Identification of overlap between KDM3A and FOXA1 regulated transcriptome in the ER positive breast cancer cell line MCF-7. Identification of overlap between KDM3A and FOXA1 regulated transcriptome in the ER positive breast cancer cell line MCF-7

To interrogate the extent of overlap between KDM3A and FOXA1 regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM3A-depleted and FOXA1-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. We identified that 43% of the KDM3A regulated transcriptome was also regulated by FOXA1 and that 43% of the FOXA1 regulated transcriptome was also regulated by KDM3A. Genes co-regulated by KDM3A and FOXA1 were involved in ER-signalling and the cell growth. We also identified that depletion of KDM3A was required for the deposition of FOXA1 on chromatin. Overall design: MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) a KDM3A targeting siRNA (siKDM3A#1), or a FOXA1 targeting siRNA (siFOXA1#1) using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 48 hours prior to treatment with 10 nM E2 for 6 hours before RNA extraction using TRIzol (Ambion, Life Technologies) and hybridization of triplicate samples to an Illumine HT-12 v4 BeadChip array.