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. 1995 Nov;15(11):6178–6187. doi: 10.1128/mcb.15.11.6178

Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer.

P P Walter 1, T A Owen-Hughes 1, J Côté 1, J L Workman 1
PMCID: PMC230869  PMID: 7565770

Abstract

To investigate the mechanisms by which transcription factors invade nucleosomal DNA and replace histones at control elements, we have examined the response of the histone octamer to transcription factor binding in the presence of histone-binding proteins (i.e., nucleosome assembly factors). We found that yeast nucleosome assembly protein 1 (NAP-1) stimulated transcription factor binding and nucleosome displacement in a manner similar to that of nucleoplasmin. In addition, disruption of the histone octamer was required both for the stimulation of transcription factor binding to nucleosomal DNA and for transcription factor-induced nucleosome displacement mediated by nucleoplasmin or NAP-1. While NAP-1 and nucleoplasmin stimulated the binding of a fusion protein (GAL4-AH) to control nucleosome cores, this stimulation was lost upon covalent histone-histone cross-linking within the histone octamers. In addition, both NAP-1 and nucleoplasmin were able to mediate histone displacement upon the binding of five GAL4-AH dimers to control nucleosome cores; however, this activity was also forfeited when the histone octamers were cross-linked. These data indicate that octamer disruption is required for both stimulation of factor binding and factor-dependent histone displacement by nucleoplasmin and NAP-1. By contrast, transcription factor-induced histone transfer onto nonspecific competitor DNA did not require disruption of the histone octamer. Thus, histone displacement in this instance occurred by transfer of complete histone octamers, a mechanism distinct from that mediated by the histone-binding proteins nucleoplasmin and NAP-1.

