CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [ChIP-seq]. Homo sapiens

In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). We observed that CTCF binding correlates with ER-mediated transcription and its depletion can affect ER-ER loop formation and subsequently gene expression. Overall design: Examination of CTCF, ER, FOXA1 and Lamin B chromatin binding in MCF7 cells upon estrogen stimulation for 0h, 45min or 3h.