Estradiol-dependent 3D chromatin structure changes in MCF7 cells assessed by Capture-C, covering GREB1 and NRIP1 gene and enhancer regions
Estrogen-receptor alpha (ERa)-dependent enhancers in the human breast cancer cell line MCF7 are a well-studied model system that allows high temporal resolution tracking of the different molecular events after hormone treatment and in which the enhancer and their target genes, as well as many of the molecular mechanisms operating in enhancer activation, are well defined. We use Capture-C to look at enhancer-promoter contact frequencies of GREB1 and NRIP1 genes across a time course (5, 30 and 60 min) after E2 addition to MCF7 cells which had been extensively starved of hormone. Additionally, ee look at the E2-dependent enhancer-promoter contact frequencies at these two loci in different contexts: in cells where the enhancer regions have been deleted; in cells treated with tamoxifen as well as with estradiol to assess the effect of different ERa ligands; and in cells pre-treated with the transcription inhibitors Flavopiridol and Triptolide to assess the role of active transcription. Overall design: Capture-C of MCF7 cells, hormone starved for 4 days and treated with vehicle or E2 for 5, 30 or 60 minutes. Two biological replicates were done. Capture-C of  WT, GREB1 enhancer deleted or NRIP1 enhancer deleted MCF7 cells, hormone starved for 4 days and treated with vehicle or E2 for 30 min. Two clones per deletion were analyzed; two biological replicates were done. Capture-C of MCF7 cells, hormone starved for 4 days and treated with vehicle, E2 or Tamoxifen 30 minutes. Two biological replicates were done. Capture-C of MCF7 cells, hormone starved for 4 days and treated with DMSO, Flavopiridol or Triptolide for 5 min and then with Vehicle or E2 for 30 additional minutes. Two biological replicates were done.