Quantitative mapping of RNA-mediated nuclear Estrogen Receptor β interactome in human breast cancer cells

The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concert with ERβ to control key cellular functions, including gene transcription, RNA splicing and post-transcriptional mRNA regulation. These studies revealed an involvement of RNA in ERβ interactome assembly and functions. By applying native protein complex purification followed by nano LC-MS/MS before and after in vitro RNA removal, we identified here a large set of nuclear ERβ-interactors, including a sizeable fraction associating with the receptor via RNA bridging. Combining label-free quantitation and GO analysis revealed several cellular functions involving the nuclear interactome mapped here. The data presented will be useful for studies aiming at elucidating the role of ERβ, nuclear RNAs and the other proteins identified here in BC and other cell types.