Ballare, CeciliaCastellano, GiancarloGaveglia, LauraAlthammer, SonjaGonzalez-Vallinas, JuanEyras, EduardoLe Dily, FrancoisZaurin, RoserSoronellas, DanielVicent, Guillermo P.Beato, Miguel2025-12-192025-12-191097-2765WOS:000313607300008PubMed:23177737ORCID:/0000-0003-0793-6218/work/162948923https://hdl.handle.net/1885/733796714Elucidating the global function of a transcription factor implies the identification of its target genes and genomic binding sites. The role of chromatin in this context is unclear, but the dominant view is that factors bind preferentially to nucleosome-depleted regions identified as DNasel-hypersensitive sites (DHS). Here we show by ChIP, MNase, and DNasel assays followed by deep sequencing that the progesterone receptor (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 of these sites encompassed several copies of the hexanucleotide TGTYCY, which is highly abundant in the genome. We found that functional PRbs accumulate around progesterone-induced genes, mainly in enhancers. Most of these sites overlap with 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 are crucial for PR binding and hormonal gene regulation.We thank Stefan Dimitrov, Grenoble, for the histone antibodies; Heinz Himmelbauer and the CRG Ultrasequencing Facility for help in establishing various sequencing protocols; and Fatima Gebauer, Luciano Di Croce, Juan Valcarcel, and members of the Chromatin and Gene Expression group for help with the manuscript. The experimental work was supported by grants from the Spanish government (BMC 2003-02902 and 2010-15313; CSD2006-00049), the European Union (IP HEROIC), and the Catalan government (AGAUR). L.G. was a recipient of a fellowship from the International PhD program of LaCaixa; G.P.V. was a recipient of a fellowship from the Ramon y Cajal program. We thank the ENCODE Project Consortium for making their data publicly available.13enGlucocorticoid-receptor-bindingTumor virus promoterPredictive chromatin signaturesProgesterone-receptorEstrogen-receptorAndrogen receptorChip-seqIn-vivoNuclear factor-1Prostate-cancer2013-01-1010.1016/j.molcel.2012.10.01984872269321