If altered cell-specificity of PR underlies the deleterious effect of progestins on breast cancer risk, the determinants of cell-specificity of progestin action require elucidation. The DNA sequence of the response elements to which PR binds, the availability of transcriptional cofactors, and the chromatin architecture of the target cell are likely to have a combined effect on the specificity of the PR transcriptome. To determine the contribution of these variables to the cell-specificity of PR in normal breast and breast cancer cells, we used genomewide PR chromatin immunoprecipitation, coupled with highthroughput sequencing to compare PR interaction on genomic DNA in two cell lines: T-47D cells and in MCF-10A immortalized normal breast cells stably expressing both PR isoforms. We report here on the discovery and characterisation of strikingly different PR cistromes in these two cell lines. The majority of BKM120 PI3K inhibitor regulated genes in both cell lines and 749/1249 in AB32, Figure 2A and B, Table 1) had one or more PR binding region within 100 kb. There was a stronger association between PR binding and transcriptional regulation at earlier time points after ORG treatment, suggesting that genes that are directly regulated by PR are more likely to be detected early at the transcriptional level than those that are indirect targets . This relationship was strongest in T- 47D cells, and in AB32 cells was true only for binding regions that were relatively near the TSS of regulated genes, as shown by the higher representation of promoter proximal PR binding regions at earlier times in both cell lines . The overall distribution of PR binding regions with respect to intragenic and intergenic regions was similar in both cell lines : the greatest proportion of PR binding regions was observed upstream and in the 59UTR of regulated genes, representing 43�C45% of regions associated with regulated genes. Self-organizing map clustering of progestin-regulated transcripts associated with PR binding regions in T-47D cells and analysis of corresponding binding regions showed that PR binding regions were significantly closer to the TSSs of rapidly up-regulated genes, than to TSSs of down-regulated genes, or genes regulated at a later time point . Self-organizing map clustering of all progestin regulated transcripts revealed a pattern of regulation that was overall similar to that observed with the subset of genes associated with PR binding . However, a cluster of 26 transcripts was detected in the larger dataset representing transcripts that were decreased at all time points, but showed some LY294002 recovery at 24 h. Although 12 transcripts in this cluster were also present in the set of transcripts associated with PR binding, 14 were found only in the full progestin regulated transcriptome, and represented transcripts that were regulated early but largely recovered by 24 h, suggesting that transcriptional silencing mediated by direct PR binding may be more sustained than indirect regulation.