Yeast telomeric sequences function as chromosomal anchorage points in vivo

EMBO Journal

Volumn 16, Issue 3, 1997, Pages 523-533

  Mirabella, Allyson ^a   Gartenberg, Marc R ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

DNA topoisomerases; R recombinase; RAP1 gene; SIR gene; Transcriptional supercoiling

Indexed keywords

DNA FRAGMENT; DNA TOPOISOMERASE;

ARTICLE; CHROMOSOME; DNA REPLICATION; ESCHERICHIA COLI; GENE MUTATION; IMMOBILIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; SACCHAROMYCES CEREVISIAE; TELOMERE; YEAST;

BINDING SITES; CHROMOSOMES; DNA; DNA TOPOISOMERASES, TYPE I; DNA, SUPERHELICAL; DNA-BINDING PROTEINS; ELECTROPHORESIS, AGAR GEL; ESCHERICHIA COLI; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; TELOMERE;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE; STAPHYLOCOCCUS PHAGE 3A;

EID: 0031014229     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.3.523     Document Type: Article

References (73)

1. 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.
2. Belotserkovskii, B.P., Johnston, B.H., Gaillard, C. and Strauss, F. (1996) Polypropylene tube surfaces may induce denaturation and multimerization of DNA. Science, 271, 222-223.
3. Benyajati, C. and Worcel, A. (1976) Isolation, characterization, and structure of the folded interphase genome of D.melanogaster. Cell, 9, 393-407.
4. Bickmore, W.A. and Oghene, K. (1996) Visualizing the spatial relationships between defined DNA sequences and the axial region of extracted metaphase chromosomes. Cell, 84, 95-104.
5. Braunstein, M., Rose, A.B., Holmes, S.G., Allis, C.D. and Broach, J.R. (1993) Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev., 7, 592-604.
6. 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 S.cerevisiae. Mol. Cell. Biol., 8, 210-225.
7. Button, L.L. and Astell, C.R. (1986) The S.cerevisiae chromosome III left telomere has a type X, but not a type Y′, ARS region. Mol. Cell. Biol., 6, 1352-1356.
8. Chikashige, Y. et al. (1994) Telomere-led premeiotic chromosome movement in fission yeast. Science, 264, 270-273.
9. Chung, H.-M.M., Shea, C., Fields, S., Taub, R.N., Van der Ploeg, L.H.T. and Tse, D.B. (1990) Architectual organization in the interphase nucleus of the protozoan T.brucei: location of telomeres and minichromosomes. EMBO J., 9, 2611-2619.
10. Cockell, M. et al. (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.
11. Cockerill, P.N. and Garrard, W.T. (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell, 44, 273-282.
12. Conrad, M.N., Wright, J.H., Wolf, A.J. and Zakian, V.A. (1990) RAP1 protein interacts with yeast telomeres in vivo: overproduction alters telomere structure and decreases chromosome stability. Cell, 63, 739-750.
13. de Lange, T. (1992) Human telomeres are attached to the nuclear matrix. EMBO J., 11, 717-724.
14. de Lara, J., Wydner, K.L., Hyland, K.M. and Ward, W.S. (1993) Fluorescent in situ hybridization of the telomere repeat sequence in hamster sperm nuclear structures. J. Cell. Biochem., 53, 213-221.
15. Delius, H. and Worcel, A. (1974) Electron microscopic visualization of the folded chromosome of E.coli. J. Mol. Biol., 82, 107-109.
16. Enomoto, S., Longtine, M.S. and Berman, J. (1994) Enhancement of telomere-plasmid segregation by the X-telomere associated sequence in S.cerevisiae involves SIR2, SIR3, SIR4, and ABF1. Genetics, 136, 757-767.
17. Erhart, E. and Hollenberg, C.P. (1983) The presence of a defective LEU2 gene on 2 micron recombinant plasmids of S.cerevisiae is responsible for curing and high copy number. J. Bacteriol., 156, 625-635.
18. Funabiki, H., Hagan, I., Uzawa, S. and Yanagida, M. (1993) Cell cycle-dependent specific positioning and clustering of centromeres and telomeres in fission yeast. J. Cell Biol., 121, 961-976.
19. Gartenberg, M.R. and Wang, J.C. (1992) Positive supercoiling of DNA greatly diminishes mRNA synthesis in yeast. Proc. Natl Acad. Sci. USA, 89, 11461-11465.
