In vivo footprinting of specific protein-DNA interactions

The authors describe in this chapter a method for mapping the pattern of cleavages within specific unique DNA sequences in a complex genome at near single base resolution. The method has been used to accurately map the sites of sequence-specific protein-nuclei acid interactions upon regulatory sequences in various members of the α- and β-globin gene families within chicken cells and cell nuclei. They examined the pattern of cleavages introduced into the genomic copies of β- and α-globin gene promoters by exogenously added nuclease, but any reagent that cleaves DNA is a candidate for this analysis. The method can be applied to the study of any gene for which in vivo structural information is desirable. The method described here is an improved version of that previously published