DNA protein-interactions at the Saccharomyces cerevisiae 35 S rRNA promoter and in its surrounding region

Journal of Molecular Biology

Volumn 275, Issue 2, 1998, Pages 197-209

  Vogelauer, M ^a   Cioci, F ^a   Camilloni, G ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Chromatin; DNA topoisomerase I; In vivo footprinting; rDNA; Yeast

Indexed keywords

DNA DIRECTED RNA POLYMERASE; FUNGAL DNA; FUNGAL PROTEIN; RIBOSOME RNA; RNA 5S;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; CULTURE MEDIUM; DNA FOOTPRINTING; FUNGUS GROWTH; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; SACCHAROMYCES CEREVISIAE;

FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 0032536159     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1451     Document Type: Article

References (46)

1. Almer, A. & Hörz, W. (1986). Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J. 5, 2681-2687.
2. Bell, S. P., Jantzen, H. M. & Tjian, R. (1990). Assembly of alternative multiprotein complexes directs rRNA promoter selectivity. Genes Dev. 4, 943-954.
3. Bonven, B. J., Gocke, E. & Westergaard, O. (1985). A high affinity topoisomerase I binding sequence is clustered at DNAase I hypersensitive sites in Tetrahymena R-chromatin. Cell, 41, 541-551.
4. Brill, S. J. & Sternglanz, R. (1988). Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants. Cell, 54, 403-411.
5. Brill, S. J., DiNardo, S., Voelkel-Meiman, K. & Sternglanz, R. (1987). Need for DNA topoisomerase activity as a swivel for DNA replication for transcription of ribosomal RNA. Nature 326, 414-416.
6. Bryk, M., Banerjee, M., Murphy, M., Knudsen, K. E., Garfinkel, D. J. & Curcio, M. J. (1997). Transcriptional silencing of TY1 elements in the RDN1 locus of yeast. Genes Dev. 11, 255-269.
7. Busk, H., Thomsen, B., Bonven, B. J., Kjeldsen, E., Nielsen, O. F. & Westergaard, O. (1987). Preferential relaxation of supercoiled DNA containing a hexadecameric recognition sequence for topoisomerase I. Nature, 327, 638-640.
8. Buttinelli, M., Di, Mauro E. & Negri, R. (1993). Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5 S rRNA gene in vitro and in vivo. Proc. Natl Acad. Sci. USA, 90, 9315-9319.
9. Cavalli, G., Bachmann, D. & Thoma, F. (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. Christman, M. F., Dietrich, F. S. & Fink, G. R. (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.
11. Christman, M. F., Dietrich, F. S., Levin, N A., Sadoff, B. U. & Fink, G. R. (1993). The rRNA-encoding DNA array has an altered structure in topoisomerase I mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 90, 7637-7641.
12. Comai, L., Tanese, N & Tjian, R. (1992). The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1. Cell, 68, 965-976.
13. Dammann, R., Lucchini, R., Koller, T. & Sogo, J. M. (1993). Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucl. Acids Res. 21, 2331-2338.
14. Dammann, R., Lucchini, R., Koller, T. & Sogo, J. M. (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.
15. Fedor, M. J., Lue, N. F. & Kornberg, R. D. (1988). Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J. Mol. Biol. 204, 109-127.
16. Jacob, S. T. (1995). Regulation of ribosomal gene transcription. Biochem. J. 306, 617-626.
17. Keys, D. A., Vu, L., Steffan, J. S., Dodd, J. A., Yamamoto, R. T., Nogi, Y. & Nomura, M. (1994). RRN6 and RRN7 encode subunits of a multiprotein complex essential for the initiation of rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae. Genes Dev. 8, 2349-2362.
18. Keys, D. A., Lee, B. S., Dodd, J. A., Nguyen, T. T., Vu, L., Fantino, E., Burson, L. M., Nogi, Y. & Nomura, M. (1996). Multiprotein transcription factor UAF interacts with the upstream element of the yeast RNA polymerase I promoter and forms a stable preinitiation complex. Genes Dev. 10, 887-903.
19. Kulkens, T., Riggs, D. L., Heck, J. D., Planta, R. J. & Nomura, M. (1991). The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro. Nucl. Acids Res. 19, 5363-5370.
20. Kulkens, T., van der Sande, C. A., Dekker, A. F., van Heerikhuizen, H. & Planta, R. J. (1992). A system to study transcription by yeast RNA polymerase I within the chromosomal context: functional analysis of the ribosomal DNA enhancer and the RBP1/ REB1 binding sites. EMBO J. 11, 4665-4674.
21. Lucchini, R. & Sogo, J. M. (1995). Replication of transcriptionally active chromatin. Nature, 374, 276-280.
22. Morrow, B. E., Johnson, S. P. & Warner, J. R. (1989). Proteins that bind to the yeast rDNA enhancer. J. Biol. Chem. 264, 9061-9068.
23. Musters, W., Knol, J., Maas, P., Dekker, A. F., van Heerikhuizen, H. & Planta, R. J. (1989). Linker scanning of the yeast RNA polymerase I promoter. Nucl. Acids Res. 17, 9661-9678.
24. Nogi, Y., Vu, L. & Nomura, M. (1991). An approach for isolation of mutants defective in 35 S ribosomal RNA synthesis in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 88, 7026-7030.
25. Nogi, Y., Yano, R., Dodd, J., Carles, C. & Nomura, M. (1993). Gene RRN4 in Saccharomyces cerevisiae encodes the A12.2 subunit of RNA polymerase I and is essential only at high temperatures. Mol. Cell Biol. 13, 114-122.
26. Noll, M. (1974). Subunit structure of chromatin. Nature, 251, 249-251.
27. Petes, T. D. (1979). Yeast ribosomal genes are located on chromosome XII. Proc. Natl Acad. Sci. USA, 76, 410-414.
28. Pikaard, C. S., McStay, B., Schultz, M. C., Bell, S. P. & Reeder, R. H (1990). The Xenopus ribosomal gene enhancers bind an essential polymerase I transcription factor, xUBF. Genes Dev. 3, 1779-1788.
29. Reeder, R. H. (1989). Regulatory elements of the generic ribosomal gene. Curr. Opin. Cell Biol. 1, 466-474.
30. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning, 2nd edit., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Schultz, M. C., Brill, S. J., Ju, Q., Sternglanz, R. & Reeder, R. H (1992). Topoisomerases and yeast rRNA transcription: negative supercoiling stimulates initiation and topoisomerase activity is required for elongation. 6, pp. 1332-1341.
32. Sherman, F., Fink, G. R. & Lawrence, C. (1983). Methods in Yeast Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Shimizu, M., Roth, S. Y., Szent-Gyorgyi, C. & 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.
34. Simpson, R. T. (1978). Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry, 17, 5524-5531.
35. Simpson, R. T. (1990). Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature, 343, 387-389.
36. Smith, J. S. & Boeke, J. D. (1997). An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11, 241-254.
37. Smith, S. D., Oriahi, E., Lowe, D., Yang-Yen, H. F., O'Mahony, D., Rose, K., Chen, K. & Rothblum, L. I. (1990). Characterization of factors that direct transcription of rat ribosomal DNA. Mol. Cell. Biol. 10, 3105-3116.
38. Sollner-Webb, B. & Tower, J. (1986). Transcription of cloned eukaryotic ribosomal RNA genes. Ann. Rev. Biochem. 55, 801-830.
39. Steffan, J. S., Keys, D. A., Dodd, J. A. & Nomura, A. (1996). The role of TBP in rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae: TBP is required for upstream activation factor-dependent recruitment of core factor. Genes Dev. 10, 2551-2563.
40. Thoma, F., Bergman, L. W. & Simpson, R. T. (1984). Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 177, 715-733.
41. Thrash, C., Voelkel, K., DiNardo, S. & Sternglanz, R. (1984). Identification of Saccharomyces cerevisiae mutants deficient in DNA topoisomerase I activity. J. Biol. Chem. 259, 1375-7.
42. Venditti, S. & Camilloni, G. (1994). In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae. Mol. Gen. Genet. 242, 100-104.
43. Venditti, P., Costanzo, G., Negri, R. & Camilloni, G. (1994). ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim. Biophys. Acta, 1219, 677-689.
44. Wang, J. C. (1996). DNA topoisomerases. Annu. Rev. Biochem. 65, 635-692.
45. Wu, C. (1980). The 5′ end of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature, 286, 854-860.
46. Yamamoto, R. T., Nogi, Y., Dodd, J. A. & Nomura, M. (1996). RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J. 15, 3964-3973.