ERa mediated gene state switching regulates the extent of the single-cell estrogen response [scRNA-seq]

Gene regulation is complex, involving the coordination of hundreds of proteins to initiate transcription. At individual loci, transcriptional initiation is stochastic, resulting in short periods of nascent RNA synthesis known as transcriptional bursts. To understand how altered Estrogen Receptor a (ERa) function and cofactor recruitment regulates transcriptional bursting, we utilized single molecule imaging of estrogen responsive genes in Bisphenol A (BPA) treated cells. We observe that cells treated with BPA exhibited TFF1 burst initiation rates and sizes which were indistinguishable from cells induced with Estradiol (E2). However, we observed a 50% reduction in the number of active alleles in BPA treated cells. This effect is gene specific, as GREB1 was unperturbed. Although we observed no difference in chromatin accessibility, the TFF1 promoter exhibited an altered structure which coincided with reduced ERa and cofactor binding. Lastly, deletion of the enhancer locus removed the BPA effect, indicating that enhancer function was perturbed. Our results demonstrate gene specific effects of altered ERa recruitment and function which lead to a reduction of transcriptionally permissive states. Our work supports the model that the initial estrogen response occurs from alleles in primed transcriptionally permissive states with additional inactive alleles contributing to the cellular response over time. Overall design: CUT&Tag, ATAC-seq and RNA-seq of MCF7 cells treated with E2 and BPA. Time course scRNA-seq of MCF7 cells treated with E2.