Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast

Genes and Development

Volumn 11, Issue 2, 1997, Pages 255-269

  Bryk, Mary ^a   Banerjee, Mukti ^a   Murphy, Michael ^a   Knudsen, Karen E ^b   Garfinkel, David J ^b   Curcio, M Joan ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

chromatin; histones H2A H2B; rDNA; transcriptional silencing; Ty1; UBC2

Indexed keywords

RIBOSOME DNA;

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

SACCHAROMYCES CEREVISIAE;

EID: 0031044789     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.2.255     Document Type: Article

References (80)

1. Adams, A., D. Gottschling, and C. Kaiser. 1995. Methods in yeast genetics. A laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Akroyd, J., V.J. Fincham, A.R. Green, P. Levantis, S. Searle, and J.A. Wyke. 1987. Transcription of Rous sarcoma proviruses in rat cells is determined by chromosomal position effects that fluctuate and can operate over a long distance. Oncogene 1: 347-355.
3. Alani, E., L. Cao, and N. Kleckner. 1987. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116: 541-545.
4. Bailly, V., J. Lamb, P. Sung, S. Prakash, and L. Prakash. 1994. Specific complex formation between yeast RAD6 and RAD18 proteins: A potential mechanism for targeting RAD6 ubiquitin-conjugating activity to DNA damage sites. Genes & Dev. 8: 811-820.
5. Bedell, M.A., N.A. Jenkins, and N.G. Copeland. 1996. Good genes in bad neighbourhoods. Nature Genet. 12: 229-232.
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. 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.
8. 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.
9. 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.
10. Chalker, D.L. and S.B. Sandmeyer. 1992. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes & Dev. 6: 117-128.
11. 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.
12. Christman, M.F., F.S. Dietrich, N.A. Levin, B.U. Sadoff, and G.R. Fink. 1993. The rRNA-encoding DNA array has an altered structure in topoisomerase I mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 90: 7637-7641.
13. Clark-Adams, C.D., D. Norris, M.A. Osley, J.S. Fassler, and F. Winston. 1988. Changes in histone gene dosage alter transcription in yeast. Genes & Dev. 2: 150-159.
14. Conklin, K.F. and M. Groudine. 1986. Varied interactions between proviruses and adjacent host chromatin. Mol. Cell. Biol. 6: 3999-4007.
15. Curcio, M.J. and D.J. Garfinkel. 1991a. Regulation of retrotransposition in Saccharomyces cerevisiae. Mol. Microbiol. 5: 1823-1829.
16. _. 1991b. Single-step selection for Ty1 element retrotransposition. Proc. Natl. Acad. Sci. 88: 936-940.
17. _. 1992. Posttranslational control of Ty1 retrotransposition occurs at the level of protein processing. Mol. Cell. Biol. 12: 2813-2825.
18. _. 1994. Heterogeneous functional Ty1 elements are abundant in the Saccharomyces cerevisiae genome. Genetics 136: 1245-1259.
19. Curcio, M.J. and R.H. Morse. 1996. Tying together integration and chromatin. Trends Genet. 12: 436-438.
20. Curcio, M.J., A.M. Hedge, J.D. Boeke, and D.J. Garfinkel. 1990. Ty RNA levels determine the spectrum of retrotransposition events that activate gene expression in Saccharomyces cerevisiae. Mol. & Gen. Genet. 220: 213-221.
21. 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.
22. Dillin, A. and J. Rine. 1995. On the origin of a silencer. Trends Biochem. Sci. 20: 231-235.
23. Dohmen, R.J., K. Madura, B. Bartel, and A. Varshavsky. 1991. The N-end rule is mediated by the UBC2 (RAD6) ubiquitinconjugating enzyme. Proc. Natl. Acad. Sci. 88: 7351-7355.
24. Elder, R.T., T.P. St. John, D.T. Stinchcomb, and R.W. Davis. 1981. Studies on the transposable element Ty1 of yeast. I. RNA homologous to Ty1. Cold Spring Harbor Symp. Quant. Biol. 45: 581-584.
25. Farabaugh, P.J. 1995. Post-transcriptional regulation of transposition by Ty retrotransposons of Saccharomyces cerevisiae. J. Biol. Chem. 270: 10361-10364.
