High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLα

Molecular and Cellular Biology

Volumn 18, Issue 9, 1998, Pages 5392-5403

  Weiss, Kerstin ^a   Simpson, Robert T ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN STRUCTURE; GENE EXPRESSION; GENE LOCUS; GENE MAPPING; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; MATING; NUCLEOSOME; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

BASE SEQUENCE; CHROMATIN; CHROMOSOME MAPPING; GENES, FUNGAL; GENES, MATING TYPE, FUNGAL; NUCLEOSOMES; PEPTIDES; PHEROMONES; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; TATA BOX;

FUNGI; MYXOGASTRIA; SACCHAROMYCES CEREVISIAE;

EID: 0031813153     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (95)

1. Abraham, J. A., K. A. Nasmyth, J. N. Strathern, A. J. S. Klar, and J. B. Hicks. 1984. Regulation of mating-type information in yeast. J. Mol. Biol. 176:307-331.
2. Ansari, A., and M. R. Gartenberg. 1997. The yeast silent information regulator Sir4p anchors and partitions plasmids. Mol. Cell. Biol. 17:7061-7068.
3. Aparicio, O. M., and D. E. Gottschling. 1994. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 8:1133-1146.
4. Bell, S. P., and B. Stillman. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357:128-134.
5. Bi, X., and J. R. Broach. 1997. DNA in transcriptionally silent chromatin assumes a distinct topology that is sensitive to cell cycle progression. Mol. Cell. Biol. 17:7077-7087.
6. 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.
7. 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.
8. Braunstein, M., A. B. Rose, S. G. Holmes, C. D. Allis, and J. R. Broach. 1993. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7:592-604.
9. 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.
10. Chant, J., K. Corrado, J. R. Pringle, and I. Herskowitz. 1991. Yeast BUD5, encoding a putative GDP-GTP exchange factor, is necessary for bud site selection and interacts with bud formation gene BEM1. Cell 65:1213-1224.
11. ChenCleland, T. A., M. M. Smith, S. Y. Le, R. Sternglanz, and V. G. Allfrey. 1993. Nucleosome structural changes during derepression of silent mating-type loci in yeast. J. Biol. Chem. 268:1118-1124.
12. Chien, C. T., S. Buck, R. Sternglanz, and D. Shore. 1993. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell 75:531-541.
13. Cockell, M., F. Palladino, T. Laroche, G. Kyrion, C. Liu, A. J. Lustig, and S. M. 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.
14. Cooper, J. P., S. Y. Roth, and R. T. Simpson. 1994. The global transcriptional regulators, SSN6 and TUP1, play distinct roles in the establishment of a repressive chromatin structure. Genes Dev. 8:1400-1410.
15. Diffley, J., and B. Stillman. 1989. Transcriptional silencing and lamins. Nature 342:24.
16. Diffley, J. F. X., and B. Stillman. 1988. Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc. Natl. Acad. Sci. USA 85:21220-21124.
17. Edmondson, D. G., M. M. Smith, and S. Y. Roth. 1996. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 10:1247-1259.
18. Fox, C. A., A. E. Ehrenhofer-Murray, S. Loo, and J. Rine. 1997. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science 276:1547-1551.
19. Gavin, I. M., and R. T. Simpson. 1997. Interplay of yeast global transcriptional regulators Ssn6p-Tup1 and Swi-Snf and their effect on chromatin structure. EMBO J. 16:6263-6271.
20. Gilson, E., M. Roberge. R. Giraldo, D. Rhodes, and S. M. Gasser. 1993. Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J. Mol. Biol. 231:293-310.
21. Gottschling. D. E. 1992. Telomere-proximal DNA in Saccharomyces cerevi- siae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. USA 89:4062-4065.
22. Gottschling, D. E., O. M. Aparico, B. L. Billington, and V. A. Zakian. 1990. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751-762.
23. Graham, I. R., and A. Chambers. 1994. A Reb1p-binding site is required for efficient activation of the yeast RAP1 gene, but multiple binding sites for Rap1p are not essential. Mol Microbiol. 12:931-940.
24. Grunstein, M., A. Hecht, G. Fisher-Adams, J. Wan, R. K. Mann, S. Strahl-Bolsinger, T. Laroche, and S. Gasser. 1995. The regulation of euchromatin and heterochromatin by histones in yeast. J. Cell Sci. 19:29-36.
25. Haber, J. E., and J. P. George, 1979. A mutation that permits the expression of normally silent copies of mating type information in Saccharomyces cerevisiae. Genetics 93:13-35.
26. Hecht, A., T. Laroche, S. StrahlBolsinger, 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.
27. Hecht, A., S. StrahlBolsinger, and M. Grunstein. 1996. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383:92-96.
28. Henikoff, S. 1990. Position-effect variegation after 60 years. Trends Genet. 120:422-426.
