance of telomere position effects in yeast. Mol. Cell. Biol. 20: 7991–8000.
   PubMedGoogle Scholar
• Dekker, J., K. Rippe, M. Dekker, and N. Kleckner. 2002. Capturing chromosome conformation. Science 295: 1306–1311.
   PubMed Web of Science ®Google Scholar
• Dernburg, A. F., K. W. Broman, J. C. Fung, W. F. Marshall, J. Philips, D. A. Agard, and J. W. Sedat. 1996. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745–759.
   PubMedGoogle Scholar
• Ehrenhofer-Murray, A. E., D. H. Rivier, and J. Rine. 1997. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145: 923–934.
   PubMedGoogle Scholar
• Feuerbach, F., V. Galy, E. Trelles-Sticken, M. Fromont-Racine, A. Jacquier, E. Gilson, J. C. Olivo-Marin, H. Scherthan, and U. Nehrbass. 2002. Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast. Nat. Cell Biol. 4: 214–221.
   PubMed Web of Science ®Google Scholar
• Fourel, G., C. Boscheron, E. Revardel, E. Lebrun, Y. F. Hu, K. C. Simmen, K. Muller, R. Li, N. Mermod, and E. Gilson. 2001. An activation-independent role of transcription factors in insulator function. EMBO Rep. 2: 124–132.
   PubMedGoogle Scholar
• Fourel, G., E. Revardel, C. E. Koering, and E. Gilson. 1999. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 18: 2522–2537.
   PubMed Web of Science ®Google Scholar
• Francastel, C., M. C. Walters, M. Groudine, and D. I. Martin. 1999. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin. Cell 99: 259–269.
   PubMedGoogle Scholar
• Gotta, M., T. Laroche, A. Formenton, L. Maillet, H. Scherthan, and S. M. 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.
   PubMed Web of Science ®Google Scholar
• Gottschling, D. E. 1992. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. USA 89: 4062–4065.
   PubMed Web of Science ®Google Scholar
• Hecht, A., T. Laroche, S. Strahl-Bolsinger, S. M. Gasser, and M. 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 M. Grunstein. 1996. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383: 92–96.
   PubMed Web of Science ®Google Scholar
• Heun, P., T. Laroche, K. Shimada, P. Furrer, and S. M. Gasser. 2001. Chromosome dynamics in the yeast interphase nucleus. Science 294: 2181–2186.
   PubMed Web of Science ®Google Scholar
• Holmes, S. G., and J. R. Broach. 1996. Silencers are required for inheritance of the repressed state in yeast. Genes Dev. 10: 1021–1032.
   PubMedGoogle Scholar
• Kimmerly, W. J., and J. Rine. 1987. Replication and segregation of plasmids containing cis-acting regulatory sites of silent mating type genes in Saccharomyces cerevisiae are controlled by the SIR genes. Mol. Cell. Biol. 7: 4225–4237.
   PubMedGoogle Scholar
• Laroche, T., S. G. Martin, M. Gotta, H. C. Gorham, F. E. Pryde, E. J. Louis, and S. M. Gasser. 1998. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr. Biol. 8: 653–656.
   PubMed Web of Science ®Google Scholar
• Lebrun, E., E. Revardel, C. Boscheron, R. Li, E. Gilson, and G. Fourel. 2001. Protosilencers in Saccharomyces cerevisiae subtelomeric regions. Genetics 158: 167–176.
   PubMed Web of Science ®Google Scholar
• Longtine, M. S., S. Enomoto, S. L. Finstad, and J. Berman. 1992. Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product. Mol. Cell. Biol. 12: 1997–2009.
   PubMedGoogle Scholar
• Mahoney, D. J., and J. R. Broach. 1989. The HML mating type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers. Mol. Cell. Biol. 9: 4621–4630.
   PubMedGoogle Scholar
• Maillet, L., C. Boscheron, M. Gotta, S. Marcand, E. Gilson, and S. M. Gasser. 1996. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 10: 1796–1811.
   PubMed Web of Science ®Google Scholar
• Maillet, L., F. Gaden, V. Brevet, G. Fourel, S. G. Martin, K. Dubrana, S. M. Gasser, and E. Gilson. 2001. Ku-deficient yeast strains exhibit alternative states of silencing competence. EMBO Rep. 2: 203–210.
   PubMedGoogle Scholar
• Marcand, S., S. W. Buck, P. Moretti, E. Gilson, and D. Shore. 1996. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev. 10: 1297–1309.
   PubMedGoogle Scholar
• Martin, S. G., T. Laroche, N. Suka, M. Grunstein, and S. M. Gasser. 1999. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97: 621–633.
   PubMed Web of Science ®Google Scholar
• Michaelis, C., R. Ciosk, and K. Nasmyth. 1997. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell 91: 35–45.
   PubMed Web of Science ®Google Scholar
• Moretti, P., K. Freeman, L. Coodly, and D. 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
• Palladino, F., T. Laroche, E. Gilson, A. Axelrod, L. Pillus, and S. M. Gasser. 1993. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75: 543–555.
   PubMed Web of Science ®Google Scholar
• Pirrotta, V. 1997. Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. Trends Genet. 13: 314–318.
   PubMed Web of Science ®Google Scholar
• Rose, M. D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Shore, D. 2001. Telomeric chromatin: replicating and wrapping up chromosome ends. Curr. Opin. Genet. Dev. 11: 189–198.
   PubMedGoogle Scholar
• Sikorski, R. S., and P. 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
• Strahl-Bolsinger, S., A. Hecht, K. Luo, and M. 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
• Tham, W. H., J. S. Wyithe, P. K. Ferrigno, P. A. Silver, and V. A. Zakian. 2001. Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions. Mol. Cell 8: 189–199.
   PubMedGoogle Scholar
• Thompson, J. S., L. M. Johnson, and M. Grunstein. 1994. Specific repression of the yeast silent mating locus HMR by an adjacent telomere. Mol. Cell. Biol. 14: 446–455.
   PubMedGoogle Scholar
• van Steensel, B., and S. Henikoff. 2000. Identification of in vivo DNA targets of chromatin proteins with tethered dam methyltransferase. Nat. Biotechnol. 18: 424–428.
   PubMed Web of Science ®Google Scholar
• Vega-Palas, M. A., S. Venditti, and E. Di Mauro. 1997. Telomeric transcriptional silencing in a natural context. Nat. Genet. 15: 232–233.
   PubMedGoogle Scholar
• Wach, A., A. Brachat, R. Pohlmann, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10: 1793–1808.
   PubMed Web of Science ®Google Scholar
• Xu, E. Y., S. Kim, and D. H. Rivier. 1999. SAS4 and SAS5 are locus-specific regulators of silencing in Saccharomyces cerevisiae. Genetics 153: 25–33.
   PubMedGoogle Scholar