Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
J Proteomics. 2019 Feb 20;193:173-183. doi: 10.1016/j.jprot.2018.10.007. Epub 2018 Oct 16.
Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules such as miRNAs or siRNAs, also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-specific and depends on internal and external stimuli. Unfortunately, the mechanisms underlying RF biogenesis and function remain unclear. To better understand them, we employed RNA pull-down and mass spectrometry methods to characterize the interactions of seven RFs originating from tRNA, snoRNA and snRNA. By integrating our results with publicly available data on physical protein-protein interactions, we constructed an RF interactome network. We determined that the RF interactome comprises proteins generally different from those that interact with their parental full length RNAs. Proteins captured by the RFs were involved in mRNA splicing, tRNA processing, DNA recombination/replication, protein biosynthesis and carboxylic acid metabolism. Our data suggest that RFs can be endogenous aptamer-like molecules and potential players in recently revealed RNA-protein regulatory networks. SIGNIFICANCE: In the recent decade it has become evident that RNAs with well-known functions (for example tRNA, snoRNA or rRNA) can be cleaved to yield short fragments, whose role in cells remains only partially characterized. At the same time, unconventional interactions between mRNA and proteins without RNA-binding domains have been demonstrated, revealing novel layers of possible RNA-mediated regulation. Considering the above, we hypothesized that RNA fragments (RFs) can be endogenous aptamer-like molecules that unconventionally interact with proteins. In this study we identified protein partners of seven selected RFs. We found that RFs bind different set of proteins than their parental full length RNAs and identified proteins differentially bound by the particular RFs. These observations suggest biological relevance of the discovered interactions. Our data provide a novel perspective on the significance of RFs and point to this pool of molecules as to a rich collection of potential components of the recently discovered RNA-protein regulatory networks.
除了相对公认的分子，如 miRNA 或 siRNA 之外，小真核 RNA 群体还包含来自所有类型组成型表达的非编码 RNA 的片段。最近已经证明，RNA 片段 (RFs) 的形成和积累是细胞/组织特异性的，并且取决于内部和外部刺激。不幸的是，RF 生物发生和功能的机制仍不清楚。为了更好地理解它们，我们使用 RNA 下拉和质谱方法来表征来自 tRNA、snoRNA 和 snRNA 的七种 RF 的相互作用。通过将我们的结果与关于物理蛋白质-蛋白质相互作用的公开可用数据集成，我们构建了一个 RF 相互作用网络。我们确定 RF 相互作用组由与它们的全长 RNA 相互作用的蛋白质通常不同的蛋白质组成。被 RF 捕获的蛋白质参与 mRNA 剪接、tRNA 加工、DNA 重组/复制、蛋白质生物合成和羧酸代谢。我们的数据表明，RFs 可以是内源性适体样分子，并且是最近揭示的 RNA-蛋白质调节网络中的潜在参与者。意义：在最近的十年中，已经很明显，具有已知功能的 RNA（例如 tRNA、snoRNA 或 rRNA）可以被切割产生短片段，其在细胞中的作用仅部分得到表征。同时，已经证明了没有 RNA 结合结构域的 mRNA 和蛋白质之间的非常规相互作用，揭示了可能的 RNA 介导调节的新层次。考虑到上述情况，我们假设 RNA 片段 (RFs) 可以是内源性适体样分子，它们与蛋白质的非常规相互作用。在这项研究中，我们鉴定了七个选定 RF 的蛋白质伙伴。我们发现 RF 与它们的全长 RNA 结合不同的蛋白质组，并且鉴定了由特定 RF 差异结合的蛋白质。这些观察结果表明所发现的相互作用具有生物学意义。我们的数据为 RFs 的重要性提供了新的视角，并指出这一组分子是最近发现的 RNA-蛋白质调节网络中潜在成分的丰富来源。
