Barrier Proteins Remodel and Modify Chromatin to Restrict Silenced Domains

Molecular and Cellular Biology

Volumn 24, Issue 5, 2004, Pages 1956-1967

  Oki, Masaya ^a   Valenzuela, Lourdes ^a   Chiba, Tomoko ^b   Ito, Takashi ^b   Kamakaka, Rohinton T ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b KANAZAWA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BARRIER PROTEIN; DNA BINDING PROTEIN; DOT1P PROTEIN; HISTONE; MEDIATOR PROTEIN; NUA3 PROTEIN; NUA4 PROTEIN; PROTEIN SUBUNIT; PROTEIN SWI; RAD6P PROTEIN; SAS I PROTEIN; SPT10P PROTEIN; TRANSCRIPTION FACTOR IID; TRANSCRIPTION FACTOR SAGA; UNCLASSIFIED DRUG;

ACETYLATION; ARTICLE; CELL NUCLEUS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN MODIFICATION; CHROMATIN STRUCTURE; DNA MODIFICATION; EUKARYOTE; GENE SILENCING; GENETIC TRANSCRIPTION; GENOME; HISTONE ACETYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; SACCHAROMYCES CEREVISIAE;

ACETYLATION; ASPARTIC ENDOPEPTIDASES; CHROMATIN; GENE EXPRESSION REGULATION, FUNGAL; GENE LIBRARY; GENE SILENCING; HISTONES; MULTIENZYME COMPLEXES; NUCLEAR PORE COMPLEX PROTEINS; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 1342346506     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.5.1956-1967.2004     Document Type: Article

References (73)

