Cooperation at a distance between silencers and proto-silencers at the yeast HML locus

EMBO Journal

Volumn 15, Issue 9, 1996, Pages 2184-2195

  Boscheron, Cécile ^a   Maillet, Laurent ^a   Marcand, Stéphane ^a,b   Tsai Pflugfelder, Monika ^c   Gasser, Susan M ^c   Gilson, Eric ^a  

^a UNIVERSITÉ DE LYON   (France)

^b Columbia University ^*  (United States)

^c SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

Author keywords

Abf1; DNA loops; ORC; Rap1; Yeast mating type

Indexed keywords

CIS ACTING ELEMENT; DNA BINDING PROTEIN; NUCLEOPROTEIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; FUNGAL GENETICS; GENE REPRESSION; MATING TYPE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; RECOMBINANT GENE; REPORTER GENE; TRANSCRIPTION REGULATION; YEAST;

EID: 0029879358     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1002/j.1460-2075.1996.tb00572.x     Document Type: Article

References (69)

1. Abraham, J., Nasmyth, A., Strathern, J.N., Klar, J.S. and Hicks, J.B. (1984) Regulation of mating type information in yeast. J. Mol. Biol., 176, 307-331.
2. Amouyal, M., Mortensen, L., Buc, H. and Hammer, K. (1989) Single and double loop formation when deoR repressor binds to its natural operator sites. Cell, 58, 545-551.
3. Aparicio, O.M., Billington, B.L. and Gottschling, D.E. (1991) Modifiers of position effect are shared between telomeric and silent mating-type loci in S.cerevisiae. Cell, 66, 1279-1287.
4. Bell, S.P., Kobayashi, R. and Stillman, B. (1993) Yeast origin recognition complex functions in transcription silencing and DNA replication Science, 262, 1844-1848.
5. Brand, A H., Micklem, G. and Nasmyth, K. (1987) A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. Cell, 51, 709-719.
6. Breeden, L. and Nasmyth, K. (1985) Regulation of the yeast HO gene Cold Spring Harbor Symp. Quant. Biol., 50, 643-650.
7. Buchman, A.R., Kimmerly, W.J., Rine, J. and Kornberg, R.D. (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.
8. Buck, S W. and Shore, D. (1995) Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes Dev., 9, 370-384.
9. Casadaban, M.J., Martinez-Arias, A., Shapira, S.K. and Chou, J. (1983) β-Galactosidase gene fusion for analyzing gene expression in Escherichia coli and yeast. Methods Enzymol., 100, 293-308.
10. Chambers, A., Stanway, C., Tsang, J.S.H., Henry, Y., Kingsman, A.J. and Kingsman, S.M. (1990) ARS binding factor 1 binds adjacent to RAP1 at the UASs of the yeast glycolytic genes PGK and PYK1. Nucleic Acids Res., 18, 5393-5399.
11. Chien, C.T., Bartel, R., Sternglanz, R. and Fields, S. (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl Acad. Sci. USA, 88, 9578-9582
12. Chien, C.T., Buck, S., Sternglanz, R. and Shore, D. (1993) Targeting of Sir1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell, 75, 531-541.
13. Cockell, M., Palladino, F., Laroche, T., Kyrion, G., Liu, C., Lustig, A J and Gasser, S.M. (1995) The C-termini of Sir4 and Rap1 affect Sir3 localization in yeast cells: evidence for a multicomponent complex required for telomeric silencing. J. Cell Biol., 129, 909-924.
14. Feldman, J., Hicks, J. and Broach, J. (1984) Identification of the sites required for repression of a silent mating type locus in yeast. J. Mol Biol., 178, 815-834.
15. Foss, M., McNally, F.J., Laurenson, P. and Rine, J. (1993) Origin replication complex (ORC) in transcriptional silencing and DNA replication in S.cerevisiae. Science, 262, 1838-1844.
16. Fox, C A., Loo, S., Rivier, D.H , Foss, M.A. and Rine, J. (1994) A transcriptional silencer as a specialized origin of replication that establishes functional domains of chromatin Cold Spring Harbor Symp Quant. Biol., 57, 443-455
17. Fox, C A., Loo, S., Dillin, A. and Rine, J. (1995) The origin recognition complex has essential functions in transcriptional silencing and chromosome replication. Genes Dev., 9, 911-924.