20. Gartenberg, M.R. and Wang, J.C. (1993) Identification of barriers to rotation of DNA segments in yeast from the topology of DNA rings excised bv an inducible site-specific recombinase. Proc. Natl Acad. Sci. USA, 90, 10514-10518.
21. Germond, J.E., Hirt, B., Oudet, P., Gross-Bellard, M. and Chambon, P. (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc. Natl Acad. Sci. USA, 72, 1843-1847.
22. Giaever, G.N. and Wang, J.C. (1988) Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell, 55, 849-856.
23. Gilson, E., Roberge, M., Giraldo, R., Rhodes, D. and Gasser, S.M. (1993) Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J. Mol. Biol., 231, 293-310.
24. Gotta, M., Laroche, T., Formenton, A., Maillet, L., Shertan, H. and Gasser, S.M. (1996) Cytological evidence for the clustering of telomeres and their colocalization with Rap1, Sir3, and Sir4 proteins in wild-type S.cerevisiae. J. Cell Biol., 134, 1349-1363.
25. Gottschling, D.E. (1992) Telomere-proximal DNA in S.cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl Acad. Sci. USA, 89, 4062-4065.
26. Gottschling, D.E., Aparicio, O.M., Billington, B.L. and Zakian, V.A. (1990) Position effect at S.cerevisiae telomeres: reversible repression of PolII transcription. Cell, 63, 751-762.
27. 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.
28. Hecht, A., Strahl-Bolsinger, S. and Grunstein, M. (1996) Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature, 383, 92-95.
29. Koo, H.-S., Claassen, L., Grossman, L. and Liu, L.F. (1991) ATP-dependent partitioning of the DNA template into supercoiled domains by E.coli UvrABC. Proc. Natl Acad. Sci. USA, 88, 1212-1216.
30. Koo, H.-S., Lau, K., Wu, H.-Y. and Liu, L.F. (1992) Identification of a DNA supercoiling activity in S.cerevisiae. Nucleic Acids Res., 20, 5067-5072.
31. Levis, R., Hazelrigg, T. and Rubin, G.M. (1985) Effects of genomic position on the expression of transduced copies of the white gene of Drosophila. Science, 29, 558-561.
32. Liu, C., Mao, X. and Lustig, A.J. (1994) Mutational analysis defines a C-terminal tail domain of RAP1 essential for telomeric silencing. Genetics, 138, 1025-1040.
33. Liu, L.F. and Wang, J.C. (1987) Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA, 84, 7024-7027.
34. Longtine, M.S., Enomoto, S., Finstad, S.L. and Berman, J. (1992) Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product. Mol. Cell. Biol. 12, 1997-2009.
35. Longtine, M.S., Enomoto, S., Finstad, S.L. and Berman, J. (1993) Telomere-mediated plasmid segregation in S.cerevisiae involves gene products required for transcriptional repression at silencers and telomeres. Genetics, 133, 171-182.
36. Louis, E.J. (1995) The chromosome ends of S.cerevisiae. Yeast, 11, 1553-1573.
37. Lustig, A.J., Kurtz, S. and Shore, D. (1990) Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length. Science, 250, 549-553.
38. Lyamichev, V.I. et al. (1989) An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH. Nature, 339, 634-637.
39. Lynch, A.S. and Wang, J.C. (1994) Use of an inducible site-specific recombinase to probe the structure of protein-DNA complexes involved in F plasmid partition in E.coli. J. Mol. Biol., 236, 679-684.
40. Marshall, M., Mahoney, D., Rose, A., Hicks, J.B. and Broach, J.B. (1987) Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol. Cell. Biol., 7, 4441-4452.
41. Matsuzaki, H., Nakajima, R., Nishiyama, J., Araki, H. and Oshima, Y. (1990) Chromosome engineering in S.cerevisiae by using a site-specific recombination system of a yeast plasmid. J. Bacteriol., 172, 610-618.
42. Mirkovitch, J., Mirault, M.-E. and Laemmli, U.K. (1984) Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell, 39, 223-232.
43. Moazed, D. and Johnson, A.D. (1996) A deubiquinating enzyme interacts with SIR4 and regulates silencing in S.cerevisiae. Cell, 86, 667-677.
44. Moens, P.B. and Pearlman, R.E. (1990) Telomere and centromere DNA are associated with the cores of meiotic prophase chromosomes. Chromosoma, 100, 8-14.
