Nucleosome-Driven Transcription Factor Binding and Gene Regulation
Nucleosome-Driven Transcription Factor Binding and Gene Regulation
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DOI：
10.1016/j.molcel.2012.10.019
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发表时间：
2013-01-10
期刊：
影响因子：
16
通讯作者：
Beato, Miguel
中科院分区：
文献类型：
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作者：
Ballare, Cecilia;Castellano, Giancarlo;Beato, Miguel
阐明转录因子的整体功能意味着识别其靶基因和基因组结合位点。染色质在此背景下的作用尚不清楚，但占主导地位的观点是，因子优先结合到被鉴定为DNA酶1超敏位点（DHS）的核小体耗尽区域。在这里，我们通过ChIP，MNase和DNase 1检测，然后进行深度测序，表明孕酮受体（PR）需要核小体才能实现最佳结合和功能。在用孕激素治疗的乳腺癌细胞中，我们确定了25，000个PR结合位点（PRbs）。这些位点中的大多数包含六核苷酸TGTYCY的几个拷贝，其在基因组中高度丰富。我们发现，功能PRBs积累周围的甾醇诱导的基因，主要是在增强子。这些位点中的大多数与DHS重叠，但表现出高的核小体占有率。孕激素刺激导致这些核小体的重塑，组蛋白H1和H2 A/H2 B二聚体的位移。我们的研究结果强烈表明，核小体是至关重要的PR结合和激素基因调控。
Elucidating 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.