Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Mol Cell Proteomics. 2013 Jul;12(7):1900-11. doi: 10.1074/mcp.M112.025783. Epub 2013 Apr 2.
MicroRNAs (miRNAs) are key post-transcriptional regulators that inhibit gene expression by promoting mRNA decay and/or suppressing translation. However, the relative contributions of these two mechanisms to gene repression remain controversial. Early studies favor a translational repression-centric scenario, whereas recent large-scale studies suggest a dominant role of mRNA decay in miRNA regulation. Here we generated proteomics data for nine colorectal cancer cell lines and integrated them with matched miRNA and mRNA expression data to infer and characterize miRNA-mediated regulation. Consistent with previous reports, we found that 8mer site, site positioning within 3'UTR, local AU-rich context, and additional 3' pairing could all help boost miRNA-mediated mRNA decay. However, these sequence features were generally not correlated with increased translational repression, except for local AU-rich context. Thus the contribution of translational repression might be underestimated in recent studies in which the analyses were based primarily on the response of genes with canonical 7-8 mer sites in 3'UTRs. Indeed, we found that translational repression was involved in more than half, and played a major role in one-third of all predicted miRNA-target interactions. It was even the predominant contributor to miR-138 mediated regulation, which was further supported by the observation that differential expression of miR-138 in two genetically matched cell lines corresponded to altered protein but not mRNA abundance of most target genes. In addition, our study also provided interesting insights into colon cancer biology such as the possible contributions of miR-138 and miR-141/miR-200c in inducing specific phenotypes of SW480 and RKO cell lines, respectively.
微小 RNA（miRNA）是关键的转录后调控因子，通过促进 mRNA 降解和/或抑制翻译来抑制基因表达。然而，这两种机制对基因抑制的相对贡献仍存在争议。早期的研究倾向于以翻译抑制为中心的情景，而最近的大规模研究表明 mRNA 降解在 miRNA 调控中起主导作用。在这里，我们生成了 9 种结直肠癌细胞系的蛋白质组学数据，并将其与匹配的 miRNA 和 mRNA 表达数据进行了整合，以推断和描述 miRNA 介导的调控。与之前的报道一致，我们发现 8mer 位点、3'UTR 内的位点定位、局部 AU 丰富的上下文和额外的 3'配对都可以帮助促进 miRNA 介导的 mRNA 降解。然而，这些序列特征通常与增加的翻译抑制无关，除了局部 AU 丰富的上下文。因此，在最近的研究中，翻译抑制的贡献可能被低估了，这些研究主要基于对具有典型 3'UTR 7-8mer 位点的基因的分析。事实上，我们发现翻译抑制参与了超过一半的预测 miRNA 靶标相互作用，并且在三分之一的预测 miRNA 靶标相互作用中起主要作用。这甚至是 miR-138 介导调控的主要贡献者，这进一步得到了观察的支持，即两种遗传匹配的细胞系中 miR-138 的差异表达与大多数靶基因的蛋白质而不是 mRNA 丰度的改变相对应。此外，我们的研究还为结肠癌生物学提供了有趣的见解，例如 miR-138 和 miR-141/miR-200c 分别在诱导 SW480 和 RKO 细胞系特定表型中的可能贡献。
