Current methods for determining RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here we present RNA structure analysis using nanopore sequencing (PORE-cupine), which combines structure probing using chemical modifications with direct long-read RNA sequencing and machine learning to detect secondary structures in cellular RNAs. PORE-cupine also captures global structural features, such as RNA-binding-protein binding sites and reactivity differences at single-nucleotide variants. We show that shared sequences in different transcript isoforms of the same gene can fold into different structures, highlighting the importance of long-read sequencing for obtaining phase information. We also demonstrate that structural differences between transcript isoforms of the same gene lead to differences in translation efficiency. By revealing isoform-specific RNA structure, PORE-cupine will deepen understanding of the role of structures in controlling gene regulation.

当前使用短读长测序确定 RNA 结构的方法无法捕获不同转录本异构体之间的大部分差异。在这里，我们介绍了使用纳米孔测序 (PORE-cupine) 进行的 RNA 结构分析，它将使用化学修饰的结构探测与直接长读长 RNA 测序和机器学习相结合，以检测细胞 RNA 中的二级结构。PORE-cupine 还捕获全局结构特征，例如 RNA 结合蛋白结合位点和单核苷酸变体的反应性差异。我们表明，同一基因的不同转录本亚型中的共享序列可以折叠成不同的结构，突出了长读长测序对于获取相位信息的重要性。我们还证明同一基因的转录本异构体之间的结构差异导致翻译效率的差异。通过揭示异构体特异性 RNA 结构，PORE-cupine 将加深对结构在控制基因调控中的作用的理解。