Kininis Miltiadis, Chen Benjamin S, Diehl Adam G, Isaacs Gary D, Zhang Tong, Siepel Adam C, Clark Andrew G, Kraus W Lee
Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, USA.
Mol Cell Biol. 2007 Jul;27(14):5090-104. doi: 10.1128/MCB.00083-07. Epub 2007 May 21.
To explore the global mechanisms of estrogen-regulated transcription, we used chromatin immunoprecipitation coupled with DNA microarrays to determine the localization of RNA polymerase II (Pol II), estrogen receptor alpha (ERalpha), steroid receptor coactivator proteins (SRC), and acetylated histones H3/H4 (AcH) at estrogen-regulated promoters in MCF-7 cells with or without estradiol (E2) treatment. In addition, we correlated factor occupancy with gene expression and the presence of transcription factor binding elements. Using this integrative approach, we defined a set of 58 direct E2 target genes based on E2-regulated Pol II occupancy and classified their promoters based on factor binding, histone modification, and transcriptional output. Many of these direct E2 target genes exhibit interesting modes of regulation and biological activities, some of which may be relevant to the onset and proliferation of breast cancers. Our studies indicate that about one-third of these direct E2 target genes contain promoter-proximal ERalpha-binding sites, which is considerably more than previous estimates. Some of these genes represent possible novel targets for regulation through the ERalpha/AP-1 tethering pathway. Our studies have also revealed several previously uncharacterized global features of E2-regulated gene expression, including strong positive correlations between Pol II occupancy and AcH levels, as well as between the E2-dependent recruitment of ERalpha and SRC at the promoters of E2-stimulated genes. Furthermore, our studies have revealed new mechanistic insights into E2-regulated gene expression, including the absence of SRC binding at E2-repressed genes and the presence of constitutively bound, promoter-proximally paused Pol IIs at some E2-regulated promoters. These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors.
为了探究雌激素调节转录的整体机制，我们运用染色质免疫沉淀结合DNA微阵列技术，来确定RNA聚合酶II（Pol II）、雌激素受体α（ERα）、类固醇受体辅激活蛋白（SRC）以及乙酰化组蛋白H3/H4（AcH）在经或未经雌二醇（E2）处理的MCF-7细胞中雌激素调节启动子上的定位。此外，我们将因子占据情况与基因表达以及转录因子结合元件的存在情况进行了关联分析。通过这种综合方法，我们基于E2调节的Pol II占据情况定义了一组58个直接E2靶基因，并根据因子结合、组蛋白修饰和转录输出对其启动子进行了分类。这些直接E2靶基因中的许多都表现出有趣的调节模式和生物学活性，其中一些可能与乳腺癌的发生和增殖有关。我们的研究表明，这些直接E2靶基因中约三分之一含有启动子近端ERα结合位点，这一比例远高于先前的估计。其中一些基因代表了通过ERα/AP-1拴系途径进行调节的可能新靶点。我们的研究还揭示了一些先前未被描述的E2调节基因表达的整体特征，包括Pol II占据情况与AcH水平之间以及E2刺激基因启动子处E2依赖性ERα和SRC募集之间的强正相关。此外，我们的研究揭示了关于E2调节基因表达的新机制见解，包括E2抑制基因处不存在SRC结合以及一些E2调节启动子处存在组成性结合、启动子近端暂停的Pol II。这些机制见解可能与理解多种核受体的基因调节相关。
