In AB32 cells more transcripts were decreased than increased and there was no significant difference in mean binding region to TSS distance observed between regulation clusters . Of the 6312 regions bound by PR in T-47D and 8117 in AB32, just 1824 binding regions were common to both cell lines, representing 29% of binding regions in T-47D and 22% of AB32 binding regions . The binding regions common to both cell lines were not more AZD2281 likely to be associated with regulated genes: of the 1824 binding regions found in both AB32 and T-47D, 431 were associated with progestin regulation in AB32 and 345 in T-47D – similar to the association of all binding regions with regulated genes shown in Table 1. Just 157 binding regions were associated with regulated genes in both cell lines . Examples of binding peaks detected exclusively in one cell line or common to both are shown in Figure S6. Directed ChIP confirmed the differential patterns of PR binding to genes regulated in AB32, T- 47D or both cell lines . Moreover, direct examination of the overlap between PR binding in T-47D and AB32 cells with another PR cistrome in T-47D cells revealed a markedly higher overlap in binding regions between the two T-47D data sets than to the AB32 PR data set . The lack of overlap in binding sites between the two cell lines was reflected in a similarly low overlap in transcriptional profiles at 2, 6 and 24 h of progestin treatment . The small overlap in progestin targets in the two cell lines was similar at all time points examined . This lack of overlap was confirmed in two additional cell lines, ZR-75-1 breast cancer cells and an additional PR+MCF-10A clone, AB9, which revealed a similarly low overlap of progestin response when compared directly with each other or with the T-47D or AB32 cells. These categories included genes such as transforming growth factor b3, CD44 and basic fibroblast growth factor, suggesting a broader developmental function. Surprisingly, a large proportion of transcripts that were regulated when FOXA1 was not present , lost regulation upon expression of the pioneer factor and were evident in multiple clusters . Functional analysis revealed a major impact of FOXA1 expression on genes involved in negative regulation of apoptosis: these had been increased by progestins in absence of FOXA1, but lost progestin responsiveness when FOXA1 was expressed . Genes in this category that were decreased by progestin were unchanged by FOXA1 expression, suggesting that the net Torin 1 mTOR inhibitor effect of FOXA1 was to promote apoptosis in response to progestin. The dampening effect of FOXA1 expression on progestin regulation suggested that the pioneer factor may play a dual role in PR action, similar to its role in androgen receptor signalling where it acts as an activator on a subset of androgen targets and a corepressor on others . The progestin regulation of just 168 transcripts was unaffected by changed FOXA1 levels .