Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Cell Rep. 2012 Jan 26;1(1):69-82. doi: 10.1016/j.celrep.2011.10.002.
The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.
RNA 的二级结构对于其成熟、调控、加工和功能至关重要。然而，真核生物中 RNA 折叠的全局影响仍不清楚。在这里，我们使用一种高通量、基于测序、结构映射的方法来鉴定果蝇和秀丽隐杆线虫转录组的配对（双链 RNA [dsRNA]）和非配对（单链 RNA [ssRNA]）成分，这使我们能够鉴定后生动物 RNA 二级结构的保守特征。通过这项分析，我们发现 ssRNAs 和 dsRNAs 与特定的表观遗传修饰显著相关。此外，我们在蛋白质编码转录本中发现了关键的结构模式，表明 RNA 折叠划定了蛋白质翻译的区域，并可能影响动物中 miRNA 对 mRNAs 的调控。最后，我们鉴定并描述了 546 个 mRNAs，它们在这些后生动物之间的折叠模式显著相关，这表明它们的结构具有一定的功能。总的来说，我们的研究结果提供了对动物中 RNA 折叠的全面评估。
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