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ncRNA
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Research on RNA Modification
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Research on RNA Modification

A topical collection in Non-Coding RNA (ISSN 2311-553X).

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Editors

Dr. Clément Carré

E-Mail Website
Guest Editor
Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
Interests: sncRNAs (si, mi and piRNAs); RNA methylation; 2’-0-methylation; epitranscriptomic; chromatin
Dr. Damien Brégeon

E-Mail Website
Guest Editor
ukaryotic translation, Sorbonne Université, CNRS, Biology of adaptation and aging, Institut de Biologie Paris-Seine, UMR8256, 75005 Paris, France
Interests: RNA modification; methylation; dihydrouridine; tRNA

Topical Collection Information

Dear Colleagues,

RNA modifications, including RNA editing, are today well recognized to play an essential role in the regulation of gene expression through several mechanisms. They have been shown to be involved in many different steps, including regulation of their stability/degradation, localization, transport in and out of the cells, protein interaction, and their role in translational regulation. Post-transcriptional modifications affect virtually all types of RNA (mRNA as well as non-coding RNA such as tRNA, rRNA, sncRNA, lncRNA, circRNA, etc.) in all known kingdoms of life as well as in viral RNAs.

The aim of this Special Issue is to cover all molecular aspects of RNA modification and RNA editing, including biosynthesis of these modified nucleotides, enzymes, and partners involved in their formation, detection methods developed for the analysis of RNA modifications, as well as molecular and cellular mechanisms, for which those modifications are important.

Finally, and excitingly, regarding the nature of RNA and its involvement in epigenetics transmission (e.g., sncRNA), the aspect of RNA modifications on epigenetics mechanisms (epitranscriptomics) will also be covered in this Special Issue.

For this Special Issue, we ask for comprehensive reviews, editorials, original research manuscripts or methodological articles.

Dr. Clément Carré
Dr. Damien Brégeon
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA modification
  • RNA editing
  • Modification biosynthesis
  • Modifications detections
  • Modifications functions
  • Modification diseases
  • Epitranscriptomics

Published Papers (4 papers)

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2022

Jump to: 2021

14 pages, 1839 KiB  
Article
Staphylococcus aureus Small RNAs Possess Dephospho-CoA 5′-Caps, but No CoAlation Marks
by Christian Löcherer, Nadja Bühler, Pascal Lafrenz and Andres Jäschke
Non-Coding RNA 2022, 8(4), 46; https://doi.org/10.3390/ncrna8040046 - 28 Jun 2022
Cited by 2 | Viewed by 2414
Abstract
Novel features of coenzyme A (CoA) and its precursor, 3′-dephospho-CoA (dpCoA), recently became evident. dpCoA was found to attach to 5′-ends of small ribonucleic acids (dpCoA-RNAs) in two bacterial species (Escherichia coli and Streptomyces venezuelae). Furthermore, CoA serves, in addition to [...] Read more.
Novel features of coenzyme A (CoA) and its precursor, 3′-dephospho-CoA (dpCoA), recently became evident. dpCoA was found to attach to 5′-ends of small ribonucleic acids (dpCoA-RNAs) in two bacterial species (Escherichia coli and Streptomyces venezuelae). Furthermore, CoA serves, in addition to its well-established coenzymatic roles, as a ubiquitous posttranslational protein modification (‘CoAlation’), thought to prevent the irreversible oxidation of cysteines. Here, we first identified and quantified dpCoA-RNAs in the small RNA fraction of the human pathogen Staphylococcus aureus, using a newly developed enzymatic assay. We found that the amount of dpCoA caps was similar to that of the other two bacteria. We furthermore tested the hypothesis that, in the environment of a cell, the free thiol of the dpCoA-RNAs, as well as other sulfur-containing RNA modifications, may be oxidized by disulfide bond formation, e.g., with CoA. While we could not find evidence for such an ‘RNA CoAlation’, we observed that CoA disulfide reductase, the enzyme responsible for reducing CoA homodisulfides in S. aureus, did efficiently reduce several synthetic dpCoA-RNA disulfides to dpCoA-RNAs in vitro. This activity may imply a role in reversing RNA CoAlation. Full article
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2021

Jump to: 2022

19 pages, 1624 KiB  
Review
The Importance of the Epi-Transcriptome in Translation Fidelity
by Charlène Valadon and Olivier Namy
Non-Coding RNA 2021, 7(3), 51; https://doi.org/10.3390/ncrna7030051 - 27 Aug 2021
Cited by 6 | Viewed by 4307
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly [...] Read more.
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases. Full article
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15 pages, 8026 KiB  
Article
Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum
by Anne Hoffmann, Lieselotte Erber, Heike Betat, Peter F. Stadler, Mario Mörl and Jörg Fallmann
Non-Coding RNA 2021, 7(2), 32; https://doi.org/10.3390/ncrna7020032 - 28 May 2021
Viewed by 4619
Abstract
Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators [...] Read more.
Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifications from reverse transcriptase signatures in chemically untreated RNA-seq data at single-nucleotide resolution. It avoids the comparison of treated and untreated RNA-seq data using reverse transcription arrest patterns at nucleotides in the neighborhood of a putative modification site as internal control. We find that nucleotide modification sites in D. discoideum tRNAs largely conform to the modification patterns observed throughout the eukaroytes. However, there are also previously undescribed modification sites. We observe substantial dynamic changes of both expression levels and modification patterns of certain tRNA types during fruiting body development. Beyond the specific application to D. discoideum our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq. Full article
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11 pages, 1995 KiB  
Article
Evaluation of the Interplay between the ADAR Editome and Immunotherapy in Melanoma
by Marina Tusup, Phil F. Cheng, Ernesto Picardi, Austeja Raziunaite, Reinhard Dummer, Mitchell P. Levesque, Lars E. French, Emmanuella Guenova, Thomas M. Kundig and Steve Pascolo
Non-Coding RNA 2021, 7(1), 5; https://doi.org/10.3390/ncrna7010005 - 12 Jan 2021
Cited by 3 | Viewed by 4241 | Correction
Abstract
Background: RNA editing is a highly conserved posttranscriptional mechanism that contributes to transcriptome diversity. In mammals, it includes nucleobase deaminations that convert cytidine (C) into uridine (U) and adenosine (A) into inosine (I). Evidence from cancer studies indicates that RNA-editing enzymes promote certain [...] Read more.
Background: RNA editing is a highly conserved posttranscriptional mechanism that contributes to transcriptome diversity. In mammals, it includes nucleobase deaminations that convert cytidine (C) into uridine (U) and adenosine (A) into inosine (I). Evidence from cancer studies indicates that RNA-editing enzymes promote certain mechanisms of tumorigenesis. On the other hand, recoding editing in mRNA can generate mutations in proteins that can participate in the Major Histocompatibility Complex (MHC) ligandome and can therefore be recognized by the adaptive immune system. Anti-cancer treatment based on the administration of immune checkpoint inhibitors enhance these natural anti-cancer immune responses. Results: Based on RNA-Seq datasets, we evaluated the editome of melanoma cell lines generated from patients pre- and post-immunotherapy with immune checkpoint inhibitors. Our results reveal a differential editing in Arthrobacter luteus (Alu) sequences between samples pre-therapy and relapses during therapy with immune checkpoint inhibitors. Conclusion: These data pave the way towards the development of new diagnostics and therapies targeted to editing that could help in preventing relapses during immunotherapies. Full article
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