Long non-coding RNAs (lncRNAs) can affect multiple layers of gene expression to control crucial cellular functions. We have previously demonstrated that the lncRNA EPR, by controlling gene expression at different levels, affects cell proliferation and migration in cultured mammary gland cells and impairs breast tumor formation in an orthotopic transplant model in mice. Here, we used ChIRP-Seq to identify EPR binding sites on chromatin of NMuMG mammary gland cells overexpressing EPR and identified its trans binding sites in the genome. Then, with the purpose of relating EPR/chromatin interactions to the reshaping of the epitranscriptome landscape, we profiled histone activation marks at promoter/enhancer regions by ChIP-Seq. Finally, we integrated data derived from ChIRP-Seq, ChIP-Seq as well as RNA-Seq in a comprehensive analysis and we selected a group of bona fide direct transcriptional targets of EPR. Among them, we identified a subset of EPR targets whose expression is controlled by TGF-β with one of them—Arrdc3—being able to modulate Epithelial to Mesenchymal Transition. This experimental framework allowed us to correlate lncRNA/chromatin interactions with the real outcome of gene expression and to start defining the gene network regulated by EPR as a component of the TGF-β pathway.

中文翻译：

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全面的多组学分析发现了lncRNA EPR直接转录靶标中的一组TGF-β调控基因。

长的非编码RNA（lncRNA）可以影响多层基因表达，以控制关键的细胞功能。我们以前已经证明，lncRNA EPR通过控制不同水平的基因表达来影响培养的乳腺细胞中的细胞增殖和迁移，并损害小鼠原位移植模型中的乳腺肿瘤形成。在这里，我们使用ChIRP-Seq识别过表达EPR的NMuMG乳腺细胞染色质上的EPR结合位点，并确定其在基因组中的反式结合位点。然后，为了使EPR /染色质相互作用与表观转录组景观的重塑相关，我们通过ChIP-Seq在启动子/增强子区域分析了组蛋白活化标记。最后，我们整合了来自ChIRP-Seq的数据，真正的EPR直接转录靶标。其中，我们鉴定了EPR靶标的子集，其表达受TGF-β控制，其中一个Arrdc3能够调节上皮向间质转化。该实验框架使我们能够将lncRNA /染色质相互作用与基因表达的真实结果相关联，并开始定义由EPR调控的基因网络，作为TGF-β途径的组成部分。