MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in disease such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin primary microRNAs are challenging to study in clinical samples where input material is limited. Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA that requires relatively few RNA sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma. We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease. With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.

中文翻译：

---

通过靶向 pri-miR 测序确定临床样本中的初级 microRNA 加工

MicroRNA 表达对于基因调控很重要，并且经常在癌症等疾病中观察到失调的 microRNA 表达。初级 microRNA 转录本的加工是 microRNA 生物发生的重要调控步骤。由于低表达水平和与染色质初级 microRNA 的关联，在输入材料有限的临床样本中进行研究具有挑战性。在这里，我们提出了一种高灵敏度的靶向方法，可以从需要相对较少的 RNA 测序读取的总 RNA 中确定数百个初级 microRNA 的处理效率。我们使用来自 HeLa 细胞的 RNA 验证了该方法，并通过分析来自正常肝脏和肝细胞癌的 RNA 显示了对临床样本的适用性。我们鉴定了从正常肝脏到肝细胞癌的加工效率显着变化的 24 种初级 microRNA，其中高度表达的 miRNA-122 和 miRNA-21，表明初级 microRNA 的差异加工正在发生并且可能与疾病有关。通过我们在此介绍的方法，我们提供了从临床样本中研究疾病中 pri-miRNA 加工的方法。