Localization of curved DNA and its association with nucleosome phasing in the promoter region of the human estrogen receptor alpha gene

We determined DNA bend sites in the promoter region of the human estrogen r eceptor (ER) gene by the circular permutation assay. A total of five sites (ERB-4 to -1, and ERB+1) mapped in the 3 kb region showed an average distan ce of 688 bp, Most of the sites were accompanied by short poly(dA).poly(dT) tracts including the potential bend core sequence A(2)N(8)A(2)N(8)A(2) (A/ A/A), Fine mapping of the ERB-2 site indicated that this A/A/A and the 20 b p immediate flanking sequence containing one half of the estrogen response element were the sites of DNA curvature. All of the experimentally mapped b end sites corresponded to the positions of DNA curvature as well as to nucl eosomes predicted by computer analysis. In vitro nucleosome mapping at ERB- 2 revealed that the bend center was located 10-30 bp from the experimental and predicted nucleosome dyad axes. (C) 1999 Federation of European Biochem ical Societies.