More help than hindrance: nucleosomes aid transcriptional regulation

A major challenge of modern human biology is to understand how a differentiated somatic cell integrates the response to external signals in the complex context of basic metabolic and tissue-specific gene expression programs. This requires exploring two interconnected basic processes: the signaling network and the global function of the key transcription factors on which signaling acts to modulate gene expression. An apparently simple model to study these questions has been steroid hormones action, since their intracellular receptors both initiate signaling and are the key transcription factors orchestrating the cellular response. We have used progesterone action in breast cancer cells to elucidate the intricacies of progesterone receptor (PR) signaling crosstalk with protein kinases, histone modifying enzymes and ATP-dependent chromatin remodeling complexes. ( 1) Recently we have described the cistrome of PR in these cells at different times after addition of hormone and its relationship to chromatin structure. ( 2) The role of chromatin in transcription factor binding to the genome is still debated, but the dominant view is that factors bind preferentially to nucleosome-depleted regions, usually identified as DNaseI-hypersensitive sites (DHS). In contrast with this vision, we have shown that PR requires nucleosomes for optimal binding and function. In breast cancer cells treated with progestins we identified 25,000 PR binding sites (PRbs), the majority encompassing several copies of the hexanucleotide TGTYCY, highly abundant in the genome. We found that strong functional PRbs accumulate around progesterone-induced genes mainly in enhancers, are enriched in DHS but exhibit high nucleosome occupancy. Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes play crucial role in PR binding and hormonal gene regulation.