Advertisement

Analysis of Changes in Nucleosome Conformation Using Fluorescence Resonance Energy Transfer

  • Tina Shahian
  • Geeta J. Narlikar
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 833)

Abstract

ATP-dependent nucleosome-remodeling motors use the energy of ATP to alter the accessibility of the underlying DNA. Understanding how these motors alter nucleosome structure can be aided by following changes in histone–DNA contacts in real time. Here, we describe a fluorescence resonance energy transfer-based approach that enables visualization of such changes.

Key words

Histone ATP-dependent chromatin remodeling ACF SNF2h 

References

  1. 1.
    Clapier CR, Cairns BR: The biology of chromatin remodeling complexes. Annu Rev Biochem 2009, 78:273–304.Google Scholar
  2. 2.
    Lakowicz J: Principles of Fluoroscence Spectroscopy.: Springer; 1999.Google Scholar
  3. 3.
    Stryer L: Intramolecular resonance transfer of energy in proteins. Biochim Biophys Acta 1959, 35:242–244.Google Scholar
  4. 4.
    Yang JG, Narlikar GJ: FRET-based methods to study ATP-dependent changes in chromatin structure. Methods 2007, 41:291–295.Google Scholar
  5. 5.
    Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997, 389:251–260.Google Scholar
  6. 6.
    Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol 2002, 319:1097–1113.Google Scholar
  7. 7.
    Park YJ, Dyer PN, Tremethick DJ, Luger K: A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome. J Biol Chem 2004, 279:24274–24282.Google Scholar
  8. 8.
    Li G, Levitus M, Bustamante C, Widom J: Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 2005, 12:46–53.Google Scholar
  9. 9.
    Yang JG, Madrid TS, Sevastopoulos E, Narlikar GJ: The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat Struct Mol Biol 2006, 13:1078–1083.Google Scholar
  10. 10.
    Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K: Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol 2004, 375:23–44.Google Scholar
  11. 11.
    Luger K, Rechsteiner TJ, Richmond TJ: Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol Biol 1999, 119:1–16.Google Scholar
  12. 12.
    Lee KM, Narlikar G: Assembly of nucleosomal templates by salt dialysis. Curr Protoc Mol Biol 2001, Chapter 21:Unit 21 26.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoUSA

Personalised recommendations