45. Moretti, P., 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.
46. Murray, A.W. and Szostak, J.W. (1983) Pedigree analysis of plasmid segregation in yeast. Cell, 34, 961-970.
47. Nimmo, E.R., Cranston, G. and Allshire, R.C. (1994) Telomere-associated chromosome breakage in fission yeast results in variegated expression of adjacent genes. EMBO J., 13, 3801-3811.
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. Paulson, J.R. and Laemmli, U.K. (1977) The structure of histone-depleted metaphase chromosomes. Cell, 12, 817-828.
50. Peck, L.J. and Wang, J.C. (1983) Energetics of B-Z transition in DNA. Proc Natl Acad. Sci. USA, 80, 6206-6210.
51. Rine, J. and Hershkowitz, I. (1987) Four genes responsible for a position effect on expression from HML and HMR in S.cerevisiae. Genetics, 116, 9-22.
52. Roca, J., Gartenberg, M.R., Oshima, Y. and Wang, J.C. (1992) A hit-and-run system for targeted genetic manipulations in yeast. Nucleic Acids Res., 20, 4671-1672.
53. Runge, K.W. and Zakian, V.A. (1989) Introduction of extra telomeric DNA sequences into S.cerevisiae results in telomere elongation. Mol. Cell. Biol., 9, 1488-1497.
54. Sen, D. and Gilbert, W. (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature, 334, 364-366.
55. Shore, D. (1994) RAP1: a protean regulator in yeast. Trends Genet., 10, 408-412.
56. Shore, D., Squire, M. and Nasmyth, K.A. (1984) Characterization of two genes required for the position-effect control of yeast mating-type genes. EMBO J., 3, 2817-2823.
57. Sinden, R.R. and Pettijohn, D.E. (1981) Chromosomes in living E.coli cells are segregated into domains of supercoiling. Proc. Natl Acad. Sci. USA, 78, 224-228.
58. Stavenhagen, J.B. and Zakian, V.A. (1994) Internal tracts of telomeric DNA act as silencers in S.cerevisiae. Genes Dev., 8, 1411-1422.
59. Sundquist, W.I. and Heaphy, S. (1993) Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA. Proc. Natl Acad. Sci. USA, 90, 3393-3397.
60. Sussel, L. and Shore, D. (1991) Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc. Natl Acad. Sci. USA, 88, 7749-7753.
61. Tsao, Y.-P., Wu, H.-Y. and Liu, L.F. (1989) Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell, 56, 111-118.
62. Venczel, E.A. and Sen, D. (1993) Parallel and antiparallel G-DNA structures from a complex telomeric sequence. Biochemistry, 32, 6220-6228.
63. Wellinger, R.J., Wolf, A.J. and Zakian, V.A. (1993) Saccharomyces telomeres acquire single-strand TG1-3 tails late in S phase. Cell, 72, 51-60.
64. Wellinger, R.J., Ethier, K., Labrecque, P. and Zakian, V. (1996) Evidence for a new step in telomere maintenance. Cell, 85, 423-433.
65. Wiley, E.A. and Zakian, V.A. (1995) Extra telomeres, but not internal tracts of telomeric DNA, reduce transcriptional repression at Saccharomyces telomeres. Genetics, 139, 67-79.
66. Williamson, J.R. (1994) G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct., 23, 703-730.
67. Williamson, J.R., Raghuraman, M.K. and Cech, T.R. (1989) Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell, 59, 871-880.
68. Worcel, A. and Burgi, E. (1972) On the structure of the folded chromosome of E.coli. J. Mol. Biol., 71, 127-147.
69. Wright, J.H. and Zakian, V.A. (1995) Protein-DNA interactions in soluble telosomes from S.cerevisiae. Nucleic Acids Res., 23, 1454-1460.
70. Wright, J.H., Gottschling, D.E. and Zakian, V.A. (1992) Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes Dev., 6, 197-210.
71. Yokota, H., van den Engh, G., Hearst, J.E., Sachs, R.K. and Trask, B.J. (1995) Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus. J. Cell Biol., 130, 1239-1249.
72. Zakian, V.A. (1995) Telomeres: beginning to understand the end. Science, 270, 1601-1607.
73. Zhang, H., Jesse, C.B. and Liu, L.F. (1990) A protein factor from Xenopous oocytes with simian virus 40 large tumor antigen-like DNA supercoiling activity. Proc. Natl Acad. Sci. USA, 87, 9078-9082.