Detecting RNA modification using direct RNA sequencing: A systematic review

Xichen Zhao, Yuxin Zhang, Daiyun Hang, Jia Meng, Zhen Wei*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

8 Citations (Scopus)


Post-transcriptional RNA modifications are involved in a range of important cellular processes, including the regulation of gene expression and fine-tuning of the functions of RNA molecules. To decipher the context-specific functions of these post-transcriptional modifications, it is crucial to accurately determine their transcriptomic locations and modification levels under a given cellular condition. With the newly emerged sequencing technology, especially nanopore direct RNA sequencing, different RNA modifications can be detected simultaneously with a single molecular level resolution. Here we provide a systematic review of 15 published RNA modification prediction tools based on direct RNA sequencing data, including their computational models, input–output formats, supported modification types, and reported performances. Finally, we also discussed the potential challenges and future improvements of nanopore sequencing-based methods for RNA modification detection.

Original languageEnglish
Pages (from-to)5740-5749
Number of pages10
JournalComputational and Structural Biotechnology Journal
Publication statusPublished - Jan 2022


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