Noncoding RNAs play a crucial role in various cellular processes in living organisms, and RNA functions heavily depend on molecule structures composed of stems, loops, and various tertiary motifs. Among those, the most frequent are A-minor interactions, which are often involved in the formation of more complex motifs such as kink-turns and pseudoknots. We present a novel classification of A-minors in terms of RNA secondary structure where each nucleotide of an A-minor is attributed to the stem or loop, and each pair of nucleotides is attributed to their relative position within the secondary structure. By analyzing classes of A-minors in known RNA structures, we found that the largest classes are mostly homogeneous and preferably localize with known A-minor co-motifs, such as tetraloop–tetraloop receptor and coaxial stacking. Detailed analysis of local A-minors within internal loops revealed a novel recurrent RNA tertiary motif, the across-bulged motif. Interestingly, the motif resembles the previously known GAAA/11nt motif but with the local adenines performing the role of the GAAA-tetraloop. By using machine learning, we show that particular classes of local A-minors can be predicted from sequence and secondary structure. The proposed classification is the first step toward automatic annotation of not only A-minors and their co-motifs but various types of RNA tertiary motifs as well.

中文翻译：

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RNA二级结构的局部上下文注释改进了A-minors的分类和预测

非编码 RNA 在生物体的各种细胞过程中发挥着至关重要的作用，RNA 的功能在很大程度上取决于由茎、环和各种三级基序组成的分子结构。其中，最常见的是 A-minor 相互作用，它们通常参与更复杂的基序的形成，例如扭结和假结。我们根据 RNA 二级结构提出了一种新的 A-minor 分类，其中 A-minor 的每个核苷酸都归因于茎或环，并且每对核苷酸都归因于它们在二级结构中的相对位置。通过分析已知 RNA 结构中的 A-minor 类别，我们发现最大的类别大多是同质的，并且最好定位于已知的 A-minor 共基序，例如四环-四环受体和同轴堆叠。对内部环内局部 A-minors 的详细分析揭示了一种新的反复出现的 RNA 三级基序，即跨凸出基序。有趣的是，该基序类似于以前已知的 GAAA/11nt 基序，但局部腺嘌呤起着 GAAA-四环的作用。通过使用机器学习，我们表明可以从序列和二级结构中预测特定类别的局部 A-minor。所提出的分类是迈向自动注释的第一步，不仅是 A-minors 及其共同基序，而且是各种类型的 RNA 三级基序。我们表明，可以从序列和二级结构中预测特定类别的局部 A 小调。所提出的分类是迈向自动注释的第一步，不仅是 A-minors 及其共同基序，而且是各种类型的 RNA 三级基序。我们表明，可以从序列和二级结构中预测特定类别的局部 A 小调。所提出的分类是迈向自动注释的第一步，不仅是 A-minors 及其共同基序，而且是各种类型的 RNA 三级基序。