DNaseI hypersensitivity analysis of chromatin structure.

Transcriptionally inactive DNA is packaged into condensed chromatin such that it is unavailable to the transcription initiation complex. Activation of the silenced genes during processes such as differentiation first requires that the chromatin structure be remodeled into a transcriptionally permissive configuration, with the DNA "exposed" and accessible to transcription factors. The change in chromatin structure associated with transcriptional competence can be detected as increased sensitivity of the exposed DNA to digestion with DNaseI. This increased susceptibility is referred to as DnaseI-hypersensitivity. DNaseI hypersensitive sites are often located in the recognition sites for transcription factors, including promoters and enhancers. This chapter describes the protocols necessary to perform and analyze DNaseI hypersensitivity assays, a technique becoming increasingly important given the rapid advances in our understanding of the chromatin remodeling processes.