Estrogen Receptor α Controls a Gene Network in Luminal-like Breast Cancer Cells Comprising Multiple Transcription Factors and microRNAs.

Luminal-like breast tumor cells express estrogen receptor alpha (ER-alpha) , a member of the nuclear receptor family of ligand-activated transcription factors that controls their proliferation, survival, and functional status. To identify the molecular determinants of this hormone-re- sponsive tumor phenotype , a comprehensive genome- wide analysis was performed in estrogen stimulated MCF-7 and ZR-75.1 cells by integrating time-course mRNA expression profiling with global mapping of genomic ER-alpha binding sites by chromatin immunopre- cipitation coupled to massively parallel sequencing , mi- croRNA expression profiling, and in silico analysis of transcription units and receptor binding regions iden- tified. All 1270 genes that were found to respond to 17beta-estradiol in both cell lines cluster in 33 highly con- cordant groups , each of which showed defined kinetics of RNA changes. This hormone-responsive gene set in- cludes several direct targets of ER-alpha and is organized in a gene regulation cascade , stemming from ligand-acti- vated receptor and reaching a large number of down- stream targets via AP-2-gamma, B-cell activating transcription factor, E2F1 and 2, E74-like factor 3, GTF2IRD1, hairy and enhancer of split homologue-1 , MYB , SMAD3 , RAR-alpha, and RXR-alpha transcription factors. MicroRNAs are also integral components of this gene regulation net- work because miR-107, miR-424, miR-570, miR-618, and miR-760 are regulated by 17beta-estradiol along with other microRNAs that can target a significant number of transcripts belonging to one or more estrogen-respon- sive gene clusters.