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Review

Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update

1
Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
2
Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
*
Authors to whom correspondence should be addressed.
Academic Editor: Carine Tisne
Genes 2021, 12(2), 278; https://doi.org/10.3390/genes12020278
Received: 15 December 2020 / Revised: 11 February 2021 / Accepted: 12 February 2021 / Published: 16 February 2021
(This article belongs to the Special Issue Functions and Dynamics of RNA Modifications)
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 m6A 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. View Full-Text
Keywords: RNA modification; epitranscriptome; deep sequencing; massive parallel sequencing; single-molecule sequencing; nanopores; RT signature; antibody; methylation; pseudouridine; 2’-O-methylation RNA modification; epitranscriptome; deep sequencing; massive parallel sequencing; single-molecule sequencing; nanopores; RT signature; antibody; methylation; pseudouridine; 2’-O-methylation
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MDPI and ACS Style

Motorin, Y.; Marchand, V. Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update. Genes 2021, 12, 278. https://doi.org/10.3390/genes12020278

AMA Style

Motorin Y, Marchand V. Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update. Genes. 2021; 12(2):278. https://doi.org/10.3390/genes12020278

Chicago/Turabian Style

Motorin, Yuri, and Virginie Marchand. 2021. "Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update" Genes 12, no. 2: 278. https://doi.org/10.3390/genes12020278

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