MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Argonaute [Ago]-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3′ UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122-dependent binding revealed a G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma.

MicroRNA-122 是一种丰富且保守的肝脏特异性 miRNA，可调节肝脏代谢并发挥肿瘤抑制因子的作用，但对 miR-122 靶网络的系统和直接生化阐明仍然不完整。为此，我们在 miR-122 敲除和对照小鼠肝脏以及匹配的人肝细胞癌 (HCC) 和良性肝组织中进行了 Argonaute 交联免疫沉淀 (Argonaute [Ago]-CLIP) 测序，以鉴定 miRNA 靶位点转录组。广泛分两种。我们观察到大部分 miR-122 结合在 3' UTR 和编码外显子上，然后广泛结合到其他基因和非基因位点。对 miR-122 依赖性结合的基序分析揭示了除了典型基序之外还有 G 凸出基序。大量 miR-122 靶标被发现具有物种特异性。几种常见的小鼠和人类靶标（尤其是 BCL9）的上调可预测 HCC 患者的生存。这些结果广泛定义了肝细胞癌中 miR-122 下调的分子后果。