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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022004706 |
| _version_ | 1797978176364740608 |
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| author | Xichen Zhao Yuxin Zhang Daiyun Hang Jia Meng Zhen Wei |
| author_facet | Xichen Zhao Yuxin Zhang Daiyun Hang Jia Meng Zhen Wei |
| author_sort | Xichen Zhao |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T05:18:49Z |
| format | Article |
| id | doaj.art-c3e12629fc744832bcce9ea962f5fc48 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:18:49Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-c3e12629fc744832bcce9ea962f5fc482022-12-24T04:54:51ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012057405749Detecting RNA modification using direct RNA sequencing: A systematic reviewXichen Zhao0Yuxin Zhang1Daiyun Hang2Jia Meng3Zhen Wei4Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, ChinaDepartment of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, China; Institute of Systems, Molecular and Integrative Biology, L69 7ZB Liverpool, UKDepartment of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, China; Department of Computer Science, University of Liverpool, L69 7ZB Liverpool, UKDepartment of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, China; AI University Research Centre, Xi’an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, China; Institute of Systems, Molecular and Integrative Biology, L69 7ZB Liverpool, UKDepartment of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, China; Institute of Life Course and Medical Sciences, L69 7ZB Liverpool, UK; Corresponding author at: Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 215123 Suzhou, Jiangsu, ChinaPost-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.http://www.sciencedirect.com/science/article/pii/S2001037022004706 |
| spellingShingle | Xichen Zhao Yuxin Zhang Daiyun Hang Jia Meng Zhen Wei Detecting RNA modification using direct RNA sequencing: A systematic review Computational and Structural Biotechnology Journal |
| 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 |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022004706 |
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