26. Feinstein, S.C., S.R. Ross, and K.R. Yamamoto. 1982. Chromosomal position effects determine transcriptional potential of integrated mammary tumor virus DNA. J. Mol. Biol. 156: 549-566.
27. Garfinkel, D.J., M.F. Mastrangelo, N.J. Sanders, B.K. Shafer, and J.N. Strathern. 1988. Transposon tagging using Ty elements in yeast. Genetics 120: 95-108.
28. Gerring, S.L., C. Connelly, and P. Hieter. 1991. Positional mapping of genes by chromosome blotting and chromosome fragmentation. In Guide to yeast genetics and molecular biology (ed. C. Guthrie and G.R. Fink), pp. 57-76. Academic Press, San Diego, CA.
29. Gietz, D., A. St. Jean, R.A. Woods, and R.H. Schiestl. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20: 1425.
30. 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.
31. Gottschling, D.E. 1992. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. 89: 4062-4065.
32. Han, M. and M. Grunstein. 1988. Nucleosome loss activates yeast downstream promoters in vivo. Cell 55: 1137-1145.
33. Han, M., M. Chang, U.J. Kim, and M. Grunstein. 1987. Histone H2B repression causes cell-cycle-specific arrest in yeast: Effects on chromosomal segregation, replication, and transcription. Cell 48: 589-597.
34. Hirschhorn, J.N., S.A. Brown, C.D. Clark, and F. Winston. 1992. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes & Dev. 6: 2288-2298.
35. Jentsch, S., J.P. McGrath, and A. Varshavsky. 1987. The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme. Nature 329: 131-134.
36. 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.
37. Kang, X.L., F. Yadao, R.D. Gietz, and B.A. Kunz. 1992. Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C → T.A transversions as well as transposition of the Ty element: Implications for the control of spontaneous mutation. Genetics 130: 285-294.
38. Klar, A.I.S., S. Fogel, and K. MacLeod. 1979. MAR1-A regulator of HMa and HMα loci in Saccharomyces cerevisiae. Genetics 93: 37-50.
39. Laurenson, P. and J. Rine. 1992. Silencers, silencing, and heritable transcriptional states. Microbiol. Rev. 56: 543-560.
40. Lawrence, C. 1994. The RAD6 DNA repair pathway in Saccharomyces cerevisiae: What does it do, and how does it do it? BioEssays 16: 253-258.
41. Lea, D.E. and C.A. Coulson. 1949. The distribution of the numbers of mutants in bacterial populations. J. Genet. 49: 264-285.
42. Lee, D.Y., J.J. Hayes, D. Pruss, and A.P. Wolffe. 1993. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72: 73-84.
43. Liebman, S.W. and G. Newnam. 1993. A ubiquitin-conjugating enzyme, RAD6, affects the distribution of Ty1 retrotransposon integration positions. Genetics 133: 499-508.
44. Lohe, A.R. and A.J. Hilliker. 1995. Return of the H-word (heterochromatin). Curr. Opin. Genet. Dev. 5: 746-755.
45. Loo, S. and J. Rine. 1994. Silencers and domains of generalized repression. Science 264: 1768-1771.
46. Madura, K., R.J. Dohmen, and A. Varshavsky. 1993. N-recognin/Ubc2 interactions in the N-end rule pathway. J. Biol. Chem. 268: 12046-12054.
47. Moazed, D. and A.D. Johnson. 1996. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86: 667-677.
48. Moore, G.D., D.A. Sinclair, and T.A. Grigliatti. 1983. Histone gene multiplicity and position effect variegation in Drosophila melanogaster. Genetics 105: 327-344.
49. Morrison, A., E.J. Miller, and L. Prakash. 1988. Domain structure and functional analysis of the carboxyl-terminal polyacidic sequence of the RAD6 protein of Saccharomyces cerevisiae. Mol. Cell. Biol. 8: 1179-1185.
50. 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.
51. Norris, D. and M.A. Osley. 1987. The two gene pairs encoding H2A and H2B play different roles in the Saccharomyces cerevisiae life cycle. Mol. Cell. Biol. 7: 3473-3481.
52. Norris, D., B. Dunn, and M.A. Osley. 1988. The effect of histone gene deletions on chromatin structure in Saccharomyces cerevisiae. Science 242: 759-761.
53. Olson, M.V. 1991. Genome structure and organization in Saccharomyces cerevisiae. In The molecular and cellular biology of the yeast Saccharomyces (ed. J.R. Broach, J.R. Pringle, and E.W. Jones), pp. 1-40. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
