In silico and experimental approaches for validating RNA editing events in transcriptomes
As a typical RNA virus, SARS-CoV-2 is subjected to RNA editing in host cells. While some researchers believe that a traditional variant calling pipeline retrieves all true-positive RNA editing events from the transcriptome, others argue that conventional methods identify many false-positive sites. H...
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| Aineistotyyppi: | Artikkeli |
| Kieli: | English |
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Taylor & Francis Group
2024-12-01
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| Sarja: | RNA Biology |
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| Linkit: | https://www.tandfonline.com/doi/10.1080/15476286.2024.2432729 |
| _version_ | 1826937815578968064 |
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| author | Lai Wei |
| author_facet | Lai Wei |
| author_sort | Lai Wei |
| collection | DOAJ |
| description | As a typical RNA virus, SARS-CoV-2 is subjected to RNA editing in host cells. While some researchers believe that a traditional variant calling pipeline retrieves all true-positive RNA editing events from the transcriptome, others argue that conventional methods identify many false-positive sites. Here, I describe several additional in silico and experimental approaches to validate the authenticity of RNA editing in SARS-CoV-2. These approaches include requiring strand-specific sequencing, analysis of hyperedited reads, linkage analysis, orthogonal methods like mass spectrometry, and the use of ADAR-deficient host cells. These findings may improve future analyses on the identification of RNA editing, especially in RNA viruses. |
| first_indexed | 2025-02-17T18:46:36Z |
| format | Article |
| id | doaj.art-0f73a28686ec4b51ba88a40bcc76e12c |
| institution | Directory Open Access Journal |
| issn | 1547-6286 1555-8584 |
| language | English |
| last_indexed | 2025-02-17T18:46:36Z |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj.art-0f73a28686ec4b51ba88a40bcc76e12c2024-12-11T08:20:17ZengTaylor & Francis GroupRNA Biology1547-62861555-85842024-12-012111269127410.1080/15476286.2024.2432729In silico and experimental approaches for validating RNA editing events in transcriptomesLai Wei0College of Life Sciences, Beijing Normal University, Beijing, ChinaAs a typical RNA virus, SARS-CoV-2 is subjected to RNA editing in host cells. While some researchers believe that a traditional variant calling pipeline retrieves all true-positive RNA editing events from the transcriptome, others argue that conventional methods identify many false-positive sites. Here, I describe several additional in silico and experimental approaches to validate the authenticity of RNA editing in SARS-CoV-2. These approaches include requiring strand-specific sequencing, analysis of hyperedited reads, linkage analysis, orthogonal methods like mass spectrometry, and the use of ADAR-deficient host cells. These findings may improve future analyses on the identification of RNA editing, especially in RNA viruses.https://www.tandfonline.com/doi/10.1080/15476286.2024.2432729RNA editingSARS-CoV-2in silicoexperimentvalidation |
| spellingShingle | Lai Wei In silico and experimental approaches for validating RNA editing events in transcriptomes RNA Biology RNA editing SARS-CoV-2 in silico experiment validation |
| title | In silico and experimental approaches for validating RNA editing events in transcriptomes |
| title_full | In silico and experimental approaches for validating RNA editing events in transcriptomes |
| title_fullStr | In silico and experimental approaches for validating RNA editing events in transcriptomes |
| title_full_unstemmed | In silico and experimental approaches for validating RNA editing events in transcriptomes |
| title_short | In silico and experimental approaches for validating RNA editing events in transcriptomes |
| title_sort | in silico and experimental approaches for validating rna editing events in transcriptomes |
| topic | RNA editing SARS-CoV-2 in silico experiment validation |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2024.2432729 |
| work_keys_str_mv | AT laiwei insilicoandexperimentalapproachesforvalidatingrnaeditingeventsintranscriptomes |