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RNA Editing

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (28 February 2020) | Viewed by 7593

Special Issue Editor

Japan Advanced Institute of Science and Technology, Area of Bioscience and Biotechnology, Nomi, Japan
Interests: RNA splicing; RNA editing; gene expression; genetic code restration

Special Issue Information

Dear Colleagues,

RNA editing is a physiological process during which RNA nucleobases are excised, inserted, or post-transcriptionally modified, resulting in changes in the genetic code and expansion of the coding capacity of the genome. RNA editing was first observed in Trypanosoma as the deletion and insertion of nucleobases in RNA. Today, RNA editing is considered a universal phenomenon in higher eukaryotes. In mammalia, RNA editing is caused by nucleobase deamination, resulting in A-to-I and C-to-U conversions, and occurs in a wide range of tissues and is catalyzed by adenosine deaminase acting on RNA (ADAR) and APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family enzymes. However, RNA editing is not limited to only these two types, and U-to-C, U-to-A, and A-to-U conversions resulting from RNA editing are found in plant mitochondria and plastids. The editosome in plants comprises pentatricopeptide repeat (PPR) proteins, multiple organellar RNA editing factors (MORFs), and zinc finger proteins. Cytidine deaminase motifs for C-to-U conversion are found within the DYW domain of PPR proteins. Despite these advances, it is entirely possible that we have only scraped the surface and that many other enzymes catalyzing RNA editing still remain to be discovered.

Recently, RNA editing machineries have started to attract considerable attention because of their potential therapeutic applications in the treatment of genetic diseases. However, it is nearly impossible to perform genome editing in patients because RNA editing machineries cannot be delivered easily to trillions of cells while at the same time ensuring that they work correctly in the cells they were designed to treat. Even if the RNA editing machinery could be delivered to patient cells, mutated RNAs might be expressed. If it were possible to fix or restore mutated RNAs via artificial RNA editing, patient symptoms might be reduced. In this Special Issue, we would like to summarize the current state of knowledge on RNA editing, particularly with respect to its future clinical applications.

Prof. Toshifumi Tsukahara
Guest Editor

Manuscript Submission Information

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Keywords

  • deaminase
  • guide RNA
  • point mutation
  • genetic code
  • artificial enzyme
  • editosome
  • PPR proteins
  • ADAR
  • APOBEC

Published Papers (2 papers)

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Research

16 pages, 1635 KiB  
Article
APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival
by Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe and Santosh K. Patnaik
Int. J. Mol. Sci. 2019, 20(22), 5621; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225621 - 10 Nov 2019
Cited by 45 | Viewed by 4372
Abstract
APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. These enzymes are also capable of converting C bases at specific positions of RNAs to U. However, the prevalence and significance of this C-to-U RNA editing in any cancer is currently unknown. We developed [...] Read more.
APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. These enzymes are also capable of converting C bases at specific positions of RNAs to U. However, the prevalence and significance of this C-to-U RNA editing in any cancer is currently unknown. We developed a bioinformatics workflow to determine RNA editing levels at known APOBEC3-mediated RNA editing sites using exome and mRNA sequencing data of 1040 breast cancer tumors. Although reliable editing determinations were limited due to sequencing depth, editing was observed in both tumor and adjacent normal tissues. For 440 sites (411 genes), editing was determinable for ≥5 tumors, with editing occurring in 0.6%–100% of tumors (mean 20%, SD 14%) at an average level of 0.6%–20% (mean 7%, SD 4%). Compared to tumors with low RNA editing, editing-high tumors had enriched expression of immune-related gene sets, and higher T cell and M1 macrophage infiltration, B and T cell receptor diversity, and immune cytolytic activity. Concordant with this, patients with increased RNA editing in tumors had better disease- and progression-free survivals (hazard ratio = 1.67–1.75, p < 0.05). Our study identifies that APOBEC3-mediated RNA editing occurs in breast cancer tumors and is positively associated with elevated immune activity and improved survival. Full article
(This article belongs to the Special Issue RNA Editing)
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16 pages, 1799 KiB  
Article
Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends
by Kamil Myszczyński, Monika Ślipiko and Jakub Sawicki
Int. J. Mol. Sci. 2019, 20(12), 2963; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20122963 - 18 Jun 2019
Cited by 12 | Viewed by 2781
Abstract
RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency [...] Read more.
RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes. Full article
(This article belongs to the Special Issue RNA Editing)
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