54. Oyen, T.B. and O.S. Gabrielsen. 1983. Non-random distribution of the Ty1 elements within nuclear DNA of Saccharomyces cerevisiae. FEBS Lett. 161: 201-206.
55. Paetkau, D.W., I.A. Riese, W.S. MacMorran, R.A. Woods, and R.D. Gietz. 1994. Interaction of the yeast RAD7 and SIR3 proteins: Implications for DNA repair and chromatin structure. Genes & Dev. 8: 2035-2045.
56. 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.
57. Petes, T.D. 1980. Unequal meiotic recombination within tandem arrays of yeast ribosomal DNA genes. Cell 19: 765-774.
58. Picologlou, S., N. Brown, and S.W. Liebman. 1990. Mutations in RAD6, a yeast gene encoding a ubiquitin-conjugating enzyme, stimulate retrotransposition. Mol. Cell. Biol. 10: 1017-1022.
59. Piper, P.W., A. Lockheart, and N. Patel. 1984. A minor class of 5S rRNA genes in Saccharomyces cerevisiae X2180-1B, one member of which lies adjacent to a Ty transposable element. Nucleic Acids Res. 12: 4083-4096.
60. Prakash, S., P. Sung, and L. Prakash. 1993. DNA repair genes and proteins of Saccharomyces cerevisiae. Annu. Rev. Genet. 27: 33-70.
61. 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.
62. Rivier, D.H. and L. Pillus. 1994. Silencing speaks up. Cell 76: 963-966.
63. Roest, H.P., J. van Klaveren, J. de Wit, C.G. van Gurp, M.H.M. Koken, M. Vermey, J.H. van Roijen, J.W. Hoogerbrugge, J.T.M. Vreeburg, W.M. Baarends, D. Bootsma, J.A. Grootegoed, and J.H.J. Hoeijmakers. 1996. Inactivation of the HR6B ubiquitin-conjugating DNA repair enzyme in mice causes male sterility associated with chromatin modification. Cell 86: 799-810.
64. Rustchenko, E.P. and F. Sherman. 1994. Physical constitution of ribosomal genes in common strains of Saccharomyces cerevisiae Yeast 10: 1157-1171.
65. Schmitt, M.E., T.A. Brown, and B.L. Trumpower. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 3091-3092.
66. Shore, D. 1994. RAP1: A protean regulator in yeast. Trends Genet. 10: 408-412.
67. Shore, D., M. Squire, and K.A. Nasmyth. 1984. Characterization of two genes required for the position-effect control of yeast mating-type genes. EMBO J. 3: 2817-2823.
68. Singh, J. and A.J. 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.
69. Smith, J.S. and J.D. Boeke. 1997. An unusual form of transcriptional silencing in the yeast ribosomal DNA. Genes & Dev. (this issue).
70. Sung, P., S. Prakash, and L. Prakash. 1988. The RAD6 protein of Saccharomyces cerevisiae polyubiquitinates histones, and its acidic domain mediates this activity. Genes & Dev. 2: 1476-1485.
71. Swerdlow, P.S., T. Schuster, and D. Finley. 1990. A conserved sequence in histone H2A which is a ubiquitination site in higher eucaryotes is not required for growth in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 4905-4911.
72. Szauter, P. 1984. An analysis of regional constraints on exchange in Drosophila melanogaster using recombination-defective meiotic mutants. Genetics 106: 45-71.
73. Szostak, J.W. and R. Wu. 1980. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284: 426-430.
74. Thompson, J.S., X. Ling, and M. Grunstein. 1994. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369: 245-247.
75. Thon, G., A. Cohen, and A.J. Klar. 1994. Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138: 29-38.
76. Vincent, A. and T.D. Petes. 1986. Isolation and characterization of a Ty element inserted into the ribosomal DNA of the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 14: 2939-2949.
77. Watkins, J.F., P. Sung, S. Prakash, and L. Prakash. 1993. The extremely conserved amino terminus of RAD6 ubiquitinconjugating enzyme is essential for amino-end rule-dependent protein degradation. Genes & Dev. 7: 250-261.
78. Weiler, K.S. and B.T. Wakimoto. 1995. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29: 577-605.
79. Winston, F., F. Chumley, and G.R. Fink. 1983. Eviction and transplacement of mutant genes in yeast. Methods Enzymol. 101: 211-228.
80. Wright, J.H., D.E. Gottschling, and V.A. Zakian. 1992. Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes & Dev. 6: 197-210.