A CRISPR-Cas9 screen identifies essential CTCF anchor sites for the mitogenic function of ER-alpha in breast cancer

Estrogen receptor α (ERα) is an enhancer activating transcriptional factor, a key driver of breast cancer, and a main target for cancer therapy. ER-mediated gene regulation requires proper chromatin-conformation to stimulate physical linkage between ER-bound enhancers and their target promoters. A major determinant of chromatin structure is CTCF that anchors chromatin domains. However, whether CTCF-binding elements (CBEs) are essential for ER mitogenic activity is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screening approach targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression predicted sensitivity to loss of ER, and good survival to anti-hormonal treatment. Altogether, our data show that CTCF-mediated chromatin structure is required for ER mitogenic function.