Estrogen Receptor β Binds to and Regulates Three Distinct Classes of Target Genes

Estrogen receptor beta (ER beta) has potent antiproliferative and anti-inflammatory properties, suggesting that ER beta-selective agonists might be a new class of therapeutic and chemopreventative agents. To understand how ER beta regulates genes, we identified genes regulated by the unliganded and liganded forms of ER alpha and ER beta in U2OS cells. Microarray data demonstrated that virtually no gene regulation occurred with unliganded ER alpha, whereas many genes were regulated by estradiol (E-2). These results demonstrated that ER alpha requires a ligand to regulate a single class of genes. In contrast, ER beta regulated three classes of genes. Class I genes were regulated primarily by unliganded ER beta. Class II genes were regulated only with E-2, whereas class III genes were regulated by both unliganded ER beta and E-2. There were 453 class I genes, 258 class II genes, and 83 class III genes. To explore the mechanism whereby ER beta regulates different classes of genes, chromatin immunoprecipitation-sequencing was performed to identify ER beta binding sites and adjacent transcription factor motifs in regulated genes. AP1 binding sites were more enriched in class I genes, whereas ERE, NF kappa B1, and SP1 sites were more enriched in class II genes. ER beta bound to all three classes of genes, demonstrating that ER beta binding is not responsible for differential regulation of genes by unliganded and liganded ER beta. The coactivator NCOA2 was differentially recruited to several target genes. Our findings indicate that the unliganded and liganded forms of ER beta regulate three classes of genes by interacting with different transcription factors and coactivators.