ER and ER Homodimers in the Same Cellular Context Regulate Distinct Transcriptomes and Functions

The two estrogen receptors ER alpha and ER beta are nuclear receptors that bind estrogen (E2) and function as ligand-inducible transcription factors. They are homologues and can form dimers with each other and bind to the same estrogen-response element motifs in the DNA. ER alpha drives breast cancer growth whereas ER beta has been reported to be anti-proliferative. However, they are rarely expressed in the same cells, and it is not fully investigated to which extent their functions are different because of inherent differences or because of different cellular context. To dissect their similarities and differences, we here generated a novel estrogen-dependent cell model where ER alpha homodimers can be directly compared to ER beta homodimers within the identical cellular context. By using CRISPR-cas9 to delete ER alpha in breast cancer MCF7 cells with Tet-Off-inducible ER beta expression, we generated MCF7 cells that express ER beta but not ER alpha. MCF7 (ER beta only) cells exhibited regulation of estrogen-responsive targets in a ligand-dependent manner. We demonstrated that either ER was required for MCF7 proliferation, but while E2 increased proliferation via ER alpha, it reduced proliferation through a G2/M arrest via ER beta. The two ERs also impacted migration differently. In absence of ligand, ER beta increased migration, but upon E2 treatment, ER beta reduced migration. E2 via ER alpha, on the other hand, had no significant impact on migration. RNA sequencing revealed that E2 regulated a transcriptome of around 800 genes via each receptor, but over half were specific for either ER alpha or ER beta (417 and 503 genes, respectively). Functional gene ontology enrichment analysis reinforced that E2 regulated cell proliferation in opposite directions depending on the ER, and that ER beta specifically impacted extracellular matrix organization. We corroborated that ER beta bound to cis-regulatory chromatin of its unique proposed migration-related direct targets ANXA9 and TFAP2C. In conclusion, we demonstrate that within the same cellular context, the two ERs regulate cell proliferation in the opposite manner, impact migration differently, and each receptor also regulates a distinct set of target genes in response to E2. The developed cell model provides a novel and valuable resource to further complement the mechanistic understanding of the two different ER isoforms.