REFERENCES
- Abraham, J., K. A. Nasmyth, J. N. Strathern, 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.
- Bi, X., M. Braunstein, G. J. Shei, and J. R. Broach. 1999. The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing. Proc. Natl. Acad. Sci. USA 96:11934–11939.
- Bi, X., Q. Yu, J. J. Sandmeier, and Y. Zou. 2004. Formation of boundaries of transcriptionally silent chromatin by nucleosome-excluding structures. Mol. Cell. Biol. 24:2118–2131.
- 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.
- Brand, A. H., L. Breeden, J. Abraham, R. Sternglanz, and K. Nasmyth. 1985. Characterization of a “silencer” in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer. Cell 41:41–48.
- Breier, A. M., S. Chatterji, and N. R. Cozzarelli. 2004. Prediction of Saccharomyces cerevisiae replication origins. Genome Biol. 5:R22.
- Buchman, A. R., W. J. Kimmerly, J. Rine, and R. D. Kornberg. 1988. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:210–225.
- Carmen, A. A., L. Milne, and M. Grunstein. 2001. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem. 277:4778–4781.
- Chi, M.-H., and D. Shore. 1996. SUM1-1, a dominant suppressor of SIR mutations in Saccharomyces cerevisiae, increases transcriptional silencing at telomeres and HM mating-type loci and decreases chromosome stability. Mol. Cell. Biol. 16:4281–4294.
- Chiu, Y. H., Q. Yu, J. J. Sandmeier, and X. Bi. 2003. A targeted histone acetyltransferase can create a sizable region of hyperacetylated chromatin and counteract the propagation of transcriptionally silent chromatin. Genetics 165:115–125.
- Feldman, J. B., J. B. Hicks, and J. R. Broach. 1984. Identification of sites required for repression of a silent mating type locus in yeast. J. Mol. Biol. 178:815–834.
- Fourel, G., E. Lebrun, and E. Gilson. 2002. Protosilencers as building blocks for heterochromatin. Bioessays 24:828–835.
- Grewal, S. I., and D. Moazed. 2003. Heterochromatin and epigenetic control of gene expression. Science 301:798–7802.
- Holmes, S. G., and M. M. Smith. 1989. Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3′-flanking domain. Mol. Cell. Biol. 9:5464–5472.
- Hoppe, G. J., J. C. Tanny, A. D. Rudner, S. A. Gerber, S. Danaie, S. P. Gygi, and D. Moazed. 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.
- Klar, A. J., J. N. Strathern, J. R. Broach, and J. B. Hicks. 1981. Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature 289:239–244.
- Lascaris, R. F., E. Groot, P. B. Hoen, W. H. Mager, and R. J. Planta. 2000. Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res. 28:1390–1396.
- Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327–334.
- Liou, G. G., J. C. Tanny, R. G. Kruger, T. Walz, and D. Moazed. 2005. Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121:515–527.
- Lipford, J. R., and S. P. Bell. 2001. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol. Cell 7:21–30.
- Loo, S., and J. Rine. 1994. Silencers and domains of generalized repression. Science 264:1768–1771.
- 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.
- Matecic, M., K. Martins-Taylor, M. Hickman, J. Tanny, D. Moazed, and S. G. Holmes. 18 June 2006. New alleles of SIR2 define cell cycle specific silencing functions. Genetics [Epub ahead of print.]
- Miyake, T., J. Reese, C. M. Loch, D. T. Auble, and R. Li. 2004. Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae. J. Biol. Chem. 279:34865–34872.
- Moazed, D. 2001. Enzymatic activities of Sir2 and chromatin silencing. Curr. Opin. Cell Biol. 13:232–238.
- Nasmyth, K. A., K. Tatchell, B. D. Hall, C. Astell, and M. Smith. 1981. A position effect in the control of transcription at yeast mating type loci. Nature 289:244–250.
- Palacios DeBeer, M. A., and C. A. Fox. 1999. A role for a replicator dominance mechanism in silencing. EMBO J. 18:3808–3819.
- Ravindra, A., K. Weiss, and R. T. Simpson. 1999. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating-type locus HMRa. Mol. Cell. Biol. 19:7944–7950.
- Rhode, P. R., S. Elsasser, and J. L. Campbell. 1992. Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1064–1077.
- Rivier, D. H., J. L. Ekena, and J. Rine. 1999. HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae. Genetics 151:521–529.
- Rudner, A. D., B. E. Hall, T. Ellenberger, and D. Moazed. 2005. A nonhistone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol. Cell. Biol. 25:4514–4528.
- Rusche, L. N., A. L. Kirchmaier, and J. Rine. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72:481–516.
- Ryan, M. P., G. A. Stafford, L. Yu, K. B. Cummings, and R. H. Morse. 1999. Assays for nucleosome positioning in yeast. Methods Enzymol. 304:376–399.
- Shei, G. J., and J. R. Broach. 1995. Yeast silencers can act as orientation-dependent gene inactivation centers that respond to environmental signals. Mol. Cell. Biol. 15:3496–3506.
- Siliciano, P. G., and K. Tatchell. 1984. Transcription and regulatory signals at the mating type locus in yeast. Cell 37:969–978.
- van Leeuwen, F., and D. E. Gottschling. 2002. Assays for gene silencing in yeast. Methods Enzymol. 350:165–186.
- Venditti, P., G. Costanzo, R. Negri, and G. Camilloni. 1994. ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim. Biophys. Acta 1219:677–689.
- Walker, S. S., S. C. Francesconi, and S. Eisenberg. 1990. A DNA replication enhancer in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 87:4665–4669.
- Weiss, K., and R. T. Simpson. 1998. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLα. Mol. Cell. Biol. 18:5392–5403.
- Wyrick, J. J., F. C. Holstege, E. G. Jennings, H. C. Causton, D. Shore, M. Grunstein, E. S. Lander, and R. A. Young. 1999. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402:418–421.
- Yarragudi, A., T. Miyake, R. Li, and R. H. Morse. 2004. Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 24:9152–9164.
- Yu, L., and R. H. Morse. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:5279–5288.
- Zou, Y., Q. Yu, Y.-H. Chiu, and X. Bi. 18 June 2006. Position effect on the directionality of silencer function in Saccharomyces cerevisiae. Genetics [Epub ahead of print.]