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Selected References

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  1. Adams C. C., Workman J. L. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol. 1995 Mar;15(3):1405–1421. doi: 10.1128/mcb.15.3.1405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Almouzni G., Clark D. J., Méchali M., Wolffe A. P. Chromatin assembly on replicating DNA in vitro. Nucleic Acids Res. 1990 Oct 11;18(19):5767–5774. doi: 10.1093/nar/18.19.5767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Almouzni G., Méchali M., Wolffe A. P. Transcription complex disruption caused by a transition in chromatin structure. Mol Cell Biol. 1991 Feb;11(2):655–665. doi: 10.1128/mcb.11.2.655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Baer B. W., Rhodes D. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature. 1983 Feb 10;301(5900):482–488. doi: 10.1038/301482a0. [DOI] [PubMed] [Google Scholar]
  5. Becker P. B., Rabindran S. K., Wu C. Heat shock-regulated transcription in vitro from a reconstituted chromatin template. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4109–4113. doi: 10.1073/pnas.88.10.4109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Becker P. B. The establishment of active promoters in chromatin. Bioessays. 1994 Aug;16(8):541–547. doi: 10.1002/bies.950160807. [DOI] [PubMed] [Google Scholar]
  7. Chen H., Li B., Workman J. L. A histone-binding protein, nucleoplasmin, stimulates transcription factor binding to nucleosomes and factor-induced nucleosome disassembly. EMBO J. 1994 Jan 15;13(2):380–390. doi: 10.1002/j.1460-2075.1994.tb06272.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Clark D. J., Felsenfeld G. A nucleosome core is transferred out of the path of a transcribing polymerase. Cell. 1992 Oct 2;71(1):11–22. doi: 10.1016/0092-8674(92)90262-b. [DOI] [PubMed] [Google Scholar]
  9. Clark D. J., Wolffe A. P. Superhelical stress and nucleosome-mediated repression of 5S RNA gene transcription in vitro. EMBO J. 1991 Nov;10(11):3419–3428. doi: 10.1002/j.1460-2075.1991.tb04906.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Côté J., Quinn J., Workman J. L., Peterson C. L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994 Jul 1;265(5168):53–60. doi: 10.1126/science.8016655. [DOI] [PubMed] [Google Scholar]
  11. Dilworth S. M., Black S. J., Laskey R. A. Two complexes that contain histones are required for nucleosome assembly in vitro: role of nucleoplasmin and N1 in Xenopus egg extracts. Cell. 1987 Dec 24;51(6):1009–1018. doi: 10.1016/0092-8674(87)90587-3. [DOI] [PubMed] [Google Scholar]
  12. Earnshaw W. C., Honda B. M., Laskey R. A., Thomas J. O. Assembly of nucleosomes: the reaction involving X. laevis nucleoplasmin. Cell. 1980 Sep;21(2):373–383. doi: 10.1016/0092-8674(80)90474-2. [DOI] [PubMed] [Google Scholar]
  13. Fujii-Nakata T., Ishimi Y., Okuda A., Kikuchi A. Functional analysis of nucleosome assembly protein, NAP-1. The negatively charged COOH-terminal region is not necessary for the intrinsic assembly activity. J Biol Chem. 1992 Oct 15;267(29):20980–20986. [PubMed] [Google Scholar]
  14. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 1988 Dec 23;55(6):1137–1145. doi: 10.1016/0092-8674(88)90258-9. [DOI] [PubMed] [Google Scholar]
  15. Han M., Kim U. J., Kayne P., Grunstein M. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2221–2228. doi: 10.1002/j.1460-2075.1988.tb03061.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hayes J. J., Wolffe A. P. Histones H2A/H2B inhibit the interaction of transcription factor IIIA with the Xenopus borealis somatic 5S RNA gene in a nucleosome. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1229–1233. doi: 10.1073/pnas.89.4.1229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hirschhorn J. N., Bortvin A. L., Ricupero-Hovasse S. L., Winston F. A new class of histone H2A mutations in Saccharomyces cerevisiae causes specific transcriptional defects in vivo. Mol Cell Biol. 1995 Apr;15(4):1999–2009. doi: 10.1128/mcb.15.4.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Imbalzano A. N., Kwon H., Green M. R., Kingston R. E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature. 1994 Aug 11;370(6489):481–485. doi: 10.1038/370481a0. [DOI] [PubMed] [Google Scholar]
  19. Ishimi Y., Kikuchi A. Identification and molecular cloning of yeast homolog of nucleosome assembly protein I which facilitates nucleosome assembly in vitro. J Biol Chem. 1991 Apr 15;266(11):7025–7029. [PubMed] [Google Scholar]
