Global Chromatin Structure of 45,000 Base Pairs of Chromosome III in a- and α-Cell Yeast and during Mating-Type Switching

REFERENCES

• Anguita, E., Johnson C. A., Wood W. G., Turner B. M., and Higgs D. R.. 2001. Identification of a conserved erythroid specific domain of histone acetylation across the alpha-globin gene cluster. Proc. Natl. Acad. Sci. USA 98:12114–12119.
   PubMedGoogle Scholar
• Connolly, B., White C. I., and Haber J. E.. 1988. Physical monitoring of mating type switching in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:2342–2349.
   PubMedGoogle Scholar
• Dubey, D. D., Davis L. R., Greenfeder S. A., Ong L. Y., Zhu J., Broach J. R., Newlon C. S., and Huberman J. A.. 1991. Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins. Mol. Cell. Biol. 11:5346–5355.
   PubMedGoogle Scholar
• Haber, J. E. 1998. Mating-type gene switching in Saccharomyces cerevisiae. Annu. Rev. Genet. 32:561–599.
   PubMed Web of Science ®Google Scholar
• Hebbes, T. R., Clayton A. L., Thorne A. W., and Crane-Robinson C.. 1994. Core histone hyperacetylation comaps with generalized DNase I sensitivity in chicken beta globin chromosomal domain. EMBO J. 13:1823–1830.
   PubMed Web of Science ®Google Scholar
• Hochstrasser, M., Ellison M. J., Chau V., and Varshavsky A.. 1991. The short-lived MAT alpha2 transcriptional regulator is ubiquitinated in vivo. Proc. Natl. Acad. Sci. USA 88:4606–4610.
   PubMed Web of Science ®Google Scholar
• Holstege, F. C. P., Jennings E. G., Wyrick J. J., Lee T. I., Hengartner C. J., Green M. R., Golub T. R., Lander E. S., and Young R. A.. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717–728.
   PubMed Web of Science ®Google Scholar
• Huang, R. Y., and Kowalski D.. 1996. Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome. Nucleic Acids Res. 24:816–823.
   PubMedGoogle Scholar
• Kornberg, R. D., and Stryer L.. 1988. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16:6677–6690.
   PubMed Web of Science ®Google Scholar
• Litt, M. D., Simpson M., Recillas-Targa F., Prioleau M. N., and Felsenfeld G.. 2001. Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J. 20:2224–2235.
   PubMedGoogle Scholar
• Lutter, L. C. 1989. Digestion of nucleosomes with deoxyribonucleases I and II. Methods Enzymol. 170:264–269.
   PubMedGoogle Scholar
• Moreira, J. M., and Holmberg S.. 1998. Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators. EMBO J. 17:6028–6038.
   PubMedGoogle Scholar
• Murphy, M. R., Shimizu M., Roth S. Y., Dranginis A. M., and Simpson R. T.. 1993. DNA-protein interactions at the S. cerevisiae alpha2 operator in vivo. Nucleic Acids Res. 21:3295–3300.
   PubMedGoogle Scholar
• Oliver, S. G., van der Aart Q. J. M., Agostini-Carbone M. L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J. P. G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P. A., Bolotin-Fukuhara M., Brown A., Brown A. J. P., Buhler J. P., Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M., Demolder J., Doira C., Dubois E., Dujon B., Dusterhoft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M. C., Franco L., Frontali L., Fukuhara H., Fuller L. J., Galland P., Gent M. E., Gigot D., Gilliquet V., Goffeau A., Grenson M., Grisanti P., Grivell L. A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J., Herbert C. J., Hilger F., Hohmann S., Hollenberg C. P., Huse K., Iborra F., Indge K. J., Isono K., Jacq C., Jacquet M., James C. M., Jauniaux J. C., Jia Y., Jimenez A., Kelly A., Kleinhauns U., Kreisi P., Lanfranchi G., Lewis C., van der Linden C. G., Lucchini G., Lutzenkirchen K., Maat M. J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C. T. C., McConnell D., McKee R. A., Messenguy F., Mewes H. W., Molemans F., Montague M. A., Muzi Falconi M., Nevas L., Newlon C. S., Noone D., Pallier C., Panzeri L., Pearson B. M., Perea J., Phillippsen P., et al. 1992. The complete DNA sequence of yeast chromosome III. Nature 357:38–46.
   PubMed Web of Science ®Google Scholar
• Ravindra, A., Weiss K., and Simpson R. T.. 1999. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating-type locus HMRa. Mol. Cell. Biol. 19:7944–7950.
