Skip to main content

Equilibrium and Dynamic Nucleosome Stability

  • Protocol
Book cover Chromatin Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 119))

Abstract

Researchers often think of nucleosomes as inert and static structures. But the laws of physical chemistry—which apply to any molecular complex—remind us that this picture cannot be correct. Indeed, many early studies revealed that nucleosomes undergo a complex set of assembly/disassembly processes, and more recent studies reveal that nucleosomes also have remarkable dynamic behavior. These properties of nucleosomes have practical consequences for experiments carried out in vitro, and they have important consequences for nucleosome function in vivo. This article will not discuss specific experimental methods; rather, it will summarize several aspects of the equilibrium and dynamic behavior of real nucleosomes that are of particular importance for studies of nucleosome structure and function.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. van Holde, K. E. (1989) Chromatin. Springer-Verlag, New York.

    Google Scholar 

  2. Manning, G. S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. 11, 179–246.

    CAS  Google Scholar 

  3. Hagerman, P. J. (1988) Flexibility of DNA. Ann. Rev. Biophys. Biophys. Chem. 17, 265–286.

    Article  CAS  Google Scholar 

  4. Yager, T. D., McMurray, C. T., and van Holde, K. E. (1989) Salt-induced release of DNA from nucleosome core particles. Biochemistry 28, 2271–2281.

    Article  PubMed  CAS  Google Scholar 

  5. Godde, J. S. and Wolffe, A. P. (1995) Disruption of reconstituted nucleosomes: the effect of particle concentration, MgCl2 and KCl concentration, the histone tails and temperature. J. Biol. Chem. 270, 27,399–27,402.

    Article  PubMed  CAS  Google Scholar 

  6. Royer, C. A., Ropp, T., and Scarlata, S. F. (1992) Solution studies of the interactions between the histone core proteins and DNA using fluorescence spectros-copy. Biophys. Chem. 43, 197–211.

    Article  PubMed  CAS  Google Scholar 

  7. Voordouw, G. and Eisenberg, H. (1978) Binding of additional histones to chromatin core particles. Nature 273, 446–448.

    Article  PubMed  CAS  Google Scholar 

  8. Gallego, F., Fernandez-Busquets, X., and Daban, J. R. (1995) Mechanism of nucleosome dissociation produced by transcription elongation in a short chromatin template. Biochemistry 34, 6711–6719.

    Article  PubMed  CAS  Google Scholar 

  9. Daban, J.-R. and Cantor, C. R. (1982) Structural and kinetic study of the self-assembly of nucleosome core particles. J. Mol. Biol. 156, 749–769.

    Article  PubMed  CAS  Google Scholar 

  10. Daban, J.-R. and Cantor, C. R. (1982) Role of histone pairs H2A, H2B and H3, H4 in the self-assembly of nucleosome core particles. J. Mol. Biol. 156, 771–789.

    Article  PubMed  CAS  Google Scholar 

  11. Caron, F. and Thomas, J. O. (1981) Exchange of histone H1 between segments of chromatin. J. Mol. Biol. 146, 513–537.

    Article  PubMed  CAS  Google Scholar 

  12. Louters, L. and Chalkley, R. (1984) In vitro exchange of nucleosomal histones H2a and H2b. Biochem. 23, 547–552.

    Article  CAS  Google Scholar 

  13. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Structure of the nucleosome core particle at 2.8Å pesolution. Nature 389, 251–260.

    Article  PubMed  CAS  Google Scholar 

  14. Studitsky, V. M., Clark, D. J., and Felsenfeld, G. (1995) Overcoming a nucleosomal barrier to transcription. Cell 83, 19–27.

    Article  PubMed  CAS  Google Scholar 

  15. Scarlata, S. F., Ropp, T., and Royer, C. A. (1989) Histone subunit interactions as investigated by high pressure. Biochemistry 28, 6637–6641.

    Article  PubMed  CAS  Google Scholar 

  16. Royer, C. A., Rusch, R. M., and Scarlata, S. F. (1989) Salt effects on histone subunit interactions as studied by fluorescence spectroscopy. Biochemistry 28, 6631–6637.

    Article  PubMed  CAS  Google Scholar 

  17. Karantza, V., Freire, E., and Moudrianakis, E. N. (1996) Thermodynamic studies of the core histones: pH and ionic strength effects on the stability of the (H3-H4)2 system. Biochemistry 35, 2037–2046.

    Article  PubMed  CAS  Google Scholar 

  18. Arents, G., Burlingame, R. W., Wang, B.-C., Love, W. E., and Moudrianakis, E. N. (1991) The nucleosomal core histone octamer at 3.1Å resolution: a tripartite protein assembly and a left-handed superhelix. PNAS (USA) 88, 10,148–10,152.

    Article  CAS  Google Scholar 

  19. Shrader, T. E. and Crothers, D. M. (1989) Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86, 7418–7422.

    Article  PubMed  CAS  Google Scholar 

  20. Shrader, T. E. and Crothers, D. M. (1990) Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216, 69–84.

    Article  PubMed  CAS  Google Scholar 

  21. Drew, H. R. (1991) Can one measure the free energy of binding of the histone octamer to different DNA sequences by salt-dependent reconstitution? J. Mol. Biol. 219, 391–392.

