Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomes

Adult women are typically exposed to 17β-estradiol (E2) concentrations of ~100 to 200 pM, yet most cell-based studies use 100 nM. We determined the molecular effects of E2 concentrations spanning six orders of magnitude (1 pM to 100 nM) in breast cancer cells. Estrogen receptor α (ERα) enhancers formed at low physiological doses of E2 (1 to 100 pM) are mechanistically distinct from those that form at high pharmacological doses (10 to 100 nM). They (i) form in open chromatin bound by FOXA1, (ii) are clustered within topologically associated domains, (iii) produce enhancer RNAs enriched with functional enhancer RNA regulatory motifs, and (iv) drive expression of proliferation genes with promoter-proximal paused RNA polymerase II and distinct co-regulator enrichment. Low-dose ERα enhancer usage is elevated in patients who have breast cancer with poor responses to aromatase inhibitors, likely as a continued response to low circulating levels of E2. Collectively, our results identify mechanistic differences between low- and high-dose ERα enhancers that specify distinct biological outcomes.