RNA. 2013 Nov;19(11):1461-73. doi: 10.1261/rna.037390.112.
The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.
基因的表达，无论是编码还是非编码，都可以被其相应转录物的 RNA 结构特征显著影响。现在有越来越多的实验和一些理论证据表明，体内结构的形成始于转录过程中，这种共转录折叠决定了正在形成的功能性 RNA 结构特征。几十年来的生物信息学研究已经产生了广泛的计算方法来预测 RNA 二级结构。然而，几乎所有在预测准确性方面处于领先地位的方法完全忽略了结构形成的过程，而只专注于最终的 RNA 结构。这篇综述旨在弥补这一空白。我们总结了共转录折叠的现有证据，然后回顾了不同的、目前用于 RNA 二级结构预测的策略。最后，我们提出了一系列想法，即如何通过显式捕捉共转录结构形成过程，从而潜在地改进最先进的方法。