    Article  PubMed  CAS  Google Scholar 

  22. Lowary, P. T. and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42.

    Article  PubMed  CAS  Google Scholar 

  23. Widom, J. (1998) Structure, dynamics, and function of chromatin In Vitro. Annu. Rev. Biophys. Biomol. Struc. 27, 285–327.

    Article  CAS  Google Scholar 

  24. Pennings, S., Meersseman, G., and Bradbury, M.E. (1991) Mobility of positioned nucleosomes on 5S rDNA. J. Mol. Biol. 220, 101–110.

    Article  PubMed  CAS  Google Scholar 

  25. Meersseman, G., Pennings, S., and Bradbury, E. M. (1992) Mobile nucleosomes: a general behavior. EMBO J. 11, 2951–2959.

    PubMed  CAS  Google Scholar 

  26. Varga-Weisz, P. D., Blank, T. A., and Becker, P. B. (1995) Energy-dependent chromatin assembly and nucleosome mobility in a cell-free system. EMBO J. 14, 2209–2216.

    PubMed  CAS  Google Scholar 

  27. Ura, K., Hayes, J. J., and Wolffe, A. P. (1995) A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones. EMBO J. 14, 3752–3765.

    PubMed  CAS  Google Scholar 

  28. Pennings, S., Meersseman, G., and Bradbury, E. M. (1994) Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc. Natl. Acad. Sci. USA 91, 10,275–10,279.

    Article  PubMed  CAS  Google Scholar 

  29. Pazin, M. J., Bhargava, P., Geiduschek, E. P., and Kadonaga, J. T. (1997) Nucleo-some mobility and the maintenance of nucleosome positioning. Science 276, 809–812.

    Article  PubMed  CAS  Google Scholar 

  30. Fragoso, G., John, S., Roberts, M. S., and Hager, G. L. (1995) Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 9, 1933–1947.

    Article  PubMed  CAS  Google Scholar 

  31. Lowary, P. T. and Widom, J. (1997) Nucleosome packaging and nucleosome Popitioning of genomic DNA. Proc. Natl. Acad. Sci. USA 94, 1183–1188.

    Article  PubMed  CAS  Google Scholar 

  32. Yao, J., Lowary, P. T., and Widom, J. (1993) Twist constraints on linker DNA in the 30nm chromatin fiber: Implications for nucleosome phasing. Proc. Natl. Acad. Sci. USA 90, 9364–9368.

    Article  PubMed  CAS  Google Scholar 

  33. Polach, K. J. and Widom, J. (1995) Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130–149.

    Article  PubMed  CAS  Google Scholar 

  34. Polach, K. J. and Widom, J. (1996) A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258, 800–812.

    Article  PubMed  CAS  Google Scholar 

  35. Protacio, R. U., Polach, K. J., and Widom, J. (1998) Coupled enzymatic assays for the rate and mechanism of DNA site-exposure in a nucleosome. J. Mol. Biol. 274, 708–721.

    Article  Google Scholar 

  36. Workman, J. L. and Kingston, R. E. (1992) Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome vomplex. Science 258, 1780–1784.

    Article  PubMed  CAS  Google Scholar 

  37. Stager, D. J. and Workman, J. L. (1997) Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer. EMBO J. 16, 2463–2472.

    Article  Google Scholar 

  38. Widom, J. (1997) Chromatin: the Nucleosome Unwrapped. Curr. Biol. 7, R653–655.

    Article  PubMed  CAS  Google Scholar 

  39. Owen-Hughes, T., Utley, R. T., Cote, J., Peterson, C. L., and Workman, J. L. (1996) Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273, 513–516.

    Article  PubMed  CAS  Google Scholar 

  40. Owen-Hughes, T. and Workman, J. L. (1996) Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones. EMBO J 15, 4702–4712.

    PubMed  CAS  Google Scholar 

  41. Adams, C. C. and Workman, J. L. (1995) Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol. Cell. Biol. 15, 1405–1421.

    PubMed  CAS  Google Scholar 

  42. Kornberg, R. D. and Lorch, Y. (1992) Chromatin structure and transcription. Annu. Rev. Cell Biol. 8, 563–587.

    Article  PubMed  CAS  Google Scholar 

  43. Kornberg, R. D. and Lorch, Y. (1995) Interplay between chromatin structure and transcription. Curr. Opinion Cell Biol. 7, 371–375.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1999 Humana Press Inc.

About this protocol

Cite this protocol

Widom, J. (1999). Equilibrium and Dynamic Nucleosome Stability. In: Becker, P.B. (eds) Chromatin Protocols. Methods in Molecular Biology™, vol 119. Humana Press. https://doi.org/10.1385/1-59259-681-9:61

Download citation

  • DOI: https://doi.org/10.1385/1-59259-681-9:61

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-665-9

  • Online ISBN: 978-1-59259-681-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics