Nucleosome binding by the polymerase I transactivator upstream binding factor displaces linker histone H1

Molecular and Cellular Biology

Volumn 17, Issue 10, 1997, Pages 5833-5842

  Kermekchiev, Milko ^a   Workman, Jerry L ^b   Pikaard, Craig S ^a,c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; HISTONE H1; RIBOSOME RNA; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA CONFORMATION; HUMAN; HUMAN CELL; MOLECULAR INTERACTION; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA BINDING; RNA GENE;

VERTEBRATA;

EID: 0030812751     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.17.10.5833     Document Type: Article

References (75)

1. Bazett-Jones, D., B. Leblanc, M. Herfort, and T. Moss. 1994. Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF. Science 264:1134-1137.
2. Berk, A. J., and P. A. Sharp. 1977. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12:721-732.
3. Boseley, P., T. Moss, M. Machler, R. Portmann, and M. Birnstiel. 1979. Sequence organization of the spacer DNA in a ribosomal gene unit of X. laevis. Cell 17:19-31.
4. Buratowski, S., S. Hahn, L. Guarente, and P. Sharp. 1989. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56:549-561.
5. Busby, S. J., and R. H. Reeder. 1983. Spacer sequences regulate transcription of ribosomal gene plasmids injected into Xenopus embryos. Cell 34:989-996.
6. Clark, D. J., R. Ghirlando, G. Felsenfeld, and H. Eisenberg. 1993. Effect of positive supercoiling on DNA compaction by nucleosome cores. J. Mol. Biol. 234:297-301.
7. Conconi, A., R. M. Widmer, T. Koller, and J. M. Sogo. 1989. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57:753-761.
8. Copenhaver, G. P., C. D. Putnam, M. L. Denton, and C. S. Pikaard. 1994. The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids. Nucleic Acids Res. 22:2651-2657.
9. Cote, J., R. T. Utley, and J. L. Workman. 1995. Basic analysis of transcription factor binding to nucleosomes. Methods Mol. Genet. 6:108-128.
10. 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.
11. Dammann, R., R. Lucchini, T. Koller, and J. M. Sogo. 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.
12. Dimitrov, S., G. Almouzni, M. Dasso, and A. P. Wolffe. 1993. Chromatin transitions during early Xenopus embryogenesis: changes in histone H4 acetylation and in linker histone type. Dev. Biol. 160:214-227.
13. Ding, H. F., S. Rimsky, S. C. Batson, M. Bustin, and U. Hansen. 1994. Stimulation of RNA polymerase II elongation by chromosomal protein HMG-14. Science 265:796-799.
14. Elgin, S. C. R. 1990. Chromatin structure and gene activity. Curr. Opin. Cell Biol. 2:437-445.
15. Felsenfeld, G. 1992. Chromatin as an essential part of the transcriptional mechanism. Nature 355:219-224.
16. Finch, J. T., and A. Klug. 1976. Solenoid model for superstructure in chromatin. Proc. Natl. Acad. Sci. USA 73:1897-1901.
17. Grossbach, U. 1995. Selective distribution of histone H1 variants and high mobility group proteins in chromosomes. Semin. Cell Biol. 6:237-246.
18. Hamkalo, J. B. R. B. A. 1978. Higher order structure in metaphase chromosomes. I. The 250 A fiber. Chromosoma 69:363-372.
19. Hu, C. H., B. McStay, S.-W. Jeong, and R. H. Reeder. 1994. xUBF, an RNA polymerase I transcription factor, binds crossover DNA with low sequence specificity. Mol. Cell. Biol. 14:2871-2882.
20. Jantzen, H. M., A. Admon, S. P. Bell, and R. Tjian. 1990. Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. Nature 344:830-836.
21. Juan, L.-J., R. T. Utley, M. Vignali, L. Bohm, and J. L. Workman. 1997. Histone H1 repression of transcription factor binding to a stably positioned nucleosome. J. Biol. Chem. 272:3635-3640.
22. Khochbin, S., and A. P. Wolffe. 1994. Developmentally regulated expression of linker-histone variants in vertebrates. Eur. J. Biochem. 225:501-510.
23. Kornberg, R. 1974. Chromatin structure: a repeating unit of histones and DNA. Science 184:868-871.
24. Kornberg, R. D., and Y. Lorch. 1995. Interplay between chromatin structure and transcription. Curr. Opin. Cell Biol. 7:371-375.
