Terasaka Naohiro, Futai Kazuki, Katoh Takayuki, Suga Hiroaki
Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
JST, CREST, The University of Tokyo, Tokyo 113-0033, Japan.
RNA. 2016 Dec;22(12):1918-1928. doi: 10.1261/rna.057737.116. Epub 2016 Oct 21.
RNA aptamers are structured motifs that bind to specific molecules. A growing number of RNAs bearing aptamer elements, whose functions are modulated by direct binding of metabolites, have been found in living cells. Recent studies have suggested that more small RNAs binding to metabolites likely exist and may be involved in diverse cellular processes. However, conventional methods are not necessarily suitable for the discovery of such RNA aptamer elements in small RNAs with lengths ranging from 50 to 200 nucleotides, due to the far more abundant tRNAs in this size range. Here, we describe a new in vitro selection method to uncover naturally occurring small RNAs capable of binding to a ligand of interest, referred to as small RNA transcriptomic SELEX (smaRt-SELEX). By means of this method, we identified a motif in human precursor microRNA 125a (hsa-pre-miR-125a) that interacts with folic acid. Mutation studies revealed that the terminal loop region of hsa-pre-miR-125a is important for this binding interaction. This method has potential for the discovery of new RNA aptamer elements or catalytic motifs in biological small RNA fractions.
RNA适体是与特定分子结合的结构化基序。在活细胞中发现了越来越多带有适体元件的RNA，其功能受代谢物直接结合的调节。最近的研究表明，可能存在更多与代谢物结合的小RNA，并且它们可能参与多种细胞过程。然而，由于在这个长度范围（50至200个核苷酸）内tRNA的数量要多得多，传统方法不一定适用于发现此类小RNA中的RNA适体元件。在此，我们描述了一种新的体外筛选方法，以发现能够与感兴趣的配体结合的天然存在的小RNA，称为小RNA转录组SELEX（smaRt-SELEX）。通过这种方法，我们在人源前体微小RNA 125a（hsa-pre-miR-125a）中鉴定出一个与叶酸相互作用的基序。突变研究表明，hsa-pre-miR-125a的末端环区域对于这种结合相互作用很重要。该方法具有发现生物小RNA组分中新的RNA适体元件或催化基序的潜力。
