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Detecting RNA modification using direct RNA sequencing: A systematic review
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 accu...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9619219/ https://www.ncbi.nlm.nih.gov/pubmed/36382183 http://dx.doi.org/10.1016/j.csbj.2022.10.023 |
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author | Zhao, Xichen Zhang, Yuxin Hang, Daiyun Meng, Jia Wei, Zhen |
author_facet | Zhao, Xichen Zhang, Yuxin Hang, Daiyun Meng, Jia Wei, Zhen |
author_sort | Zhao, Xichen |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9619219 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-96192192022-11-14 Detecting RNA modification using direct RNA sequencing: A systematic review Zhao, Xichen Zhang, Yuxin Hang, Daiyun Meng, Jia Wei, Zhen Comput Struct Biotechnol J Review Article 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. Research Network of Computational and Structural Biotechnology 2022-10-21 /pmc/articles/PMC9619219/ /pubmed/36382183 http://dx.doi.org/10.1016/j.csbj.2022.10.023 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Article Zhao, Xichen Zhang, Yuxin Hang, Daiyun Meng, Jia Wei, Zhen Detecting RNA modification using direct RNA sequencing: A systematic review |
title | Detecting RNA modification using direct RNA sequencing: A systematic review |
title_full | Detecting RNA modification using direct RNA sequencing: A systematic review |
title_fullStr | Detecting RNA modification using direct RNA sequencing: A systematic review |
title_full_unstemmed | Detecting RNA modification using direct RNA sequencing: A systematic review |
title_short | Detecting RNA modification using direct RNA sequencing: A systematic review |
title_sort | detecting rna modification using direct rna sequencing: a systematic review |
topic | Review Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9619219/ https://www.ncbi.nlm.nih.gov/pubmed/36382183 http://dx.doi.org/10.1016/j.csbj.2022.10.023 |
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