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. 1997 Sep 15;25(18):3733–3742. doi: 10.1093/nar/25.18.3733

Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1.

K Eisfeld 1, R Candau 1, M Truss 1, M Beato 1
PMCID: PMC146933  PMID: 9278498

Abstract

To analyse the role of rotational orientation and translational positioning of nucleosomal DNA on transcription factor binding we have generated a series of mutant MMTV promoters containing insertions of various lengths between the hormone-responsive region and the binding site for NF1. These various MMTV promoter fragments were assembled in mononucleosomes and used for structural studies and binding experiments. We show that the insertions change the rotational phase and translational positioning of the NF1 site as predicted if the sequences upstream of the insertion site were the main determinants of nucleosome phasing. In band shift experiments with recombinant NF1 we cannot detect binding of the protein to NF1 sites included within the limits of a nucleosome, independent of their rotational orientation. Moving the NF1 site closer to the nucleosome border also did not permit NF1 binding. This behaviour probably reflects the way NF1 binds DNA, namely it almost completely surrounds the circumference of the double helix establishing a large number of contacts with the bases and the backbone. In contrast to the wild-type and short insertion mutants, NF1 bound readily to nucleosomes containing 30 or 50 bp insertions which placed the NF1 site at the nucleosome edge or within linker DNA. NF1 binding to the linker DNA was unaffected by incorporation of histone H1 into the nucleosome particle. These findings are discussed in relation to chromatin remodelling initiated by steroid hormones during induction of the MMTV promoter.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allan J., Hartman P. G., Crane-Robinson C., Aviles F. X. The structure of histone H1 and its location in chromatin. Nature. 1980 Dec 25;288(5792):675–679. doi: 10.1038/288675a0. [DOI] [PubMed] [Google Scholar]
  2. Beato M., Eisfeld K. Transcription factor access to chromatin. Nucleic Acids Res. 1997 Sep 15;25(18):3559–3563. doi: 10.1093/nar/25.18.3559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beato M. Transcriptional regulation of mouse mammary tumor virus by steroid hormones. Crit Rev Oncog. 1991;2(3):195–210. [PubMed] [Google Scholar]
  4. 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]
  5. Blomquist P., Li Q., Wrange O. The affinity of nuclear factor 1 for its DNA site is drastically reduced by nucleosome organization irrespective of its rotational or translational position. J Biol Chem. 1996 Jan 5;271(1):153–159. doi: 10.1074/jbc.271.1.153. [DOI] [PubMed] [Google Scholar]
  6. Boulikas T., Wiseman J. M., Garrard W. T. Points of contact between histone H1 and the histone octamer. Proc Natl Acad Sci U S A. 1980 Jan;77(1):127–131. doi: 10.1073/pnas.77.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bresnick E. H., Bustin M., Marsaud V., Richard-Foy H., Hager G. L. The transcriptionally-active MMTV promoter is depleted of histone H1. Nucleic Acids Res. 1992 Jan 25;20(2):273–278. doi: 10.1093/nar/20.2.273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brüggemeier U., Rogge L., Winnacker E. L., Beato M. Nuclear factor I acts as a transcription factor on the MMTV promoter but competes with steroid hormone receptors for DNA binding. EMBO J. 1990 Jul;9(7):2233–2239. doi: 10.1002/j.1460-2075.1990.tb07393.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chalepakis G., Arnemann J., Slater E., Brüller H. J., Gross B., Beato M. Differential gene activation by glucocorticoids and progestins through the hormone regulatory element of mouse mammary tumor virus. Cell. 1988 May 6;53(3):371–382. doi: 10.1016/0092-8674(88)90157-2. [DOI] [PubMed] [Google Scholar]
  10. Chávez S., Candau R., Truss M., Beato M. Constitutive repression and nuclear factor I-dependent hormone activation of the mouse mammary tumor virus promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Dec;15(12):6987–6998. doi: 10.1128/mcb.15.12.6987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cordingley M. G., Riegel A. T., Hager G. L. Steroid-dependent interaction of transcription factors with the inducible promoter of mouse mammary tumor virus in vivo. Cell. 1987 Jan 30;48(2):261–270. doi: 10.1016/0092-8674(87)90429-6. [DOI] [PubMed] [Google Scholar]
  12. Felsenfeld G. Chromatin unfolds. Cell. 1996 Jul 12;86(1):13–19. doi: 10.1016/s0092-8674(00)80073-2. [DOI] [PubMed] [Google Scholar]
  13. Fragoso G., John S., Roberts M. S., Hager G. L. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 1995 Aug 1;9(15):1933–1947. doi: 10.1101/gad.9.15.1933. [DOI] [PubMed] [Google Scholar]
  14. Hayes J. J., Pruss D., Wolffe A. P. Contacts of the globular domain of histone H5 and core histones with DNA in a "chromatosome". Proc Natl Acad Sci U S A. 1994 Aug 2;91(16):7817–7821. doi: 10.1073/pnas.91.16.7817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kalff M., Gross B., Beato M. Progesterone receptor stimulates transcription of mouse mammary tumour virus in a cell-free system. Nature. 1990 Mar 22;344(6264):360–362. doi: 10.1038/344360a0. [DOI] [PubMed] [Google Scholar]
  16. Li Q., Wrange O. Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol Cell Biol. 1995 Aug;15(8):4375–4384. doi: 10.1128/mcb.15.8.4375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lutter L. C. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J Mol Biol. 1978 Sep 15;124(2):391–420. doi: 10.1016/0022-2836(78)90306-6. [DOI] [PubMed] [Google Scholar]
  18. Meersseman G., Pennings S., Bradbury E. M. Chromatosome positioning on assembled long chromatin. Linker histones affect nucleosome placement on 5 S rDNA. J Mol Biol. 1991 Jul 5;220(1):89–100. doi: 10.1016/0022-2836(91)90383-h. [DOI] [PubMed] [Google Scholar]
  19. Miksicek R., Borgmeyer U., Nowock J. Interaction of the TGGCA-binding protein with upstream sequences is required for efficient transcription of mouse mammary tumor virus. EMBO J. 1987 May;6(5):1355–1360. doi: 10.1002/j.1460-2075.1987.tb02375.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Muchardt C., Yaniv M. A human homologue of Saccharomyces cerevisiae SNF2/SWI2 and Drosophila brm genes potentiates transcriptional activation by the glucocorticoid receptor. EMBO J. 1993 Nov;12(11):4279–4290. doi: 10.1002/j.1460-2075.1993.tb06112.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pennings S., Meersseman G., Bradbury E. M. Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10275–10279. doi: 10.1073/pnas.91.22.10275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Piña B., Barettino D., Truss M., Beato M. Structural features of a regulatory nucleosome. J Mol Biol. 1990 Dec 20;216(4):975–990. doi: 10.1016/S0022-2836(99)80015-1. [DOI] [PubMed] [Google Scholar]
  24. Piña B., Brüggemeier U., Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell. 1990 Mar 9;60(5):719–731. doi: 10.1016/0092-8674(90)90087-u. [DOI] [PubMed] [Google Scholar]
  25. Piña B., Truss M., Ohlenbusch H., Postma J., Beato M. DNA rotational positioning in a regulatory nucleosome is determined by base sequence. An algorithm to model the preferred superhelix. Nucleic Acids Res. 1990 Dec 11;18(23):6981–6987. doi: 10.1093/nar/18.23.6981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pruss D., Bartholomew B., Persinger J., Hayes J., Arents G., Moudrianakis E. N., Wolffe A. P. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science. 1996 Oct 25;274(5287):614–617. doi: 10.1126/science.274.5287.614. [DOI] [PubMed] [Google Scholar]
  27. Richard-Foy H., Hager G. L. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J. 1987 Aug;6(8):2321–2328. doi: 10.1002/j.1460-2075.1987.tb02507.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Roberts M. S., Fragoso G., Hager G. L. Nucleosomes reconstituted in vitro on mouse mammary tumor virus B region DNA occupy multiple translational and rotational frames. Biochemistry. 1995 Sep 26;34(38):12470–12480. doi: 10.1021/bi00038a046. [DOI] [PubMed] [Google Scholar]
  29. Siebenlist U., Gilbert W. Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980 Jan;77(1):122–126. doi: 10.1073/pnas.77.1.122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Simpson R. T. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry. 1978 Dec 12;17(25):5524–5531. doi: 10.1021/bi00618a030. [DOI] [PubMed] [Google Scholar]
  31. Staynov D. Z., Crane-Robinson C. Footprinting of linker histones H5 and H1 on the nucleosome. EMBO J. 1988 Dec 1;7(12):3685–3691. doi: 10.1002/j.1460-2075.1988.tb03250.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Truss M., Bartsch J., Schelbert A., Haché R. J., Beato M. Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 1995 Apr 18;14(8):1737–1751. doi: 10.1002/j.1460-2075.1995.tb07163.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Truss M., Beato M. Steroid hormone receptors: interaction with deoxyribonucleic acid and transcription factors. Endocr Rev. 1993 Aug;14(4):459–479. doi: 10.1210/edrv-14-4-459. [DOI] [PubMed] [Google Scholar]
  34. Truss M., Chalepakis G., Beato M. Contacts between steroid hormone receptors and thymines in DNA: an interference method. Proc Natl Acad Sci U S A. 1990 Sep;87(18):7180–7184. doi: 10.1073/pnas.87.18.7180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Tsukiyama T., Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell. 1995 Dec 15;83(6):1011–1020. doi: 10.1016/0092-8674(95)90216-3. [DOI] [PubMed] [Google Scholar]
  37. Walter P. P., Owen-Hughes T. A., Côté J., Workman J. L. Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer. Mol Cell Biol. 1995 Nov;15(11):6178–6187. doi: 10.1128/mcb.15.11.6178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Winston F., Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 1992 Nov;8(11):387–391. doi: 10.1016/0168-9525(92)90300-s. [DOI] [PubMed] [Google Scholar]
  39. Yoshinaga S. K., Peterson C. L., Herskowitz I., Yamamoto K. R. Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. Science. 1992 Dec 4;258(5088):1598–1604. doi: 10.1126/science.1360703. [DOI] [PubMed] [Google Scholar]
  40. Zaret K. S., Yamamoto K. R. Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element. Cell. 1984 Aug;38(1):29–38. doi: 10.1016/0092-8674(84)90523-3. [DOI] [PubMed] [Google Scholar]
  41. de Vries E., van Driel W., van den Heuvel S. J., van der Vliet P. C. Contactpoint analysis of the HeLa nuclear factor I recognition site reveals symmetrical binding at one side of the DNA helix. EMBO J. 1987 Jan;6(1):161–168. doi: 10.1002/j.1460-2075.1987.tb04734.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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