Analysis of DNaseI Hypersensitive Sites in Chromatin by Cleavage in Permeabilized Cells

Treatment of nuclei with limited amounts of DNaseI can be used to reveal sites in chromatin that are hypersensitive (HS) to the nuclease (1 ,2 ). DNaseI HS sites are thought to correspond to sites where the regular nucleosome structure is perturbed, e.g., by binding of proteins to chromatin such that DNA becomes more accessible to the nuclease. Some HS sites have indeed been reconstituted in vitro during assembly of nucleosomes in the presence of transcription factors. Mapping of DNaseI HS sites and monitoring their time course of appearance (or disappearance) has been successfully used to identify many regulatory elements. Analysis of HS sites is an attractive method when searching for regulatory regions because one can scan genomic regions without detailed prior assumptions of where to look.