25. Kuhn, A., and I. Grummt. 1992. Dual role of the nucleolar transcription factor UBF: trans-activator and antirepressor. Proc. Natl. Acad. Sci. USA 89:7340-7344.
26. Kuhn, A., R. Voit, V. Stefanovsky, R. Evers, M. Bianchi, and I. Grummt. 1994. Functional differences between the two splice variants of the nucleolar transcription factor UBF: the second HMG box determines specificity of DNA binding and transcriptional activity. EMBO J. 13:416-424.
27. Labhart, P., and R. H. Reeder. 1984. Enhancer-like properties of the 60/81 bp elements in the ribosomal gene spacer of Xenopus laevis. Cell 37:285-289.
28. Laudet, V., D. Stehelin, and H. Clevers. 1993. Ancestry and diversity of the HMG box superfamily. Nucleic Acids Res. 21:2493-2501.
29. Laybourn, P. J., and J. T. Kadonaga. 1991. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science 254:238-245.
30. Leblanc, B., C. Read, and T. Moss. 1993. Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction. EMBO J. 12:513-525.
31. Lorch, Y., J. W. LaPointe, and R. D. Kornberg. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203-210.
32. McKnight, S. L., and O. L. Miller. 1976. Ultrastructural patterns of RNA synthesis during early embryogenesis of Drosophila melanogaster. Cell 8:305-319.
33. McStay, B., M. W. Frazier, and R. H. Reeder. 1991. xUBF contains a novel dimerization domain essential for RNA polymerase I transcription. Genes Dev. 5:1957-1968.
34. McStay, B., G. J. Sullivan, and C. Cairns. 1997. The Xenopus RNA polymerase I transcription factor, UBF, has a role in transcriptional enhancement distinct from that at the promoter. EMBO J. 16:396-405.
35. Moss, T. 1983. A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis. Nature 302:223-228.
36. Moss, T., and V. Y. Stefanovsky. 1995. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. Prog. Nucleic Acid Res. Mol. Biol. 50:25-66.
37. Mougey, E. B., L. K. Pape, and B. Sollner-Webb. 1996. Virtually the entire Xenopus laevis rDNA multikilobase intergenic spacer serves to stimulate polymerase I transcription. J. Biol. Chem. 271:27138-27145.
38. Neil, K. J., R. A. Ridsdale, B. Rutherford, L. Taylor D. E. Larson, M. Glibetic, L. Rothblum, and G. Harauz. 1996. Structure of recombinant UBF by electron image analysis and homology modelling. Nucleic Acids Res. 24:1472-1480.
39. Neubauer, B., and W. Horz. 1989. Analysis of nucleosome positioning by in vitro reconstitution, p. 630-644. In P. M. Wassarman and R. D. Kornberg (ed.), Nucleosomes, vol. 170. Academic Press, Inc., San Diego, Calif.
40. Nightingale, K., S. Dimitrov, R. Reeves, and A. P. Wolffe. 1996. Evidence for a shared structural role for HMG1 and linker histones B4 and H1 in organizing chromatin. EMBO J. 15:548-561.
41. Noll, M., and R. D. Kornberg. 1977. Action of micrococcal nuclease on chromatin and the location of histone H1. J. Mol. Biol. 109:393-404.
42. Olins, A. L., and D. E. Olins. 1974. Spheroid chromatin units (υ-bodies). Science 183:330-332.
43. Owen-Hughes, T., and J. L. Workman. 1994. Experimental analysis of chromatin function in transcription control. Crit. Rev. Eukaryot. Gene Expr. 4:403-441.
44. Paranjape, S. M., R. T. Kamakaka, and J. T. Kadonaga. 1994. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu. Rev. Biochem. 63:265-297.
45. Paranjape, S. M., A. Krumm, and J. T. Kadonaga. 1995. HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation. Genes Dev. 9:1978-1991.
46. Paule, M. R. 1994. Transcription of ribosomal RNA by eukaryotic RNA polymerase I, p. 83-106. In R. C. Conaway and J. W Conaway (ed.), Transcription: mechanisms and regulation. Raven Press, Ltd., New York, N.Y.
47. Pennings, S., G. Meersseman, and E. M. Bradbury. 1994. Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc. Natl. Acad. Sci. USA 91:10275-10279.
48. Pikaard, C. S., B. McStay, M. C. Schultz, S. P. Bell, and R. H. Reeder. 1989. The Xenopus ribosomal gene enhancers bind an essential polymerase I transcription factor, xUBF. Genes Dev. 3:1779-1788.
49. Pikaard, C. S., L. K. Pape, S. L. Henderson, K. Ryan, M. H. Paalman, M. A. Lopata, R. H. Reeder, and B. Sollner-Webb. 1990. Enhancers for RNA polymerase I in mouse ribosomal DNA. Mol. Cell. Biol. 10:4816-4825.