18. Fromental, C. Kanno, M., Nomiyama, H. and Chambon, P (1988) Cooperativity and hierarchical levels of functional organization in the SV40 enhancer. Cell, 54, 943-953.
19. Giesman, D., Best, L. and Tatchell, K. (1991) The role of RAP1 in the regulation of the MATα locus. Mol. Cell. Biol., 11, 1069-1079.
20. Gilson, E. and Gasser, S.M. (1995) Repressor activator protein 1 and its ligands, organising chromatin domains Nucleic Acids Res.Mol Biol., 9, 308-327.
21. Gilson, E., Laroche, T. and Gasser, S.M. (1993a) Telomeres and the functional architecture of the nucleus. Trends Cell Biol., 3, 128-134
22. Gilson, E., Roberge, M., Giraldo, R., Rhodes, D. and Gasser, S.M. (1993b) Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J. Mol. Biol., 231, 293-310.
23. Grosveld, F., Antoniou, M., Berry, M., deBoer, E., Dillon, N., Ellis, J., Fraser, P. Hurst, J., Imam, A., Meijer, D., Philipsen, S., Pruzina, S., Strouboulis, J. and Whyatt, D. (1994) Regulation of human gene switching. Cold Spring Harbor Symp. Quant Biol., 57, 7-13.
24. Guarente, L. and Mason, T. (1983) Heme regulates transcription of the CYC1 gene of S.cerevisiae via an upstream activation site. Cell, 32, 1279-1286.
25. Hardy, C.F.J., Sussel, L. and Shore, D (1992) A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. Genes Dev., 6, 801-814.
26. Hecht, A., Laroche, T , Strahl-Bolsinger, S., Gasser, S.M. and Grunstein, M. (1995) Histone H3 and H4 N termini interact with the silent information regulators Sir3 and Sir4 in vitro a molecular model for the formation of heterochromatin in yeast. Cell, 80, 583-592.
27. Hill, J., Donald, K.A.G. and Griffiths, D.E. (1991) DMSO-enhanced whole cell yeast transformation Nucleic Acids Res., 19, 5791.
28. Hofmann, J.F.X., Laroche, T., Brand, A H. and Gasser, S.M. (1989) RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Cell, 57, 725-737.
29. Ivy, J.M., Klar, A.J S. and Hicks, J.B. (1986) Cloning and characterization of four SIR genes of S.cerevisiae. Mol. Cell. Biol., 6, 688-702.
30. Karpen, G.H. (1994) Position-effect variegation and the new biology of heterochromatin. Curr. Opin. Genet. Dev., 4, 281-291.
31. Kayne, P.S , Kim, U.J., Han, M., Mullen, J.R., Yoshizaki, F. and Grunstein, M (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.
32. Kimmerly, W., Buchman, A., Kornberg, R. and Rine, J. (1988) Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeast silencer. EMBO J., 7, 2241-2253.
33. Kurtz, S. and Shore, D. (1991) RAP1 protein activates and silences transcription of mating type genes in yeast Genes Dev., 5, 5264-5268.
34. Kyrion, G., Liu, K. and Lustig, A.J. (1993) RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev., 7, 1146-1159.
35. Laemmli, U.K., Käs, E., Poljak, L. and Adachi, Y. (1992) Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains Curr. Opin. Genet. Dev., 2, 275-285.
36. Laurenson, P. and Rine, J. (1992) Silencers, silencing and heritable transcriptional states. Microbiol. Rev., 56, 543-560.
37. Liu, C , Mao, X. and Lustig, A.J. (1994) Mutational analysis defines a C-terminal tail domain of RAP1 essential for telomeric silencing in S.cerevisiae. Genetics, 138, 1025-1040.
38. Locke, J., Kotarsky, M.A. and Tartof, K D. (1988) Dosage-dependent modifiers of position effect variegation in Drosophila and a mass-action model that explains their effects. Genetics, 120, 181-198.
39. Loo, S. and Rine, J. (1994) Silencers and domains of generalized repression. Science, 264, 1768-1771.
40. Mahoney, D.J. and Broach, J. (1989) The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers. Mol. Cell. Biol., 9, 4621-4630.
41. Mahoney, D.J., Marquard, R , Shei, G J , Rose, A.B. and Broach, J (1991) Mutations in the HML E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression. Genes Dev., 5, 605-615.
42. McBroom, L.D B. and Sadowski, P.D. (1994) Contacts of the ABF1 protein of S.cerevisiae with a DNA binding site at MATa J. Biol. Chem., 269, 16455-16460.
