| Title | [PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing |
|---|---|
| Author | Ari Hong1,2, Dongwan Kim1,3, V. Narry Kim1,3, and Hyeshik Chang1,2,3* |
| Address | 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 |
| Bibliography | Journal of Microbiology, 60(9),867-876, 2022, |
| DOI | 10.1007/s12275-022-2324-4 |
| Key Words | RNA virus, RNA modification, viral epitranscriptome, coronavirus, nanopore sequencing, direct RNA sequencing |
| 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. |