29. Hicks, J., J. N. Strathern, and A. J. S. Klar. 1979. Transposable mating type genes in Saccharomyces cerevisiae. Nature 282:473-478.
30. Hofmann, J. F. X., T. Laroche, A. H. Brand, and S. M. Gasser. 1989, RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Cell 57:725-737.
31. Ivy, J. M., A. J. S. Klar, and J. B. Hicks. 1986, Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:688-702.
32. Jacquet, M., J. M. Buhler, F. Iborra, M. C. Francingues-Gaillard, and C. Soustelle. 1991. The MAT locus revisited within a 9.8 kb fragment of chromosome III containing BUD5 and two new open reading frames. Yeast 7:881-888.
33. Jamieson, R. V., P. P. Tam, and M. Gardiner-Garden. 1996. X-chromosome activity: impact of imprinting and chromatin structure. Int. J. Dev. Biol. 40:1065-1080.
34. Johnson, L. M., P. S. Kayne, E. S. Kahn, and M. Grunstein. 1990. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of silent mating type loci in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 87:6286-6290.
35. Kayne, P. S., U. Kim, M. Han, J. R. Mullen, F. Yoshizaki, and M. Grunstein. 1988. Extremely conserved histone H4 N-terminus is dispensable for growth but essential for repressing the silent mating type loci in yeast. Cell 55:27-39.
36. Keleher, C. A., M. J. Redd, J. Schultz, M. Carlson, and A. D. Johnson. 1992. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell 68:709-719.
37. Kim, J. L., D. B- Nikolov, and S. K. Burley. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520-527.
38. Kim, Y., J. H. Geiger, S. Hahn, and P. B. Sigler. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512-520.
39. Klar, A. J. S., S. Fogel, and D. N. Radin. 1979. Switching of mating-type a mutant allele in budding yeast Saccharomyces cerevisiae. Genetics 92:756-776.
40. Klar, A. J. S., J. N. Strathern, and J. A. Abraham. 1984. Involvement of double-strand chromosomal breaks for mating-type switching in Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 49:77-88.
41. Komachi, K., M. J. Redd, and A. D. Johnson. 1994. The WD repeats of Tup1 interact with the homeo domain protein alpha 2. Genes Dev. 8:2857-2867.
42. Koonin, E. V., P. Bork, and C. Sander. 1994. Yeast chromosome III: new gene functions, EMBO J. 13:493-503.
43. Kostriken, R., J. N. Strathern, A. J. S. Klar, J. B. Hicks, and F. Heffron. 1983. A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae. Cell 35:167-174.
44. Kyrion, G., K. Liu, C. Liu, and A. J. Lustig. 1993. RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev. 7:1146-1159.
45. Laurenson, P., and J. Rine. 1992. Silencers, silencing, and heritable transcriptional states. Microbiol, Rev. 56:543-560.
46. Loo, S., and J. Rine. 1994. Silencers and domains of generalized repression. Science 264:1768-1771.
47. 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.
48. Mahoney, D. J., R. Marquardt, G. Shei, A. B. Rose, and J. R. Broach. 1991. Mutations in the HML-E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression. Genes Dev. 5:605-615.
49. 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.
50. Megee, P. C., B. A. Morgan, B. A. Mittman, and M. M. Smith. 1990, Genetic analysis of histone H4: essential role of lysines subject to reversible acetylation. Science 247:841-845.
51. Moazed, D., and A. D. Johnson. 1996, A deubiquinating enzyme interacts with SIR4 and regulates silencing in cerevisiae. Cell 86:667-677.
52. 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.
53. Mueller, T., E. Gilson, R. Schmidt, R. Giraldo, J. Sogo, H. Gross, and S. M. Gasser. 1994. Imaging the asymmetrical DNA bend induced by repressor activator protein 1 with scanning tunneling microscopy. J. Struct. Biol 113: 1-12.
54. Mullen, J. R., P. S. Kayne, R. P. Moerschell, S. Tsunasawa, M. Gribskov, M. Colavito-Shepanski, M. Grunstein, F. Sherman, and R. Sternglanz, 1989. Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast. EMBO J. 8:2067-2075.
55. Nasmyth, K. A. 1982. The regulation of yeast mating-type chromatin structure by SIR: an action at a distance affecting both transcription and transposition. Cell 30:567-578.
56. Oliver, S. G., et al. 1992. The complete DNA sequence of yeast chromosome III. Nature 357:38-46.
57. 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.
58. Park, E. C., and J. W. Szostak. 1990. Point mutations in the yeast histone H4 gene prevent silencing of the silent mating type locus HML. Mol. Cell. Biol. 10:4932-4934.
59. Patterton, H. G., and R. T. Simpson. 1994. Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression. Mol. Cell. Biol. 14:4002-4010.
60. 59a.Ravindra, A., K. Weiss, and R. T. Simpson. Unpublished observations.
61. Reifsnyder, C., J. Lowell, A. Clarke, and L. Pillus. 1996. Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat. Genet. 14:42-49.
