Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Position and orientation of the globular domain of linker histone H5 on the nucleosome

Nature volume 395, pages 402–405 (1998)Cite this article

Abstract

It is essential to identify the exact location of the linker histone within nucleosomes, the fundamental packing units of chromatin, in order to understand how condensed, transcriptionally inactive chromatin forms. Here, using a site-specific protein–DNA photo-crosslinking method1, we map the binding site and the orientation of the globular domain of linker histone H5 on mixed-sequence chicken nucleosomes. We show, in contrast to an earlier model2, that the globular domain forms a bridge between one terminus of chromatosomal DNA and the DNA in the vicinity of the dyad axis of symmetry of the core particle. Helix III of the globular domain binds in the major groove of the first helical turn of the chromatosomal DNA, whereas the secondary DNA-binding site on the opposite face of the globular domain of histone H5 makes contact with the nucleosomal DNA close to its midpoint. We also infer that helix I and helix II of the globular domain of histone H5 probably face, respectively, the solvent and the nucleosome. This location places the basic carboxy-terminal region of the globular domain in a position from which it could simultaneously bind the nucleosome-linking DNA strands that exit and enter the nucleosome.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: DNase I degestion of H1/H5-depleted chromatosomes.
Figure 2: Characterization of the complex formation between GH5 mutants and linker-histone-depleted chromatosomes and of dimer formation by the mutant proteins.
Figure 3: Analysis of GH5–azidophenacyl crosslinked to chromatosomal DNA.
Figure 4: Representation of the GH5 location on a chromatosome.

Similar content being viewed by others

References

  1. Pendergast, P. S., Chen, Y., Ebright, Y. W. & Ebright R. H. Determination of the orientation of a DNA binding motif in a protein–DNA complex by photocrosslinking. Proc. Natl Acad. Sci. USA> 89 10287–10291 (1992).

    Article  ADS  Google Scholar 

  2. Pruss, D.et al. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science 274, 614–617 (1996).

    Article  CAS  ADS  PubMed  Google Scholar 

  3. Thoma, F., Koller, T. & Klug, A. Involvement of histone H1 in the organisation of the nucleosome and of the salt dependent superstructure of chromatin. J. Cell Biol. 83, 403–427 (1979).

    Article  CAS  PubMed  Google Scholar 

  4. Simpson, R. Structure of the chromatosome, a chromatin particle containing 160 bp of DNA and all histones. Biochemistry 17, 5524–5531 (1978).

    Article  CAS  PubMed  Google Scholar 

  5. Allan, J., Crane-Robinson, C. & Aviles, F. X. The structure of histone H1 and its location in chromatin. Nature 288, 675–679 (1980).

    Article  CAS  ADS  PubMed  Google Scholar 

  6. Ramakrishnan, V., Finch, J. T., Graziano, V., Lee, P. L. & Sweet, R. M. Crystal structure of the globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219–223 (1993).

    Article  CAS  ADS  PubMed  Google Scholar 

  7. Cerf, C. et al. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure and comparison with the globular domain of histone H5. Biochemistry 33, 11079–11086 (1994).

    Article  CAS  PubMed  Google Scholar 

  8. Clark, K. L., Halay, E. D., Lai, E. & Burley, S. K. Co-crystal structure of the HNF-3/Fork head DNA-recognition motif resembles histone H5. Nature 364, 412–420 (1993).

    Article  CAS  ADS  PubMed  Google Scholar 

  9. Goytisolo, F. A. et al. Identification of two DNA-binding sites on the globular domain of histone H5. EMBO J. 15, 3421–3429 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Crane-Robinson, C. Where is the globular domain of linker histone located on the nucleosome? Trends Biochem. Sci. 22, 75–77 (1997).

    Article  CAS  PubMed  Google Scholar 

  11. Lambert, S. et al. Neutron scattering studies of chromatosomes. Biochem. Biophys. Res. Commun. 179, 810–816 (1991).

    Article  CAS  PubMed  Google Scholar 

  12. Muyldermans, S. & Travers, A. A. DNA sequence organization in chromatosomes. J. Mol. Biol. 235, 855–870 (1994).

    Article  CAS  PubMed  Google Scholar 

  13. Travers, A. A. & Muyldermans, S. ADNA sequence for positioning chromatosomes. J. Mol. Biol. 257, 486–491 (1996).

    Article  CAS  PubMed  Google Scholar 

  14. Hayes, J. J. Site-directed cleavage of DNA by a linker histone–Fe(II) EDTA conjugate: localization of a globular domain binding site within a nucleosome. Biochemistry 35, 11931–11937 (1996).

    Article  CAS  PubMed  Google Scholar 

  15. Segers, A., Muyldermans, S. & Wyns, L. The interaction of histone H5 and its globular domain with core particles, depleted chromatosomes, polynucleosomes, and a DNA decamer. J. Biol. Chem. 266, 1502–1508 (1991).

    CAS  PubMed  Google Scholar 

  16. Lutter, L. C. Precise location of DNase I cutting sites on the nucleosome core determined by high resolution gel electrophoresis. Nucleic Acids Res. 6, 41–56 (1979).

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  17. Hayes, J. J. & Wolffe, A. P. Preferential and asymmetric interaction of linker histones with 5S DNA in the nucleosome. Proc. Natl Acad. Sci. USA 90, 6415–6419 (1993).

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  18. Thomas, J. O. & Wilson, C. M. Selective radiolabeling and identification of a strong nucleosome binding site on the globular domain of histone H5. EMBO J. 5, 3531–3537 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).

    Article  CAS  ADS  PubMed  Google Scholar 

  20. An, W., van Holde, K. & Zlatanova, J. Linker histone protection of chromatosomes reconstituted on 5S rDNA from Xenopus borealis: a reinvestigation. Nucleic Acids Res. (in the press).

  21. Thomas, J. O., Rees, C. & Finch, J. T. Cooperative binding of the globular domains of histones H1 and H5 to DNA. Nucleic Acids Res. 20, 187–194 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Drwe, H. R. & McCall, M. J. Structural analysis of a reconstituted DNA containing three histone octamers and histone H5. J. Mol. Biol. 197, 485–511 (1987).

    Article  Google Scholar 

  23. Staynov, D. Z. & Crane-Robinson, C. Footprinting of linker histones H5 and H1 on the nucleosome. EMBO J. 7, 3685–3691 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Pehrson, J. R. Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin. Proc. Natl Acad. Sci. USA 86, 9149–9153 (1989).

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  25. Mirzabekov, A., Pruss, D. & Ebralidse, K. K. Chromatin superstructure dependent crosslinking with DNA of the histone H5 residues Thr1, His25 and His62. J. Mol. Biol. 211, 479–491 (1989).

    Article  Google Scholar 

  26. Hamiche, A., Schulz, P., Ramakrishnan, V., Oudet, P. & Prunell, A. Linker histone dependent DNA structure in mononucleosomes. J. Mol. Biol. 257, 30–42 (1996).

    Article  CAS  PubMed  Google Scholar 

  27. 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. USA 91, 7817–7821 (1994).

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  28. Howe, L. & Ausió, J. Nucleosome translational position, not histone acetylation, determines TFIIIA binding to nucleosomes Xenopus laevis rRNA genes. Mol. Cell. Biol. 18, 1156–1162 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Pannetta, G., Buttinelli, M., Flaus, A., Richmond, T. J. & Rhodes, D. Differential nucleosome positioning on Xenopus oocyte and somatic 5S RNA genes determines both RFIIA and H1 binding: a mechanism for selective H1 repression. J. Mol. Biol. (in the press).

Download references

Acknowledgements

We thank T. Hamelryck and Y. Geunes for help with figures, and L. Wyns for helpful discussions. Z.Y.B. received a grant from the VlAB. V.R. was supported by a Public Health Service grant from the NIH. This work was supported by grants from (N)FWO and the OZR-VUB.

Author information

Authors and Affiliations

  1. Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640, Sint Genesius Rode, Belgium

    Y.-B. Zhou & Serge Muyldermans

  2. Biology Department, Brookhaven National Laboratory, Upton, 11973, New York, USA

    Sue Ellen Gerchman

  3. Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, 84132, Utah, USA

    V. Ramakrishnan

  4. MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK

    Andrew Travers

Authors
  1. Y.-B. Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sue Ellen Gerchman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. Ramakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrew Travers
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Serge Muyldermans
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Serge Muyldermans.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhou, YB., Gerchman, S., Ramakrishnan, V. et al. Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature 395, 402–405 (1998). https://doi.org/10.1038/26521

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/26521

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing