Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.

中文翻译：

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Argonaute 在人核 RNA 中的结合及其对可变剪接的影响

哺乳动物 RNA 干扰 (RNAi) 通常与细胞质中基因表达的调节有关。然而，合成的 RNA 也可以通过 RNAi 途径调节转录和剪接。虽然合成 RNA 的核调节可能很稳健，但一个尚未解决的关键问题是哺乳动物细胞中是否存在核 RNAi 的内源性功能。使用增强交联免疫沉淀 (eCLIP) 结合 RNA 测序 (RNA-seq) 和多个AGO敲除细胞系后，我们绘制了核 RNA 内的 AGO2 蛋白结合位点。最强的 AGO2 结合位点被映射到微 RNA (miRNA)。最丰富的 miRNA 在细胞质和细胞核之间的分布相似，没有提供任何证据证明 miRNA 在一个区室与另一个区室中的定位机制。除了 miRNA，最具统计学意义的 AGO2 结合在内含子内。剪接变化由 RT-PCR 证实，并由与 AGO2 结合位点互补的合成 miRNA 模拟物概括。这些数据支持 miRNA 可以控制基因剪接的假设。虽然核 RNAi 蛋白有可能成为自然调节机制，但仍需要仔细研究以确定正常生理和疾病的关键 RNA 驱动因素。