[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing

Ari Hong; Dongwan Kim; V. Narry Kim; Hyeshik Chang

doi:10.1007/s12275-022-2324-4

Articles

Page Path: HOME > J. Microbiol > Volume 60(9); 2022 > Article

Journal Article
[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing: Ari Hong ^1,2, Dongwan Kim ^1,3, V. Narry Kim ^1,3, Hyeshik Chang ^1,2,3; Journal of Microbiology 2022;60(9):867-876.
DOI: https://doi.org/10.1007/s12275-022-2324-4
Published online: August 24, 2022

¹Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul 08826, Republic of Korea, ²Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea, ³School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea¹Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul 08826, Republic of Korea, ²Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea, ³School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea

Corresponding author: Hyeshik Chang ,

Received: 18 July 2022 • Revised: 4 August 2022 • Accepted: 5 August 2022

57 Views
0 Download
7 Web of Science
7 Crossref
6 Scopus

Full Article

Abstract

RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N6- methyladenosine, have also been found in viral transcripts and viral RNA genomes. Some of the modifications increase the viral replication efficiency while also helping the virus to evade the host immune system. Nonetheless, there are numerous examples in which the host's RNA modification enzymes function as antiviral factors. Although established methods like MeRIP-seq and miCLIP can provide a transcriptome- wide overview of how viral RNA is modified, it is difficult to distinguish between the complex overlapping viral transcript isoforms using the short read-based techniques. Nanopore direct RNA sequencing (DRS) provides both long reads and direct signal readings, which may carry information about the modifications. Here, we describe a refined protocol for analyzing the RNA modifications in viral transcriptomes using nanopore technology.

Keywords: PK/PD;Staphylococcus aureus;antibacterial activity;cefquinome;in vitro model;quantitative proteomic

Figure & Data

References

Citations

Citations to this article as recorded by

Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications
Lu Tan, Zhihao Guo, Xiaoming Wang, Dal Young Kim, Runsheng Li, Pedro H. Oliveira
mSystems.2024;[Epub] CrossRef
Current progress in strategies to profile transcriptomic m6A modifications
Yuening Yang, Yanming Lu, Yan Wang, Xianghui Wen, Changhai Qi, Weilan Piao, Hua Jin
Frontiers in Cell and Developmental Biology.2024;[Epub] CrossRef
Improved sub-genomic RNA prediction with the ARTIC protocol
Thomas Baudeau, Kristoffer Sahlin
Nucleic Acids Research.2024; 52(17): e82. CrossRef
Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases
Stephen Spatz, Claudio L. Afonso
Veterinary Sciences.2024; 11(6): 239. CrossRef
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data
Shenglun Chen, Jia Meng, Yuxin Zhang
Methods.2024; 228: 30. CrossRef
Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis
Caroline A. McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N. Klink, Miten Jain, Sara H. Rouhanifard
Gigabyte.2024; 2024: 1. CrossRef
Dissecting the effects of METTL3 on alternative splicing in prostate cancer
Lin Wang, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, Yiwei Wang, Cathy Sin-Hang Fung, Peter Ka-Fung Chiu, Chi-Fai Ng, Stephen Kwok-Wing Tsui
Frontiers in Oncology.2023;[Epub] CrossRef

Cite this Article

Cite this Article: export Copy Download Format; Close

Download Citation

Download a citation file in RIS format that can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Reference Manager.

Format:

RIS — For EndNote, ProCite, RefWorks, and most other reference management software
BibTeX — For JabRef, BibDesk, and other BibTeX-specific software

Include:

Citation for the content below
Citation and abstract for the content below

[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing

J. Microbiol. 2022;60(9):867-876. Published online August 24, 2022

DOI: https://doi.org/10.1007/s12275-022-2324-4

Related articles