Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
Gene. 2014 Jan 10;533(2):520-31. doi: 10.1016/j.gene.2013.08.005. Epub 2013 Aug 9.
MicroRNAs (miRNAs) are small non-coding RNAs mediating the regulation of gene expression in various biological contexts, including carcinogenesis. Here, we screened putative associations between 34, 45, and 103 miRNAs and 164, 391, and 81 mRNAs via Argonaute1 (Ago1) or Ago2 immunoprecipitation (IP) experiments in a colon cancer cell line. We used a combination of RIP Seq analysis. RNAs that were co-immunoprecipitated with Ago1 or Ago2 were used for massively parallel small RNA and mRNA sequencing. The detected miRNAs and mRNAs were further associated with one another based on in silico target predictions. Analysis of the putative associations indicated that, although Ago1 and Ago2 shared a similar repertory of miRNAs, the mRNAs possibly regulated by those miRNAs seemed different. The mRNAs detected with Ago1 IP were indicated to be frequently associated with genes having constitutive cellular functions, regulated by a smaller number of miRNAs, and appeared to receive more stringent translational regulation. In contrast, putative miRNA-mRNA associations detected with Ago2 IP appeared to be related to signal transduction genes, which had a larger number of possible miRNA binding sites. We then conducted a similar analysis using the colon cancer cells cultured under hypoxia and identified potential hypoxia-induced miRNA-mRNA associations, which included several well-characterized cancer-related genes as novel putative miRNA targets.
微小 RNA（miRNAs）是一种小的非编码 RNA，在包括癌症发生在内的各种生物背景下调节基因表达。在这里，我们通过 Argonaute1（Ago1）或 Ago2 免疫沉淀（IP）实验在结肠癌细胞系中筛选了 34、45 和 103 个 miRNAs 与 164、391 和 81 个 mRNAs 之间的可能关联。我们使用了 RIP Seq 分析的组合。与 Ago1 或 Ago2 共沉淀的 RNA 用于大规模平行的小 RNA 和 mRNA 测序。根据计算机目标预测进一步将检测到的 miRNAs 和 mRNAs 彼此关联。对可能的关联的分析表明，尽管 Ago1 和 Ago2 共享相似的 miRNA 谱，但那些 miRNA 可能调节的 mRNAs 似乎不同。用 Ago1 IP 检测到的 mRNAs 被指示与具有组成性细胞功能的基因频繁相关，受较少数量的 miRNAs 调节，并且似乎受到更严格的翻译调控。相比之下，用 Ago2 IP 检测到的可能的 miRNA-mRNA 关联似乎与信号转导基因有关，这些基因具有更多可能的 miRNA 结合位点。然后，我们使用在低氧条件下培养的结肠癌细胞进行了类似的分析，并确定了潜在的低氧诱导的 miRNA-mRNA 关联，其中包括几个作为新型潜在 miRNA 靶标的众所周知的癌症相关基因。
