Institut National de la Sante et de la Recherche Medicale, U590, Centre Léon Bérard, Lyon, France.
Cancer Res. 2010 May 1;70(9):3760-70. doi: 10.1158/0008-5472.CAN-09-3988. Epub 2010 Apr 20.
Alternative promoters (AP) occur in >30% protein-coding genes and contribute to proteome diversity. However, large-scale analyses of AP regulation are lacking, and little is known about their potential physiopathologic significance. To better understand the transcriptomic effect of estrogens, which play a major role in breast cancer, we analyzed gene and AP regulation by estradiol in MCF7 cells using pan-genomic exon arrays. We thereby identified novel estrogen-regulated genes (ERG) and determined the regulation of AP-encoded transcripts in 150 regulated genes. In <30% cases, APs were regulated in a similar manner by estradiol, whereas in >70% cases, they were regulated differentially. The patterns of AP regulation correlated with the patterns of estrogen receptor alpha (ERalpha) and CCCTC-binding factor (CTCF) binding sites at regulated gene loci. Interestingly, among genes with differentially regulated (DR) APs, we identified cases where estradiol regulated APs in an opposite manner, sometimes without affecting global gene expression levels. This promoter switch was mediated by the DDX5/DDX17 family of ERalpha coregulators. Finally, genes with DR promoters were preferentially involved in specific processes (e.g., cell structure and motility, and cell cycle). We show, in particular, that isoforms encoded by the NET1 gene APs, which are inversely regulated by estradiol, play distinct roles in cell adhesion and cell cycle regulation and that their expression is differentially associated with prognosis in ER(+) breast cancer. Altogether, this study identifies the patterns of AP regulation in ERGs and shows the contribution of AP-encoded isoforms to the estradiol-regulated transcriptome as well as their physiopathologic significance in breast cancer.
替代启动子 (AP) 存在于超过 30%的蛋白质编码基因中，有助于蛋白质组的多样性。然而，目前缺乏对 AP 调控的大规模分析，对其潜在的生理病理意义也知之甚少。为了更好地了解雌激素在乳腺癌中发挥主要作用的转录组效应，我们使用泛基因组外显子芯片分析了雌二醇对 MCF7 细胞中基因和 AP 调控的影响。我们因此鉴定了新的雌激素调控基因 (ERG)，并确定了 150 个调控基因中 AP 编码转录本的调控情况。在不到 30%的情况下，AP 受到雌二醇的相似调控，而在超过 70%的情况下，它们受到不同的调控。AP 调控的模式与受调控基因座上雌激素受体 α (ERα)和 CCCTC 结合因子 (CTCF) 结合位点的模式相关。有趣的是，在具有差异调控 (DR) AP 的基因中，我们发现了一些情况，其中雌二醇以相反的方式调控 AP，有时不影响全局基因表达水平。这种启动子切换是由 ERα核心调节因子 DDX5/DDX17 家族介导的。最后，具有 DR 启动子的基因优先参与特定的过程（例如，细胞结构和运动，以及细胞周期）。我们特别表明，NET1 基因 AP 编码的异构体，其受雌二醇的反向调控，在细胞黏附和细胞周期调控中发挥不同的作用，其表达与 ER(+)乳腺癌的预后差异相关。总的来说，本研究确定了 ERG 中 AP 调控的模式，并显示了 AP 编码的异构体对雌二醇调控转录组的贡献及其在乳腺癌中的生理病理意义。
