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

• Published in: FEBS letters 1999-02, Vol.444 (1), p.117-124
• Main Authors: Wada-Kiyama, Yuko, Kuwabara, Kentaro, Sakuma, Yasuo, Onishi, Yoshiaki, Trifonov, Edward N, Kiyama, Ryoiti
• Format: Article
• Language: English
• Subjects: Base Sequence; Computer Simulation; Curvature; DNA - chemistry; DNA - genetics; DNA - metabolism; DNA bend site; DNA Restriction Enzymes; Electrophoresis, Polyacrylamide Gel; Estrogen Receptor alpha; HeLa Cells; Humans; Micrococcal Nuclease; Molecular Sequence Data; Nucleic Acid Conformation; Nucleosome mapping; Nucleosomes - genetics; Nucleosomes - metabolism; Oligodeoxyribonucleotides - genetics; Oligodeoxyribonucleotides - metabolism; Promoter Regions, Genetic - genetics; Receptors, Estrogen - genetics; Response Elements - genetics; Sequence Deletion
• ISSN: 0014-5793; 1873-3468
• DOI: 10.1016/S0014-5793(99)00041-1

We determined DNA bend sites in the promoter region of the human estrogen receptor (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 distance of 688 bp. Most of the sites were accompanied by short poly(dA)·poly(dT) tracts including the potential bend core sequence A 2N 8A 2N 8A 2 (A/A/A). Fine mapping of the ERB−2 site indicated that this A/A/A and the 20 bp immediate flanking sequence containing one half of the estrogen response element were the sites of DNA curvature. All of the experimentally mapped bend sites corresponded to the positions of DNA curvature as well as to nucleosomes 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.