   PubMedGoogle Scholar
• Roth, S. Y., and Simpson R. T.. 1991. Yeast minichromosomes. Methods Cell Biol. 35:289–314.
   PubMedGoogle Scholar
• Sauer, R. T., Smith D. L., and Johnson A. D.. 1988. Flexibility of the yeast alpha2 repressor enables it to occupy the ends of its operator, leaving the center free. Genes Dev. 2:807–816.
   PubMedGoogle Scholar
• Shrader, T. E., and Crothers D. M.. 1989. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86:7418–7422.
   PubMed Web of Science ®Google Scholar
• Simpson, R. T., and Stafford D. W.. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA 80:51–55.
   PubMed Web of Science ®Google Scholar
• Spellman, P. T., Sherlock G., Zhang M. Q., Iyer V. R., Anders K., Eisen M. B., Brown P. O., Botstein D., and Futcher B.. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9:3273–3297.
   PubMed Web of Science ®Google Scholar
• Staynov, D. Z., and Proykova Y. G.. 1998. Quantitative analysis of DNase I digestion patterns of oligo- and polynucleosomes. J. Mol. Biol. 279:59–71.
   PubMedGoogle Scholar
• Strathern, J. N., and Herskowitz I.. 1979. Asymmetry and directionality in production of new cell types during clonal growth: the switching pattern of homothallic yeast. Cell 17:371–381.
   PubMed Web of Science ®Google Scholar
• Sun, K., Coic E., Zhou Z., Durrens P., and Haber J. E.. 2002. Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer. Genes Dev. 16:2085–2096.
   PubMedGoogle Scholar
• Szeto, L., Fafalios M. K., Zhong H., Vershon A. K., and Broach J. R.. 1997. Alpha2p controls donor preference during mating type interconversion in yeast by inactivating a recombinational enhancer of chromosome III. Genes Dev. 11:1899–1911.
   PubMedGoogle Scholar
• Thoma, F. 1986. Protein-DNA interactions and nuclease sensitive regions determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 190:177–190.
   PubMedGoogle Scholar
• Vujcic, M., Miller C. A., and Kowalski D.. 1999. Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast. Mol. Cell. Biol. 19:6098–6109.
   PubMedGoogle Scholar
• Wang, X., and Simpson R. T.. 2001. Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I. Nucleic Acids Res. 29:1943–1950.
   PubMed Web of Science ®Google Scholar
• Weintraub, H., and Groudine M.. 1976. Chromosomal subunits in active genes have an altered conformation. Science 193:848–856.
   PubMed Web of Science ®Google Scholar
• Weiss, K., and Simpson R. T.. 1997. Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching. EMBO J. 16:4352–4360.
   PubMedGoogle Scholar
• Weiss, K., and Simpson R. T.. 1998. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLα. Mol. Cell. Biol. 18:5392–5403.
   PubMedGoogle Scholar
• White, C. I., and Haber J. E.. 1990. Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. EMBO J. 9:663–673.
   PubMed Web of Science ®Google Scholar
• Winston, F., Dollard C., and Ricupero-Hovasse S. L.. 1995. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11:53–55.
   PubMed Web of Science ®Google Scholar
• Wu, C., and Gilbert W.. 1981. Tissue specific exposure of chromatin structure at the 5′ terminus of the rat preproinsulin gene. Proc. Natl. Acad. Sci. USA 78:1577–1580.
   PubMed Web of Science ®Google Scholar
• Wu, C., Weiss K., Yang C., Harris M. A., Tye B. K., Newlon C. S., Simpson R. T., and Haber J. E.. 1998. Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching. Genes Dev. 12:1726–1737.
   PubMedGoogle Scholar
• Wu, X., and Haber J. E.. 1996. A 700 bp cis-acting region controls mating-type dependent recombination along the entire left arm of yeast chromosome III. Cell 87:277–285.
   PubMedGoogle Scholar
• Wu, X., and Haber J. E.. 1995. MATa donor preference in yeast mating-type switching: activation of a large chromosomal region for recombination. Genes Dev. 9:1922–1932.
   PubMedGoogle Scholar
• Wu, X., Moore J. K., and Haber J. E.. 1996. Mechanism of MATα donor preference during mating-type switching of Saccharomyces cerevisiae. Mol. Cell. Biol. 16:657–668.
   PubMedGoogle Scholar
• Wyrick, J. J., Holstege F. C., Jennings E. G., Causton H. C., Shore D., Grunstein M., Lander E. S., and Young R. A.. 1999. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402:418–421.
   PubMed Web of Science ®Google Scholar
• Yu, L., and Morse R. H.. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:5279–5288.
   PubMed Web of Science ®Google Scholar