Glucocorticoid receptor DNA-binding specificity is increased by the organization of DNA in nucleosomes

A DNA fragment containing glucocorticoid receptor binding sites in the mouse mammary tumor virus promoter was reconstituted in vitro with histones to form nucleosome cores, which become positioned on the DNA fragment in a sequence-specific manner. Glucocorticoid receptor binding to specific DNA sequences was analyzed by quantitative DNase I footprinting. The receptor interacted with surprisingly high affinity with one of the binding sites in the reconstituted promoter, although it was reduced by a factor of approximately 2 compared with the same site in protein-free DNA. By contrast, the affinity for random genomic nucleosomal sites was drastically reduced compared with histone-free DNA. Thus, reconstituting the promoter in vitro resulted in a 60- to 70-fold increase in binding specificity. Such an increase in selective binding may help to explain the ability of glucocorticoid receptor to effectively locate its target sites in chromatin.