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High-Throughput
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Emerging Topics in Epitranscriptomics (RNA Modifications)
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Emerging Topics in Epitranscriptomics (RNA Modifications)

A special issue of High-Throughput (ISSN 2571-5135).

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 4043

Special Issue Editor

Prof. Dr. Shizuka Uchida

E-Mail Website
Guest Editor
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark
Interests: bioinformatics; cardiovascular system; circRNA; database; epitranscriptomics; lncRNA; miRNA; non-coding RNA

Special Issue Information

Dear Colleagues,

Despite our early understanding of RNA as an enabling messenger, it is not simply a static reflection of genetic activation. Upon transcription from the DNA template, RNA can be modified by various enzymes, which results in over 140 different types of RNA modifications across various organisms. These RNA modifications include N1-methyladenosine (m1A), 5-methylcytosine (m5C), N6-methyladenosine (m6A), pseudouridine (Ψ), and RNA editing. These chemical modifications of RNA influence cellular activities, such as conformational/structural changes of RNAs, nuclear–cytoplasmic shuttling, RNA stability, splicing, and translation efficiencies.

Owing greatly to high-throughput techniques (e.g., microarrays, next generation sequencing, mass spectrometry), the field of epitranscriptomics (the study of RNA modifications) has flourished in recent years. Because of their functional importance, dysregulations in RNA modifications have been linked to various diseases (e.g., cancer, cardiovascular disease, neuromuscular disease). To further understand this exciting area of study, in this Special Issue, we invite manuscripts regarding methods for detecting epitranscriptomic marks, analyzing epitranscriptomic data, screening assays for understanding the importance of RNA modifications in cellular activities, and how such dysregulations are linked to various diseases.

Dr. Shizuka Uchida
Guest Editor

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 special issue 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. High-Throughput is an international peer-reviewed open access quarterly 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 1000 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

  • bioinformatics
  • expression profiling
  • epitranscriptomics
  • gene regulation
  • next generation sequencing
  • RNA-seq
  • RNA modifications

Published Papers (1 paper)

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Research

12 pages, 1185 KiB  
Article
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
by Tyler Weirick, Giuseppe Militello, Mohammed Rabiul Hosen, David John, Joseph B. Moore IV and Shizuka Uchida
High-Throughput 2019, 8(4), 19; https://doi.org/10.3390/ht8040019 - 29 Nov 2019
Cited by 2 | Viewed by 3430
Abstract
Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by [...] Read more.
Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems. Full article
(This article belongs to the Special Issue Emerging Topics in Epitranscriptomics (RNA Modifications))
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