Chemical modifications of RNA nucleotides change their identity and characteristics and thus alter genetic and structural information encoded in the genomic DNA. tRNA and rRNA are probably the most heavily modified genes, and often depend on derivatization or isomerization of their nucleobases in order to correctly fold into their functional structures. Recent RNomics studies, however, report transcriptome wide RNA modification and suggest a more general regulation of structuredness of RNAs by this so called epitranscriptome. Modification seems to require specific substrate structures, which in turn are stabilized or destabilized and thus promote or inhibit refolding events of regulatory RNA structures. In this review, we revisit RNA modifications and the related structures from a computational point of view. We discuss known substrate structures, their properties such as sub-motifs as well as consequences of modifications on base pairing patterns and possible refolding events. Given that efficient RNA structure prediction methods for canonical base pairs have been established several decades ago, we review to what extend these methods allow the inclusion of modified nucleotides to model and study epitranscriptomic effects on RNA structures.

中文翻译：

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结构预测中的 RNA 修饰——现状和未来挑战

RNA 核苷酸的化学修饰改变了它们的身份和特征，从而改变了基因组 DNA 中编码的遗传和结构信息。tRNA 和 rRNA 可能是修饰最严重的基因，并且通常依赖于其核碱基的衍生化或异构化，以便正确折叠成其功能结构。然而，最近的 RNomics 研究报告了转录组范围内的 RNA 修饰，并建议通过这种所谓的表观转录组对 RNA 的结构进行更一般的调节。修饰似乎需要特定的底物结构，这些结构反过来稳定或不稳定，从而促进或抑制调节性 RNA 结构的重折叠事件。在这篇综述中，我们从计算的角度重新审视了 RNA 修饰和相关结构。我们讨论已知的衬底结构，它们的特性，例如子基序以及对碱基配对模式和可能的重折叠事件进行修改的结果。鉴于经典碱基对的有效 RNA 结构预测方法已经在几十年前建立，我们回顾了这些方法在多大程度上允许包含修饰的核苷酸来模拟和研究对 RNA 结构的表观转录组学影响。