Abstract
This chapter focuses on the analysis of hypersensitive sites in chromatin. Although the precise cause and effect of the phenomenon of nuclease hypersensitivity in chromatin remains to be fully elucidated, the identification of nuclease hypersensitive sites in cellular chromatin is useful as a marker of nonnucleosomal organization that could also reflect an underlying sequence-specific protein-DNA interaction. The sequence of experiments can serve as a general strategy for surveying the chromatin organization of a eukaryotic gene or region of special interest, with the intention of further analyzing those regions in which the break in nucleosomal arrangement is reflected by a change in nuclease sensitivity. Such an in vivo analysis is an important study of gene regulation as it provides information on the protein-DNA interactions that are actually occurring in the cell nucleus. This chapter concludes with describing the various properties of restriction endonuclease protection and limitations of the ExoIII protection techniques.
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