50. Pikaard, C. S., and R. H. Reeder. 1988. Sequence elements essential for function of the Xenopus laevis ribosomal DNA enhancers. Mol. Cell. Biol. 8:4282-4288.
51. Postnikov, Y. V., V. V. Shick, A. V. Belyavsky, K. R. Khrapko, K. L. Brodolin, T. A. Nikolskaya, and A. D. Mirzabekov. 1991. Distribution of high mobility group proteins 1/2, E and 14/17 and linker histones H1 and H5 on transcribed and non-transcribed regions of chicken erythrocyte chromatin. Nucleic Acids Res. 19:717-725.
52. Pruss, D., J. J. Hayes, and A. P. Wolffe. 1994. Nucleosomal anatomy - where are the histones? BioEssays 17:161-170.
53. Putnam, C. D., G. P. Copenhaver, M. L. Denton, and C. S. Pikaard. 1994. The RNA polymerase I transactivator UBF requires its dimerization domain and HMG-box 1 to bend, wrap, and positively supercoil enhancer DNA. Mol. Cell. Biol. 14:6476-6488.
54. Putnam, C. D., and C. S. Pikaard. 1992. Cooperative binding of the Xenopus RNA polymerase I transcription factor xUBF to repetitive ribosomal gene enhancers. Mol. Cell. Biol. 12:4970-4980.
55. Quinn, J., A. M. Fyrberg, R. W. Ganster, M. C. Schmidt, and C. L. Peterson. 1996. DNA-binding properties of the yeast SWI/SNF complex. Nature 379: 844-847.
56. Ratnner, J. B., and B. A. Hamkalo. 1978. Higher order structure in metaphase chromosomes. II. The relationship between the 250 A fiber, superbeads and beads-on-a-string. Chromosoma 69:373-379.
57. Reeder, R. H. 1984. Enhancers and ribosomal gene spacers. Cell 38:349-351.
58. Reeder, R. H. (ed.). 1992. Regulation of transcription by RNA polymerase I, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
59. Reeder, R. H., C. S. Pikaard, and B. McStay. 1995. UBF an architectural element for RNA polymerase I promoters. Nucleic Acids Mol. Biol. 9:251-263.
60. Rhodes, D., and R. A. Laskey. 1989. Assembly of nucleosomes and chromatin in vitro. Methods Enzymol. 170:575-585.
61. 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.
62. Studitsky, V. M., D. J. Clark, and G. Felsenfeld. 1994. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76:371-382.
63. Studitsky, V. M., D. J. Clark, and G. Felsenfeld. 1995. Overcoming a nucleosomal barrier to transcription. Cell 83:19-27.
64. Thoma, F., T. Koller, and A. Klug. 1979. Involvement of H1 in the organization of the nucleosome and of salt-dependent superstructures of chromatin. J. Cell Biol. 83:403-427.
65. Towbin, H., T. Staehelin, and J. Gordon. 1979. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc. Natl. Acad. Sci. USA 76:4350-4354.
66. Treiber, D. K., X. Zhai, H.-M. Jantzen, and J. M. Essigman. 1994. Cisplatin-DNA adducts are molecular decoys for the ribosomal RNA transcription factor hUBF. Proc. Natl. Acad. Sci. USA 91:5672-3676.
67. Ura, K., J. J. Hayes, and A. P. Wolffe. 1995. A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones. EMBO J. 14:3752-3765.
68. Ura, K., and A. P. Wolffe. 1996. Reconstitution of transcriptionally active and silent chromatin. Methods Enzymol. 274:257-271.
69. Utley, R. T., T. A. Owen-Hughes, L.-J. Juan, J. Cote, C. C. Adams, and J. L. Workman. 1996. In vitro analysis of transcription factor binding to nucleosomes and nucleosome disruption/displacement. Methods Enzymol. 274: 276-291.
70. Varga-Weisz, P., K. van Holde, and J. Zlatanova. 1994. Competition between linker histones and HMG1 for binding to four-way junction DNA: implications for transcription. Biochem. Biophys. Res. Commun. 203:1904-1911.
71. Vettese-Dadey, M., P. A. Grant, T. R. Hebbes, C. Crane-Robinson, C. D. Allis and J. L. Workman. 1996. Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J 15:2508-2518.
72. Weintraub, H. 1984. Histone-H1-dependent chromatin superstructures and the suppression of gene activity. Cell 38:17-27.
73. Woodcock, C. L., and R. A. Horowitz. 1995. Chromatin organization reviewed. Trends Cell Biol. 5:272-277.
74. Workman, J. L., et al. Unpublished results.
75. Zlatanova, J., and K. Van Holde. 1996. The linker histones and chromatin structure: new twists. Prog. Nucleic Acid Res. Mol. Biol. 52:217-259.