Estrogen Receptor Enhancers Sensitive to Low Doses of Hormone Specify Distinct Molecular and Biological Outcomes

Adult women are typically exposed to estradiol (E2) concentrations of ∼100-200 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 alpha (ERα) enhancers formed at low physiological doses of E2 (1-100 pM) are mechanistically distinct from those that form at high pharmacological doses (10-100 nM). They (1) form in open chromatin bound by FOXA1, (2) produce enhancer RNAs enriched with functional eRNA regulatory motifs (FERMs), and (3) drive expression of cell proliferation genes with promoter-proximal paused RNA polymerase II. Importantly, low dose ERα enhancer usage is elevated in breast cancer patients 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.