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Approaches for Studying Nucleosome Movement by ATP-Dependent Chromatin Remodeling Complexes

  • Swetansu K. Hota
  • Blaine BartholomewEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 809)

Abstract

Packaging DNA into compact chromatin enables eukaryotic cells to organize and regulate their genome. Packaging is achieved by wrapping ∼146–147 bp of DNA around a histone octamer to form a nucleosome, the basic unit of chromatin. Chromatin is a barrier of the bound DNA to factors involved in DNA-dependent processes such as transcription, replication, recombination, and repair. Several multisubunit protein complexes can move nucleosome to different positions on DNA utilizing energy derived from ATP hydrolysis and thereby facilitate access to DNA. Several methods are described for measuring nucleosome movement both in vivo and in vitro which provide important insights into the remodeling process.

Key words

Nucleosome position Indirect end-labeling Chromatin remodeling Histone-DNA cross-linking SWI/SNF ISW2 

References

  1. 1.
    Clapier, C. R. and Cairns, B. R. (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem. 78 273–304.Google Scholar
  2. 2.
    Gangaraju, V. K. and Bartholomew, B. (2007) Mechanisms of ATP dependent chromatin remodeling. Mutat Res. 618 3–17.Google Scholar
  3. 3.
    Kagalwala, M. N., Glaus, B. J., Dang, W., Zofall, M. and Bartholomew, B. (2004) Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23 2092–2104.Google Scholar
  4. 4.
    Dechassa, M. L., Sabri, A., Pondugula, S., Kassabov, S. R., Chatterjee, N., Kladde, M. P. and Bartholomew, B. (2010) SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell. 38 590–602.Google Scholar
  5. 5.
    Mizuguchi, G., Shen, X., Landry, J., Wu, W. H., Sen, S. and Wu, C. (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 303 343–348.Google Scholar
  6. 6.
    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.Google Scholar
  7. 7.
    Kent, N. A., Karabetsou, N., Politis, P. K. and Mellor, J. (2001) In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 15 619–626.Google Scholar
  8. 8.
    Flaus, A., Luger, K., Tan, S. and Richmond, T. J. (1996) Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. Proc Natl Acad Sci USA. 93 1370–1375.Google Scholar
  9. 9.
    Kassabov, S. R. and Bartholomew, B. (2004) Site-directed histone-DNA contact mapping for analysis of nucleosome dynamics. Methods Enzymol. 375 193–210.Google Scholar
  10. 10.
    Kassabov, S. R., Henry, N. M., Zofall, M., Tsukiyama, T. and Bartholomew, B. (2002) High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol Cell Biol. 22 7524–7534.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Southern Illinois University School of MedicineCarbondaleUSA

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