A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation

Estrogen receptor alpha (ER alpha) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ER alpha-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ER alpha-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ER alpha-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ER alpha-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ER alpha target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ER alpha-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ER alpha-driven breast cancer cell proliferation.