  20. Ishimi Y., Kojima M., Yamada M., Hanaoka F. Binding mode of nucleosome-assembly protein (AP-I) and histones. Eur J Biochem. 1987 Jan 2;162(1):19–24. doi: 10.1111/j.1432-1033.1987.tb10535.x. [DOI] [PubMed] [Google Scholar]
  21. Ishimi Y., Yasuda H., Hirosumi J., Hanaoka F., Yamada M. A protein which facilitates assembly of nucleosome-like structures in vitro in mammalian cells. J Biochem. 1983 Sep;94(3):735–744. doi: 10.1093/oxfordjournals.jbchem.a134414. [DOI] [PubMed] [Google Scholar]
  22. Izban M. G., Luse D. S. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 1991 Apr;5(4):683–696. doi: 10.1101/gad.5.4.683. [DOI] [PubMed] [Google Scholar]
  23. Jackson V. In vivo studies on the dynamics of histone-DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry. 1990 Jan 23;29(3):719–731. doi: 10.1021/bi00455a019. [DOI] [PubMed] [Google Scholar]
  24. Kamakaka R. T., Bulger M., Kadonaga J. T. Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly. Genes Dev. 1993 Sep;7(9):1779–1795. doi: 10.1101/gad.7.9.1779. [DOI] [PubMed] [Google Scholar]
  25. Kleinschmidt J. A., Fortkamp E., Krohne G., Zentgraf H., Franke W. W. Co-existence of two different types of soluble histone complexes in nuclei of Xenopus laevis oocytes. J Biol Chem. 1985 Jan 25;260(2):1166–1176. [PubMed] [Google Scholar]
  26. Kleinschmidt J. A., Seiter A., Zentgraf H. Nucleosome assembly in vitro: separate histone transfer and synergistic interaction of native histone complexes purified from nuclei of Xenopus laevis oocytes. EMBO J. 1990 Apr;9(4):1309–1318. doi: 10.1002/j.1460-2075.1990.tb08240.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kwon H., Imbalzano A. N., Khavari P. A., Kingston R. E., Green M. R. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature. 1994 Aug 11;370(6489):477–481. doi: 10.1038/370477a0. [DOI] [PubMed] [Google Scholar]
  28. Laskey R. A., Honda B. M., Mills A. D., Finch J. T. Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA. Nature. 1978 Oct 5;275(5679):416–420. doi: 10.1038/275416a0. [DOI] [PubMed] [Google Scholar]
  29. Lee D. Y., Hayes J. J., Pruss D., Wolffe A. P. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell. 1993 Jan 15;72(1):73–84. doi: 10.1016/0092-8674(93)90051-q. [DOI] [PubMed] [Google Scholar]
  30. Li Q., Wrange O. Translational positioning of a nucleosomal glucocorticoid response element modulates glucocorticoid receptor affinity. Genes Dev. 1993 Dec;7(12A):2471–2482. doi: 10.1101/gad.7.12a.2471. [DOI] [PubMed] [Google Scholar]
  31. Lin Y. S., Carey M. F., Ptashne M., Green M. R. GAL4 derivatives function alone and synergistically with mammalian activators in vitro. Cell. 1988 Aug 26;54(5):659–664. doi: 10.1016/s0092-8674(88)80010-2. [DOI] [PubMed] [Google Scholar]
  32. O'Neill T. E., Smith J. G., Bradbury E. M. Histone octamer dissociation is not required for transcript elongation through arrays of nucleosome cores by phage T7 RNA polymerase in vitro. Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):6203–6207. doi: 10.1073/pnas.90.13.6203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Owen-Hughes T., Workman J. L. Experimental analysis of chromatin function in transcription control. Crit Rev Eukaryot Gene Expr. 1994;4(4):403–441. [PubMed] [Google Scholar]
  34. Paranjape S. M., Kamakaka R. T., Kadonaga J. T. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu Rev Biochem. 1994;63:265–297. doi: 10.1146/annurev.bi.63.070194.001405. [DOI] [PubMed] [Google Scholar]
  35. Pazin M. J., Kamakaka R. T., Kadonaga J. T. ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. Science. 1994 Dec 23;266(5193):2007–2011. doi: 10.1126/science.7801129. [DOI] [PubMed] [Google Scholar]
  36. Perlmann T., Wrange O. Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome. EMBO J. 1988 Oct;7(10):3073–3079. doi: 10.1002/j.1460-2075.1988.tb03172.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Philpott A., Leno G. H., Laskey R. A. Sperm decondensation in Xenopus egg cytoplasm is mediated by nucleoplasmin. Cell. 1991 May 17;65(4):569–578. doi: 10.1016/0092-8674(91)90089-h. [DOI] [PubMed] [Google Scholar]
  38. Philpott A., Leno G. H. Nucleoplasmin remodels sperm chromatin in Xenopus egg extracts. Cell. 1992 May 29;69(5):759–767. doi: 10.1016/0092-8674(92)90288-n. [DOI] [PubMed] [Google Scholar]
