Detecting RNA modification using direct RNA sequencing: A systematic review



Zhao, Xichen, Zhang, Yuxin, Hang, Daiyun, Meng, Jia ORCID: 0000-0003-3455-205X and Wei, Zhen
(2022) Detecting RNA modification using direct RNA sequencing: A systematic review. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20. pp. 5740-5749.

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Abstract

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.

Item Type: Article
Depositing User: Symplectic Admin
Date Deposited: 21 Nov 2022 16:49
Last Modified: 01 Nov 2023 11:08
DOI: 10.1016/j.csbj.2022.10.023
Open Access URL: https://doi.org/10.1016/j.csbj.2022.10.023
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3166309