62. Reimer, S. K., and A. R. Buchman. 1997. Yeast silencers create domains of nuclease-resistant chromatin in an SIR4-dependent manner. Chromosoma 106:136-148.
63. Renauld, H., O. M. Aparicio, P. D. Zierath, B. L. Billington, S. K. Chablani, and D. E. 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.
64. Rine, J., and I. Herskowitz. 1987. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9-22.
65. Rine, J., J. N. Strathern, J. B. Hicks, and I. Herskowitz. 1979. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Genetics 93:877-901.
66. Rose, M. D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
67. Roth, S. Y., A. Dean, and R. T. Simpson. 1990. Yeast α2 repressor positions nucleosomes in TRP1/ARS1 chromatin. Mol. Cell. Biol. 10:2247-2260.
68. Roth, S. Y., M. Shimizu, L. Johnson, M. Grunstein, and R. T. Simpson. 1992. Stable nucleosome positioning and complete repression by the yeast α2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev. 6:411-425.
69. Schnell, R., and J. Rine. 1986. A position effect on the expression of a tRNA gene mediated by the SIR genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 6:494-501.
70. 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.
71. Shimizu, M., S. Y. Roth, C. Szent-Gyorgyi, and R. T. Simpson. 1991. Nu-cleosomes are positioned with base pair precision adjacent to the α2 operator in Saccharomyces cerevisiae. EMBO J. 10:3033-3041.
72. Shore, D., and K. Nasmyth. 1987. Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51:721-732.
73. Siliciano, P. G., and K. Tatchell. 1984. Transcription and regulatory signals at the mating type locus in yeast. Cell 37:969-978.
74. Simpson, R. T. 1990. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 343:387-389.
75. Simpson, R. T., S. Y. Roth, R. H. Morse, H.-G. Patterton, J. P. Cooper, M. R. Murphy, M. P. Kladde, and M. Shimizu. 1993. Nucleosome positioning and transcription. Cold Spring Harbor Symp. Quant. Biol. 58:237-245.
76. Singh, J., and A. J. S. Klar. 1992. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev. 6:186-196.
77. Smith, D. L., A. B. Desai, and A. D. Johnson. 1995. DNA bending by the al and alpha 2 homeodomain proteins from yeast. Nucleic Acids Res. 23:1239-1243.
78. Stone, E. M., M. J. Swanson, A. M. Romeo, J. B. Hicks, and R. Sternglanz. 1991. The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Mol. Cell. Biol. 11:2253-2262.
79. StrahlBolsinger, S., A. Hecht, K. H. Luo, and M. Grunstein. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83-93.
80. Strathern, J. N., J. Hicks, and I. Herskowitz. 1981. Control of cell type in yeast by the mating type locus. The alpha 1-alpha 2 hypothesis. J. Mol. Biol. 147:357-372.
81. Strathern, J. N., A. J. S. Klar, J. B. Hicks, J. A. Abraham, J. M. Ivy, K. Nasmyth, and C. Gill. 1982. Homothallic switching of yeast mating-type is initiated by a double-stranded cut in the MAT locus. Cell 31:183-192.
82. Strathern, J. N., C. S. Newlon, I. Herskowitz, and J. B. Hicks. 1979. Isolation of a circular derivative of yeast chromosome III: implication for the mechanism of mating type interconversion. Cell 18:309-319.
83. Surani, M. A. 1994. Genomic imprinting: control of gene expression by epigenetic inheritance. Curr. Opin. Cell Biol. 6:390-395.
84. Svaren, J., and W. Hörz. 1997. Transcription factors vs nucleosomes: regulation of the PH05 promoter in yeast. Trends Biochem. Sci. 22:93-97.
85. Sypes, M. A., and D. S. Gilmour. 1994. Protein/DNA crosslinking of TFIID complex reveals novel interactions downstream of the transcription start. Nucleic Acids Res. 22:807-814.
86. Szent-Gyorgyi, C., and I. Isenberg. 1983. The organization of oligonucleosomes in yeast. Nucleic Acids Res. 11:3717-3736.
87. Tatchell, K., K. A. Nasmyth, B. D. Hall, C. Astell, and M. Smith. 1981. In vitro mutation analysis of the mating-type locus in yeast. Cell 27:25-35.
88. Thompson, J. S., A. Hecht, and M. Grunstein. 1993. Histones and the regulation of heterochromatin in yeast. Cold Spring Harbor Symp. Quant. Biol. 58:247-256.
89. 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.
90. Triolo, T., and R. Sternglanz. 1996. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381:251-253.
91. Tsukagoshi, Y. T., and R. T. Simpson. Unpublished data.
92. Turner, B. M. 1995. Histone H4, the cell cycle and a question of integrity. Bioessays 17:1013-1015.
93. Verdone, L., G. Camilloni, E. Di Mauro, and M. Caserta. 1996. Chromatin remodelling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16:1978-1988.
94. Weiss, K., and R. T. Simpson. 1997. Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching. EMBO J. 16:4352-4360.
95. Whiteway, M., R. Freedman, S. Van Arsdell, J. W. Szostak, and J. Thorner. 1987. The yeast ARD1 gene product is required for repression of cryptic mating-type information at the HML locus. Mol. Cell. Biol. 7:3713-3722.