Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update
The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m<sup>6</sup>A methylation in mRNAs,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/2/278 |
| _version_ | 1797396444131360768 |
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| author | Yuri Motorin Virginie Marchand |
| author_facet | Yuri Motorin Virginie Marchand |
| author_sort | Yuri Motorin |
| collection | DOAJ |
| description | The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m<sup>6</sup>A methylation in mRNAs, dozens of deep sequencing-based methods and protocols were proposed for the analysis of various RNA modifications, allowing us to considerably extend the list of detectable modified residues. Many of the currently used methods rely on the particular reverse transcription signatures left by RNA modifications in cDNA; these signatures may be naturally present or induced by an appropriate enzymatic or chemical treatment. The newest approaches also include labeling at RNA abasic sites that result from the selective removal of RNA modification or the enhanced cleavage of the RNA ribose-phosphate chain (perhaps also protection from cleavage), followed by specific adapter ligation. Classical affinity/immunoprecipitation-based protocols use either antibodies against modified RNA bases or proteins/enzymes, recognizing RNA modifications. In this survey, we review the most recent achievements in this highly dynamic field, including promising attempts to map RNA modifications by the direct single-molecule sequencing of RNA by nanopores. |
| first_indexed | 2024-03-09T00:50:26Z |
| format | Article |
| id | doaj.art-4c22b64f0d1e4d65a32ed35a2356ca5f |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T00:50:26Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-4c22b64f0d1e4d65a32ed35a2356ca5f2023-12-11T17:12:58ZengMDPI AGGenes2073-44252021-02-0112227810.3390/genes12020278Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 UpdateYuri Motorin0Virginie Marchand1Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, FranceUniversité de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, FranceThe precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m<sup>6</sup>A methylation in mRNAs, dozens of deep sequencing-based methods and protocols were proposed for the analysis of various RNA modifications, allowing us to considerably extend the list of detectable modified residues. Many of the currently used methods rely on the particular reverse transcription signatures left by RNA modifications in cDNA; these signatures may be naturally present or induced by an appropriate enzymatic or chemical treatment. The newest approaches also include labeling at RNA abasic sites that result from the selective removal of RNA modification or the enhanced cleavage of the RNA ribose-phosphate chain (perhaps also protection from cleavage), followed by specific adapter ligation. Classical affinity/immunoprecipitation-based protocols use either antibodies against modified RNA bases or proteins/enzymes, recognizing RNA modifications. In this survey, we review the most recent achievements in this highly dynamic field, including promising attempts to map RNA modifications by the direct single-molecule sequencing of RNA by nanopores.https://www.mdpi.com/2073-4425/12/2/278RNA modificationepitranscriptomedeep sequencingmassive parallel sequencingsingle-molecule sequencingnanopores |
| spellingShingle | Yuri Motorin Virginie Marchand Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update Genes RNA modification epitranscriptome deep sequencing massive parallel sequencing single-molecule sequencing nanopores |
| title | Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update |
| title_full | Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update |
| title_fullStr | Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update |
| title_full_unstemmed | Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update |
| title_short | Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update |
| title_sort | analysis of rna modifications by second and third generation deep sequencing 2020 update |
| topic | RNA modification epitranscriptome deep sequencing massive parallel sequencing single-molecule sequencing nanopores |
| url | https://www.mdpi.com/2073-4425/12/2/278 |
| work_keys_str_mv | AT yurimotorin analysisofrnamodificationsbysecondandthirdgenerationdeepsequencing2020update AT virginiemarchand analysisofrnamodificationsbysecondandthirdgenerationdeepsequencing2020update |