Identification of the role of GATA-3 in ER-positive breast cancer cells by whole genome ChIP-Chip Free

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Breast cancer is among the most common malignancies in women. It is well established that estrogen receptor alpha (ER) is a major determinant in the development and progression of breast tumor. However, it is still not fully understood how ER affects downstream signaling pathways and cross talks with other intracellular signal transduction pathways. GATA-3, a member of the zinc-finger transcription factor family, has been shown to be strongly correlated with the ER status in breast cancer by our laboratory and others. Previously, we have identified candidate targets of GATA-3 regulation using RNA interference (RNAi) followed by cDNA microarray profiling analysis. The list of potential GATA-3 target genes consists of genes that are involved in various cellular pathways including the estrogen response pathway. To further investigate the potential role played by GATA-3 in ER-dependent gene regulation, we have used chromatin immunoprecipitation coupled with DNA microarray (ChIP-Chip) assay to examine the in vivo DNA binding by GATA-3 and ER. Whole-Genome ChIP-Chip analysis using human tiling arrays has identified large number of GATA-3 binding sites in MCF-7 breast cancer cells, which are ER-positive. GATA-3 binding sites were detected in proximal promoter regions as well as distal regions, with most located in non-proximal regions. To determine if the GATA-3 binding sites co-localize with ER binding sites, we compared our ChIP-Chip data with published results from Carroll et al. (Cell 122:33-43, 2005). The comparison revealed that a significant of portion of the GATA-3 binding sites overlaps with known ER binding sites. The list of genes with overlapping GATA-3 and ER binding sites includes TFF1, XBP1 and NRIP1, which are well-known ER-regulated genes. The ChIP-Chip data, together with the RNAi knock-down results, indicate that GATA-3 may cooperate with ER and play an important role in ER-dependent gene regulation, mammary epithelial differentiation and breast cancer development.