Over the past few years, genomic approaches have supported and expanded the concept of cooperation of hormone or signal-dependent transcription factors, such as nuclear receptors, and cell-type specific factors, in ensuring that hormone dependent gene activation occurs only in the intended cell type. As discussed below, the FoxA factors play a major role in gene activation by the glucocorticoid, androgen, and estrogen receptors.
Almost twenty years ago, Schütz and colleagues asked the question why the activation of gluconeogenic genes by glucocorticoids in response to fasting occurs only in liver and kidney, even though the glucocorticoid receptor (GR) is expressed and the ligand distributed ubiquitously. Through molecular analysis of the cis
-regulatory elements of a fasting-activated gene, tyrosine aminotransferase
), they developed the model that cell-type specific activation of the gene was achieved through juxtaposition of binding sites for FoxA and GR [40
]. They showed that mutation of the FoxA binding site in a promoter-reporter construct severely attenuated gene activation by glucocorticoids. A similar situation was shown to exist for another fasting-activated gene, Pck1
, by Daryl Granner’s group [41
However, because these studies only mutated binding sites, they could not prove that in fact FoxA factors mediate this effect, as the same sites are also bound by other winged helix proteins, chiefly of the FoxO class, activity of which is regulated by insulin signaling [44
]. Indeed, Foxo1
is required for full activation of gluconeogenic genes. However, conditional gene ablation of Foxa2
in the liver demonstrated that this factor regulates the expression of the fasting-induced genes Tat
, and Igfbp1 in vivo
. Furthermore, Zhang and colleagues showed by chromatin immunoprecipitation that GR binding to its targets in vivo
is indeed Foxa2
]. Interestingly, the targets regulated by FoxA2 in the liver depend on the physiological state of the organism, as shown by genome-wide location analysis [45
]. Thus, when mice are exposed to high cholic acid levels, the genes regulated by FoxA2 are different than those controlled in the chow-fed situation. Thus, gene regulation by FoxA2 is context-dependent.
An analogous relationship exists between FoxA1 and the sex hormone receptors, AR (androgen receptor) and ER (estrogen receptor). Matusik and colleagues, while studying the regulation of prostate-specific gene expression, discovered that AR activation depended on the presence of FoxA1 at nearby binding sites for several genes, thus establishing this new paradigm [46
]. These findings were recently extended to the genome-wide level by ChIP-on-Chip experiments, demonstrating that this cooperation between FoxA1 and AR is a wide-spread phenomenon [34
In fact, this close relationship of nuclear receptors and FoxA factors appears to be a general principle (). Brown and colleagues, determining the binding sites of the estrogen receptor to three chromosomes in human breast cancer cell lines, made the striking discovery using computational tools that ER binding sites are very frequently paired with FoxA sites [47
]. In fact, when FoxA1 expression was suppressed by shRNA, ER-mediated gene activation was blunted. Similar conclusions were reached independently by Giguere and colleagues [48
]. A very recent genetic study proved that Foxa1
is indispensable for mammary gland development, specifically the estrogen-induced mammary duct expansion [49
]. So how does Foxa1 serve two masters, ER and AR in a cell-type specific fashion? Brown and colleagues have begun to address this question, comparing FoxA1 occupancy in breast and prostate cancer cell lines. They found only partial overlap between the two sets of binding sites, suggesting again that there is no universal set of FoxA binding sites [34
]. Overall it is clear, however, that the FoxA factors have greatly expanded their range of action by cooperation with nuclear receptors in conditional gene activation.
Figure 2 Coordinate gene regulation by Foxa factors and nuclear receptors. Depending on the cell type, Foxa1 and/or Foxa2 facilitate binding of the androgen receptor (AR), estrogen receptor (ER) and glucocorticoid receptor (GR). Foxa1 also activates expression (more ...)