1. 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.
2. 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.
3. Bi, X. 2002. Domains of gene silencing near the left end of chromosome III in Saccharomyces cerevisiae. Genetics 160:1401-1407.
4. 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.
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. Bi, X., and J. R. Broach. 1999. UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev. 13:1089-1101.
7. Blanton, J., M. Gaszner, and P. Schedl. 2003. Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev. 17:664-675.
8. Cheng, T. H., and M. R. Gartenberg. 2000. Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev. 14:452-463.
9. 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.
10. Cuperus, G., and D. Shore. 2002. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162:633-645.
11. Dhillon, N., and R. T. Kamakaka. 2000. A histone variant, Htzlp, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol. Cell 6:769-780.
12. Dillin, A., and J. Rine. 1997. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics 147:1053-1062.
13. Donze, D., C. R. Adams, J. Rine, and R. T. Kamakaka. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13:698-708.
14. Donze, D., and R. T. Kamakaka. 2002. Braking the silence: how heterochromatic gene repression is stopped in its tracks. Bioessays 24:344-349.
15. Donze, D., and R. T. Kamakaka. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20:520-531.
16. Ehrenhofer-Murray, A. E., R. T. Kamakaka, and J. Rine. 1999. A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics 153:1171-1182.
17. 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.
18. Feng, Q., H. Wang, H. H. Ng, H. Erdjument-Bromage, P. Tempst, K. Struhl, and Y. Zhang. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12:1052-1058.
19. 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.
20. Fourel, G., T. Miyake, P. A. Defossez, R. Li, and E. Gilson. 2002. General regulatory factors (GRFs) as genome partitioners. J. Biol. Chem. 277:41736-41743.
21. 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.
22. Ghidelli, S., D. Donze, N. Dhillon, and R. T. Kamakaka. 2001. Sir2p exists in two nucleosome-binding complexes with distinct deacetylase activities. EMBO J. 20:4522-4535.
23. Grant, P. A., D. Schieltz, M. G. Pray-Grant, D. J. Steger, J. C. Reese, J. R. Yates III, and J. L. Workman. 1998. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94:45-53.
24. Imai, S., C. M. Armstrong, M. Kaeberlein, and L. Guarente. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795-800.
25. Ishii, K., G. Arib, C. Lin, G. Van Houwe, and U. K. Laemmli. 2002. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 109:551-562.
26. Ito, T., K. Tashiro, S. Muta, R. Ozawa, T. Chiba, M. Nishizawa, K. Yamamoto, S. Kuhara, and Y. Sakaki. 2000. Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA 97:1143-1147.
27. Ivy, J. M., A. J. Klar, and J. B. Hicks. 1986. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:688-702.
28. Kamakaka, R. T., and J. Rine. 1998. Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p. Genetics 149:903-914.
29. Kasper, L. H., P. K. Brindle, C. A. Schnabel, C. E. Pritchard, M. L. Cleary, and J. M. van Deursen. 1999. CREB binding protein interacts with nucleoporin-specific FG repeats that activate transcription and mediate NUP98-HOXA9 oncogenicity. Mol. Cell. Biol. 19:764-776.
30. Kayne, P. S., U. J. 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 loci in yeast. Cell 55:27-39.
31. Kimura, A., T. Umehara, and M. Horikoshi. 2002. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat. Genet. 32:370-377.
32. Kristjuhan, A., B. O. Wittschieben, J. Walker, D. Roberts, B. R. Cairns, and J. Q. Svejstrup. 2003. Spreading of Sir3 protein in cells with severe histone H3 hypoacetylation. Proc. Natl. Acad. Sci. USA 100:7551-7556.
33. Ladurner, A. G., C. Inouye, R. Jain, and R. Tjian. 2003. Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol. Cell 11:365-376.
34. Le, S., C. Davis, J. B. Konopka, and R. Sternglanz. 1997. Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast 13:1029-1042.
35. Lee, S., and D. S. Gross. 1993. Conditional silencing: the HMRE mating-type silencer exerts a rapidly reversible position effect on the yeast HSP82 heat shock gene. Mol. Cell. Biol. 13:727-738.
36. Lee, T. I., H. C. Causton, F. C. Holstege, W. C. Shen, N. Hannett, E. G. Jennings, F. Winston, M. R. Green, and R. A. Young. 2000. Redundant roles for the TFIID and SAGA complexes in global transcription. Nature 405:701-704.
37. 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.
38. Litt, M. D., M. Simpson, F. Recillas-Targa, M. N. Prioleau, and G. Felsenfeld. 2001. Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J. 20:2224-2235.
39. Loo, S., P. Laurenson, M. Foss, A. Dillin, and J. Rine. 1995. Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics 141:889-902.
40. Loo, S., and J. Rine. 1994. Silencers and domains of generalized repression. Science 264:1768-1771.
41. Loo, S., and J. Rine. 1995. Silencing and heritable domains of gene expression. Annu. Rev. Cell Dev. Biol. 11:519-548.
42. Lustig, A. J., C. Liu, C. Zhang, and J. P. Hanish. 1996. Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2483-2495.
43. 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.
44. Marshall, M., D. Mahoney, A. Rose, J. B. Hicks, and J. R. Broach. 1987. Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 7:4441-4452.
45. McNally, F. J., and J. Rine. 1991. A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:5648-5659.
46. Meijsing, S. H., and A. E. Ehrenhofer-Murray. 2001. The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 15:3169-3182.
47. Moreira, J. M., and S. Holmberg. 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.
48. 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.
49. Mutskov, V. J., C. M. Farrell, P. A. Wade, A. P. Wolffe, and G. Felsenfeld. 2002. The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev. 16:1540-1554.
50. 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.
51. Ng, H. H., D. N. Ciccone, K. B. Morshead, M. A. Oettinger, and K. Struhl. 2003. Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc. Natl. Acad. Sci. USA 100:1820-1825.
52. Ng, H. H., Q. Feng, H. Wang, H. Erdjument-Bromage, P. Tempst, Y. Zhang, and K. Struhl. 2002. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16:1518-1527.
53. Noma, K., C. D. Allis, and S. I. Grewal. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293:1150-1155.
54. Oki, M., and R. T. Kamakaka. 2002. Blockers and barriers to transcription: competing activities. Curr. Opin. Cell Biol. 14:299-304.
55. Osada, S., A. Sutton, N. Muster, C. E. Brown, J. R. Yates III, R. Sternglanz, and J. L. Workman. 2001. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 15:3155-3168.
56. Park, J. H., M. S. Cosgrove, E. Youngman, C. Wolberger, and J. D. Boeke. 2002. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32:273-279.
57. Pryde, F. E., and E. J. Louis. 1999. Limitations of silencing at native yeast telomeres. EMBO J. 18:2538-2550.
58. 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.
59. 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. (Erratum, 16:109, 1997.)
60. Renauld, H., O. M. Aparicio, P. D. Zierath, B. L. Billington, S. K. Chhablani, 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.
61. 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.
62. Singer, M. S., A. Kahana, A. J. Wolf, L. L. Meisinger, S. E. Peterson, C. Goggin, M. Mahowald, and D. E. Gottschling. 1998. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150:613-632.
63. 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.
64. Suka, N., K. Luo, and M. Grunstein. 2002. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat. Genet. 32:378-383.
65. Sun, F. L., M. H. Cuaycong, and S. C. Elgin. 2001. Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol. Cell. Biol. 21:2867-2879.
66. Sun, Z. W., and M. Hampsey. 1999. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152:921-932.
67. Sutton, A., W. J. Shia, D. Band, P. D. Kaufman, S. Osada, J. L. Workman, and R. Sternglanz. 2003. Sas4 and Sas5 are required for the histone acetyltransferase activity of Sas2 in the SAS complex. J. Biol. Chem. 278:16887-16892.
68. van Leeuwen, F., P. R. Gafken, and D. E. Gottschling. 2002. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109:745-756.
69. 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.
70. Wu, C. 1980. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286:854-860.
71. Xu, E. Y., S. Kim, K. Replogle, J. Rine, and D. H. Rivier. 1999. Identification of SAS4 and SAS5, two genes that regulate silencing in Saccharomyces cerevisiae. Genetics 153:13-23.
72. 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.
73. Zhang, Z., M. K. Hayashi, O. Merkel, B. Stillman, and R. M. Xu. 2002. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J. 21:4600-4611.