43. McNally, F.J. and Rine, J. (1991) A synthetic silencer mediates SIR-dependent functions in Saccaromyces cerevisae. Mol. Cell. Biol., 11, 5648-5659.
44. Moretti, R. Freeman, K., Coodly, L. and Shore, D. (1994) Evidence that a complex of SIR proteins interacts with the silencer and telomere binding protein Rap1. Genes Dev., 8, 2257-2269.
45. Müller, H.R. Sogo, J.M. and Schaffner, W. (1989) An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Cell, 58, 767-777.
46. Orlando, V. and Paro, R. (1995) Chromatin multiprotein complexes involved in the maintenance of transcription patterns. Curr. Opin. Genet. Dev. 5, 174-179.
47. Palladino, F. and Gasser, S.M. (1994) Telomere maintenance and gene repression: a common end? Curr. Opin. Cell Biol., 6, 373-380.
48. Palladino, F., Laroche, T., Gilson, E , Axelrod, A., Pillus, L. and Gasser, S M. (1993) SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell, 75, 543-555.
49. Pillus, L. and Rine, J (1989) Epigenetic inheritance of transcriptional states in S cerevisiae. Cell, 30, 567-578.
50. Pirrotta, V. (1995) Chromatin complexes regulating gene expression in Drosophila. Curr. Opin. Genet. Dev., 5, 466-472.
51. Renauld, H , Aparicio, O.M., Zierath, P.D., Billington, B.L., Chhablani, S.K. and Gottschling, D.E. (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.
52. Rose, M.D., Winston, F and Hieter, P. (1990) Methods in Yeast Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. Rudolph, H., Koening-Rauseo, I. and Hinnen, A. (1985) One-step replacement in yeast by cotransformation. Gene, 36, 87-95.
54. Sambrook, J., Fritsch, E F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
55. Shei, G.-J. and Broach, J.R (1995) Yeast silencers can act as orientation-dependent gene inactivation centers that respond to environmental signals. Mol. Cell Biol., 15, 3496-3506.
56. Shimizu, M., Roth, S.Y., Szent-Gyorgy, C. and Simpson, R.T. (1991) Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J., 10, 3033-3041.
57. Shore, D. (1994) RAP1: a protein regulator in yeast. Trends Genet., 10, 408-412.
58. Singer, M.S. and Gottschling, D.E. (1994) TLC1: template RNA component of Saccharomyces cerevisiae telomerase. Science, 266, 404-409.
59. Sikorski, R.S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in S.cerevisiae. Genetics, 122, 19-27.
60. Stavenhagen, J.B. and Zakian, V.A. (1994) Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae Genes Dev., 8, 1411-1422.
61. Stone, E.M., Swanson, M.J., Romeo, A.M., Hicks, J.B. and Sternglanz, R. (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.
62. Tartof, K.D. and Henikoff, S. (1991) Trans-sensing effects from Drosophila to humans. Cell, 65, 201-203.
63. Thierry, A., Fairhead, C. and Dujon, B. (1990) The complete sequence of the 2.8 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase. Yeast, 6, 521-534.
64. Thompson, J S , Johnson, L.M. and Grunstein, M. (1994a) Specific repression of the yeast silent mating type locus HMR by an adjacent telomere. Mol. Cell. Biol., 14, 446-455.
65. Thompson, J.S., Hecht, A. and Grunstein, M. (1994b) The histone H3 amino terminus is required for both telomeric and silent mating locus repression in yeast. Nature, 369, 235-247.
66. Tu, H. and Casadaban, M J. (1990) The upstream activating sequence for L-leucine gene regulation in S.cerevisiae. Nucleic Acids Res., 18, 3923-3931.
67. Vazquez, J., Farkas, G., Gaszner, M., Udvardy, A., Muller, M., Hagstrom, K., Gyurkovics, H., Sipos, L., Gausz, J., Galloni, M., Hogga, I., Karch, F. and Schedl, P. (1994) Genetic and molecular analysis of chromatin domains Cold Spring Harbor Symp. Quant. Biol., 57, 45-54
68. Vignais, M.L., Huet, J. and Sentenac, A. (1990) Contacts between the factor TUF and RPG sequences. J. Biol. Chem., 265, 14669-14674
69. Wright, J.H., Gottschling, D.E. and Zakian, V.A. (1992) Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes Dev., 6, 197-210.