Summary
The basic repeating unit of chromatin, the nucleosome, is known to play a critical role in regulating the process of gene transcription. The positioning of nucleosomes on a promoter is a significant determinant in its responsiveness to gene-inducing signals. For example, positioning and subsequent mobilization of nucleosomes can regulate the access of various DNA factors to underlying DNA templates. Several mechanisms have been proposed to direct the process of nucleosome displacement such as chemical histone modifications, ATP-dependent remodelling, and the incorporation of histone variants. Thus, rather than being an inert molecular structure, chromatin is highly dynamic in response to the transcription process. In this section, we describe two methodologies that allow the determination of exact nucleosome positioning within specific gene regions.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Luger, K. (2003). Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev 13, 127135.
Olins, A. L., and Olins, D. E. (1974). Spheroid chromatin units (v bodies). Science 183, 330332.
Mellor, J. (2005). The dynamics of chromatin remodeling at promoters. Mol Cell 19, 147157.
Eberharter, A., and Becker, P. B. (2004). ATP-dependent nucleosome remodelling: factors and functions. J Cell Sci 117, 37073711.
Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128, 693705.
Rando, O. J., and Ahmad, K. (2007). Rules and regulation in the primary structure of chromatin. Curr Opin Cell Biol 19, 250256.
Workman, J. L. (2006). Nucleosome displacement in transcription. Genes Dev 20, 20092017.
Guillemette, B., Bataille, A. R., Gevry, N., Adam, M., Blanchette, M., Robert, F., and Gaudreau, L. (2005). Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol 3, e384.
Lomvardas, S., and Thanos, D. (2001). Nucleosome sliding via TBP DNA binding in vivo. Cell 106, 685696.
Lomvardas, S., and Thanos, D. (2002). Modifying gene expression programs by altering core promoter chromatin architecture. Cell 110, 261271.
Metivier, R., Penot, G., Hubner, M. R., Reid, G., Brand, H., Kos, M., and Gannon, F. (2003). Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751763.
Sekinger, E. A., Moqtaderi, Z., and Struhl, K. (2005). Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 18, 735748.
The authors would like to thank BenoÃt Leblanc for his help in the artwork included in Fig. 1.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Gévry, N., Svotelis, A., Larochelle, M., Gaudreau, L. (2009). Nucleosome Mapping. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_19
Download citation
DOI: https://doi.org/10.1007/978-1-60327-015-1_19
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-014-4
Online ISBN: 978-1-60327-015-1
eBook Packages: Springer Protocols