An unusual form of transcriptional silencing in yeast ribosomal DNA

Genes and Development

Volumn 11, Issue 2, 1997, Pages 241-254

  Smith, Jeffrey S ^a   Boeke, Jef D ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

S. cerevisiae; silent mating loci; SIR genes; Transcriptional repression; yeast ribosomal DNA

Indexed keywords

RIBOSOME DNA;

ARTICLE; FUNGAL GENETICS; GENE DELETION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

SACCHAROMYCES CEREVISIAE;

EID: 0031056907     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.2.241     Document Type: Article

References (65)

1. Allshire, R.C., J.-P. Javerzat, N.J. Redhead, and G. Cranston. 1994. Position effect variegation at fission yeast centro meres. Cell 76: 157-169.
2. Aparicio, O.M., B.L. Billington, and D.E. Gottschling. 1991. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66: 1279-1287.
3. Baker, R.T., J.W. Tobias, and A. Varshavsky. 1992. Ubiquitinspecific proteases of Saccharomyces cerevisiae. Cloning ot UBP2 and UBP3. and functional analysis of the UBP gene family. J. Biol. Chem. 267: 23364-23375.
4. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21: 3329-3330.
5. Boeke, J.D., F. LaCroute, and G.R. Fink. 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-Fluoro-orotic acid resistance. Mol. & Gen. Genet. 197: 345-346.
6. Boeke, J.D., D.J. Garfinkel, C.A. Styles, and G.R. Fink. 1985. Ty elements transpose through an RNA intermediate. Cell 40: 491-500.
7. Boeke, J.D., H. Xu, and G.R. Fink. 1988. A general method for the chromosomal amplification of genes in yeast. Science 239: 280-282.
8. Brachmann, C.B., J.M. Sherman, S.E. Devine, E.E. Cameron, L. Pillus, and J.D. Boeke. 1995. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes & Dev. 9: 2888-2902.
9. 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.
10. Braunstein, M., R.E. Sobel, C.D. Allis, B.M. Turner, and J.R. Broach. 1996. Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol Cell Biol. 16: 4349-4356.
11. Brill, S.J., S. DiNardo, K. Voelkel-Meiman, and R. Sternglanz. 1987. Need for DNA topoisomerase activity as a swivel for DNA replication of ribosomal RNA. Nature 326: 414-416.
12. Bryk M., M. Banerjee, M. Murphy, K.E. Knudsen, D.J. Garfinkel, and M.J. Curcio. 1997. A specialized chromatin structure in the RDN1 locus of yeast causes transcriptional silencing of Ty1 elements. Genes & Dev. (this issue).
13. Buchman, A.R., N.F. Lue, and R.D. Kornberg. 1988. Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein. Mol. Cell. Biol. 8: 5086-5099.
14. Buck, S.W. and D. Shore. 1995. Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes & Dev. 9: 370-384.
15. Burke, W.D., F. Muller, and T.H. Eickbush. 1995. R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res. 23: 4628-4634.
16. Cavalli, G., D. Bachmann, and F. Thoma. 1996. Inactivation of topoisomerases affects transcription-dependent chromatin transitions in rDNA but not in a gene transcribed by RNA polymerase II. EMBO J. 15: 590-597.
17. Chalker, D.L. and S.B. Sandmeyer. 1990. Transfer RNA genes are genomic targets for de novo transposition of the yeast retrotransposon Ty3. Genetics 126: 837-850.
18. Chapman, K.B. and J.D. Boeke. 1991. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65: 483-492.
19. Christianson, T.W., R.S. Sikorski, M. Dante, J.H. Shero, and P. Hieter. 1992. Multifunctional yeast high-copy-number shuttle vectors. Gene 110: 119-122.
20. Christman, M.F., F.S. Dietrich, and G.R. Fink. 1988. Mitotic recombination in the rDNA of S. cerevisiae is suppressed by the combined action of DNA topoisomerases I and II. Cell 55: 413-425.
21. Cost, G.J. and J.D. Boeke. 1996. A useful colony colour phenotype associated with the yeast selectable/counterselectable marker MET15. Yeast 12: 939-941.
22. Curcio, M.J. and D.J. Garfinkel. 1991. Single-step selection for Ty1 element retrotransposition. Proc. Natl. Acad. Sci. 88: 936-940.
23. Dammann, R., R. Lucchini, T. Koller, and J.M. Sogo. 1993. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21: 2331-2338.
24. _. 1995. Transcription in the yeast rRNA gene locus: Distribution of the active gene copies and chromatin structure of their flanking regulatory sequences. Mol. Cell. Biol. 15: 5294-5303.
25. Derbyshire, M.K., K.G. Weinstock, and J.N. Strathern. 1996. HST1, a new member of the SIR2 family of genes. Yeast 12: 631-640.
26. Devine, S.E. and J.D. Boeke. 1996. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes & Dev. 10: 620-633.
27. Gangloff, S., J.P. McDonald, C. Bendixen, L. Arthur, and R. Rothstein. 1994. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: A potential eukaryotic reverse gyrase. Mol. Cell Biol. 14: 8391-8398.
28. Gotta, M. T. Laroche, A. Formenton, L. Maillet, H. Scherthan, and S.M. Gasser. 1996. The clustering of telomeres and co-localization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134: 1349-1363.
29. Gottlieb, S. and R.E. Esposito. 1989. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56: 771-776.
30. Gottschling, D.E. 1992. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. 89: 4062-4065.
31. Gottschling, D.E., O.M. Aparicio, B.L. Billington, and V.A. Zakian. 1990. Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription. Cell 63: 751-762.
32. Hecht, A., T. Laroche, S. Strahl-Bolsinger, 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.
33. Holmes, S.G., A.B. Rose, E. Saez, S. Sayegh, K. Steuerte, and J.R. Broach. 1997. Hyperactivation of the silencing proteins, Sir2p and Sir3p, causes chromosome loss. Genetics (in press).
34. Jakubczak, J.L., W.D. Burke, and T.D. Eickbush. 1991. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects, Proc. Natl. Acad. Sci. 88: 3295-3299.
35. Ji. H., D.P. Moore, M.A. Blomberg, L.T. Braiterman, D.F. Voytas, G. Natsoulis, and J.D. Boeke. 1993. Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73: 1007-1018.
36. Keil, R.L. and A.D. McWilliams. 1993. A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae. Genetics 135: 711-718.
37. Kim, R.A. and J.C. Wang. 1989. A subthreshold level of DNA topoisomerases leads to the excision of yeast rDNA as extrachromosomal rings. Cell 57: 975-985.
38. Kim, S., J. Mellor, A.J. Kingsman, and S.M. Kingsman. 1986. Multiple control elements in the TRP1 promoter of Saccharomyces cerevisiae. Mol. Cell. Biol. 6: 4251-4258.
39. Kingston, R.E., C.A. Bunker, and A.N. Imbalzano. 1996. Repression and activation by multiprotein complexes that alter chromatin structure. Genes & Dev. 10: 905-920.
40. Kostrikcn, R., J.N. Strathern, A.J.S. Klar, J.B. Hicks, and F. Heffron. 1983. A site-specific endonuclease essential formating-type switching in Saccharomyces cerevisiae. Cell 35: 167-174.
41. Loo, S. and J. Rine. 1994. Silencers and domains of generalized repression. Science 264: 1768-1771.
42. _. 1995. Silencing and heritable domains of gene expression. Annu. Rev. Biol. Dev. 11: 519-548.
43. Lorenz, M.C., R.S. Muir, E. Lim, J. McElver, S.C. Weber, and J. Heitman. 1995. Gene disruption with PCR products in Saccharomyces cerevisiae. Gene 158: 113-117.
44. 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.
45. Moazed, D. and A.D. Johnson. 1996. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86: 667-677.
46. Natsoulis, G., W. Thomas, M.-C. Roghmann, F. Winston, and J.D. Boeke. 1989. Ty1 transposition in Saccharomyces cerevisiae is nonrandom. Genetics 123: 269-279.
47. Nimmo, E.R., G. Cranston, and R.C. Allshire. 1994. Telomere-associated chromosome breakage in fission yeast results in variegated expression of adjacent genes. EMBO J. 13: 3801-3811.
48. Ono, B., N. Ishii, S. Fujino, and I. Aoyama. 1991. Role of hydro-sulfide ions in methylmercury resistance in Saccharomyces cerevisiae. Appl. Env. Microbiol. 57: 3183-3186.
49. 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.
50. Petes, T.D. and D. Botstein. 1977. Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast. Proc. Natl. Acad. Sci 74: 5091-5095.
51. Philippsen, P., M. Thomas, R.A. Kramer, and R.W. Davis. 1978. Unique arrangement of coding sequences for 5S, 5.8S, 18S, and 25S ribosomal RNA in Saccharomyces cerevisiae as determined by R-loop and hybridization analysis. J. Mol. Biol. 123: 387-404.
52. Pillus, L. and J. Rine. 1989. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell 59: 637-647.
53. Renauld, H., O.M. Aparicio, P.D. Zierath, B.L. Billington, S.K. Chhablam, 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.
54. Rose, M.D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics. A laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
55. Rustchenko, E.P. and F. Sherman. 1994. Physical constitution of ribosomal genes in common strains of Saccharomyces cerevisiae. Yeast 10: 1157-1171.
56. Schnell, R. and J. Rine. 1986. A position effect on the expression of a tRNA gene mediated by the SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6: 494-501.
57. Sikorski, R.S. and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed tor efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
58. 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.
59. Skryabin, K.G., M.A. Eldarov, V.L. Larionov, A.A. Bayev, J. Klootwijk, V.C.H. F.d. Regt, G.M. Veldman, R.J. Planta, O.I. Georgiev, and A.A. Hadjiolov. 1984. Structure and function of the nontranscribed spacer regions of yeast rDNA. Nucleic Acids Res. 12: 2955-2968.
60. Strathern, J.N., A.J. Klar, J.B. Hicks, J.A. Abraham, J.M. Ivy, K.A. Nasmyth, and C. McGill. 1982. Homothallic switching of yeast mating-type cassettes is initiated by a double-stranded cut in the MAT locus. Cell 31: 183-192.
61. Szostak, J.W. and R. Wu. 1980. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284: 426-430.
62. Thompson, J.S., A. Hecht, and M. Grunstein. 1994. Histones and the regulation of heterochromatin in yeast. Cold Spring Harbor Symp. Quant. Biol. 58: 247-256.
63. Warner, J.R. 1989. Synthesis of ribosomes in Saccharomyces cerevisiae. Microbiol. Rev. 53: 256-271.
64. Winston, F., C. Dollard, and S.L. Ricupero-Hovasse. 1995. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11: 53-55.
65. Zou, S., N. Ke, J.M. Kim, and D.F. Voytas. 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes & Dev. 10: 634-645.