ABSTRACT

The covalent modification of RNA molecules is a pervasive feature of all classes of RNAs and has fundamental roles in the regulation of several cellular processes. Mapping the location of RNA modifications transcriptome-wide is key to unveiling their role and dynamic behaviour, but technical limitations have often hampered these efforts. Nanopore direct RNA sequencing is a third-generation sequencing technology that allows the sequencing of native RNA molecules, thus providing a direct way to detect modifications at single-molecule resolution. Despite recent advances, the analysis of nanopore sequencing data for RNA modification detection is still a complex task that presents many challenges. Many works have addressed this task using different approaches, resulting in a large number of tools with different features and performances. Here we review the diverse approaches proposed so far and outline the principles underlying currently available algorithms.

摘要

RNA 分子的共价修饰是所有类别 RNA 的普遍特征，并且在多种细胞过程的调节中具有基本作用。绘制转录组范围内 RNA 修饰的位置是揭示其作用和动态行为的关键，但技术限制往往阻碍了这些努力。纳米孔直接RNA测序是第三代测序技术，可以对天然RNA分子进行测序，从而提供了一种以单分子分辨率检测修饰的直接方法。尽管最近取得了进展，但用于 RNA 修饰检测的纳米孔测序数据分析仍然是一项复杂的任务，带来了许多挑战。许多工作使用不同的方法来解决此任务，从而产生了大量具有不同功能和性能的工具。在这里，我们回顾了迄今为止提出的各种方法，并概述了当前可用算法的原理。