[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

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[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 Korea

Corresponding author: Hyeshik Chang ,

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

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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: RNA virus, RNA modification, viral epitranscriptome, coronavirus, nanopore sequencing, direct RNA sequencing

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[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

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