  39. Rhodes D. Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA. EMBO J. 1985 Dec 16;4(13A):3473–3482. doi: 10.1002/j.1460-2075.1985.tb04106.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ruiz-Carrillo A., Jorcano J. L. An octamer of core histones in solution: central role of the H3-H4 tetramer in the self-assembly. Biochemistry. 1979 Mar 6;18(5):760–768. doi: 10.1021/bi00572a004. [DOI] [PubMed] [Google Scholar]
  41. Sealy L., Burgess R. R., Cotten M., Chalkley R. Purification of Xenopus egg nucleoplasmin and its use in chromatin assembly in vitro. Methods Enzymol. 1989;170:612–630. doi: 10.1016/0076-6879(89)70068-9. [DOI] [PubMed] [Google Scholar]
  42. Smith S., Stillman B. Stepwise assembly of chromatin during DNA replication in vitro. EMBO J. 1991 Apr;10(4):971–980. doi: 10.1002/j.1460-2075.1991.tb08031.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stein A. DNA folding by histones: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones. J Mol Biol. 1979 May 15;130(2):103–134. doi: 10.1016/0022-2836(79)90421-2. [DOI] [PubMed] [Google Scholar]
  44. Studitsky V. M., Clark D. J., Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template. Cell. 1994 Jan 28;76(2):371–382. doi: 10.1016/0092-8674(94)90343-3. [DOI] [PubMed] [Google Scholar]
  45. Taylor I. C., Workman J. L., Schuetz T. J., Kingston R. E. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 1991 Jul;5(7):1285–1298. doi: 10.1101/gad.5.7.1285. [DOI] [PubMed] [Google Scholar]
  46. Tsukiyama T., Becker P. B., Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 1994 Feb 10;367(6463):525–532. doi: 10.1038/367525a0. [DOI] [PubMed] [Google Scholar]
  47. Varga-Weisz P. D., Blank T. A., Becker P. B. Energy-dependent chromatin accessibility and nucleosome mobility in a cell-free system. EMBO J. 1995 May 15;14(10):2209–2216. doi: 10.1002/j.1460-2075.1995.tb07215.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Voordouw G., Eisenberg H. Binding of additional histones to chromatin core particles. Nature. 1978 Jun 8;273(5662):446–448. doi: 10.1038/273446a0. [DOI] [PubMed] [Google Scholar]
  49. Wall G., Varga-Weisz P. D., Sandaltzopoulos R., Becker P. B. Chromatin remodeling by GAGA factor and heat shock factor at the hypersensitive Drosophila hsp26 promoter in vitro. EMBO J. 1995 Apr 18;14(8):1727–1736. doi: 10.1002/j.1460-2075.1995.tb07162.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Wechsler D. S., Papoulas O., Dang C. V., Kingston R. E. Differential binding of c-Myc and Max to nucleosomal DNA. Mol Cell Biol. 1994 Jun;14(6):4097–4107. doi: 10.1128/mcb.14.6.4097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Wolffe A. P. Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends Biochem Sci. 1994 Jun;19(6):240–244. doi: 10.1016/0968-0004(94)90148-1. [DOI] [PubMed] [Google Scholar]
  52. Workman J. L., Abmayr S. M., Cromlish W. A., Roeder R. G. Transcriptional regulation by the immediate early protein of pseudorabies virus during in vitro nucleosome assembly. Cell. 1988 Oct 21;55(2):211–219. doi: 10.1016/0092-8674(88)90044-x. [DOI] [PubMed] [Google Scholar]
  53. Workman J. L., Kingston R. E. Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex. Science. 1992 Dec 11;258(5089):1780–1784. doi: 10.1126/science.1465613. [DOI] [PubMed] [Google Scholar]
  54. Workman J. L., Roeder R. G., Kingston R. E. An upstream transcription factor, USF (MLTF), facilitates the formation of preinitiation complexes during in vitro chromatin assembly. EMBO J. 1990 Apr;9(4):1299–1308. doi: 10.1002/j.1460-2075.1990.tb08239.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Workman J. L., Taylor I. C., Kingston R. E. Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes. Cell. 1991 Feb 8;64(3):533–544. doi: 10.1016/0092-8674(91)90237-s. [DOI] [PubMed] [Google Scholar]
  56. Workman J. L., Taylor I. C., Kingston R. E., Roeder R. G. Control of class II gene transcription during in vitro nucleosome assembly. Methods Cell Biol. 1991;35:419–447. doi: 10.1016/s0091-679x(08)60582-8. [DOI] [PubMed] [Google Scholar]
  57. Zucker K., Worcel A. The histone H3/H4.N1 complex supplemented with histone H2A-H2B dimers and DNA topoisomerase I forms nucleosomes on circular DNA under physiological conditions. J Biol Chem. 1990 Aug 25;265(24):14487–14496. [PubMed] [Google Scholar]
  58. van Holde K. E., Lohr D. E., Robert C. What happens to nucleosomes during transcription? J Biol Chem. 1992 Feb 15;267(5):2837–2840. [PubMed] [Google Scholar]

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