Global Analysis of RNA Secondary Structure in Two Metazoans
Global Analysis of RNA Secondary Structure in Two Metazoans
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DOI：
10.1016/j.celrep.2011.10.002
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发表时间：
2012-01-01
期刊：
影响因子：
8.8
通讯作者：
Gregory, Brian D.
中科院分区：
文献类型：
--
作者：
Li, Fan;Zheng, Qi;Gregory, Brian D.
RNA 的二级结构是其成熟、调节、加工和功能所必需的。然而，真核生物中RNA折叠的整体影响仍不清楚。在这里，我们使用高通量、基于测序的结构作图方法来识别果蝇和秀丽隐杆线虫转录组的配对（双链 RNA [dsRNA]）和未配对（单链 RNA [ssRNA]）成分，这使我们能够识别后生动物中 RNA 二级结构的保守特征。从这个分析中，我们发现 ssRNA 和 dsRNA 与特定的表观遗传修饰显着相关。此外，我们发现蛋白质编码转录本的关键结构模式表明，RNA 折叠划分了蛋白质翻译区域，并可能影响动物体内 microRNA 介导的 mRNA 调节。最后，我们鉴定并表征了 546 个 mRNA，其折叠模式在这些后生动物之间显着相关，表明它们的结构具有某些功能。总的来说，我们的研究结果提供了对动物 RNA 折叠的全面评估。
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.