Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

RNA Modifications and Epitranscriptomics in Human Disease

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

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

Deadline for manuscript submissions: closed (15 March 2023) | Viewed by 11611

Share This Special Issue

Special Issue Editor

Dr. Yi-Ping Yang

E-Mail Website
Guest Editor

1. Division of Basic Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
2. Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11217, Taiwan
3. School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
Interests: tumor immunology; viral immunity; RNA modifications; RNA epitranscriptomics

Special Issue Information

Dear Colleagues,

Gene regulation has been known to involve dynamic and reversible biological and chemical RNA modifications in the epitranscriptome. Hundreds of RNA modifications have been identified by epitranscriptomics to date. Increasing evidence suggests that epitranscriptomic changes are important for cell differentiation, sex determination, and stress responses. As well as being non-genetically encoded, they can be reversible and involved in genetic regulation. With these recent developments, as well as the recent discovery of writers, readers, and erasers of modifications that affect a diverse range of RNAs and tissues, integrative approaches have been developed for mapping, transcriptome-wide, the modifications and protein–RNA interactions of epitranscriptome agents. RNA modulation maps and their crosstalk have revealed that they serve as signaling switches, raising suspicions that an epitranscriptomic code governs the post-transcriptional fate of RNA, which contributes to human diseases including neurological disorders, cancers, and other diseases. Through the development of single-molecule sequencing technologies and antibodies specific to various RNA modifications, transcript-specific epitranscriptomic marks can be discovered across cell types and their abnormalities in disease.

Topics of this Special Issue include, but are not limited to:

RNA modifications;
Functions of modification systems;
RNA modification mapping;
RNA modifications and RNA structure;
RNA editing, RNA adenylation, and RNA uridylation;
Methods for profiling and mapping RNA modifications;
Epitranscriptome in diseases;
Modification enzymes and their marks in diseases.

Dr. Yi-Ping Yang
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 editing
RNA modifications
epitranscriptome
human diseases
epitranscriptomic marks
approaches for mapping transcriptome

Published Papers (5 papers)

Download All Papers

Research

Jump to: Review

14 pages, 1453 KiB

Open AccessArticle

Characterization of A-to-I Editing in Pigs under a Long-Term High-Energy Diet

by Liu Yang, Lei Huang, Yulian Mu and Kui Li

Int. J. Mol. Sci. 2023, 24(9), 7921; https://doi.org/10.3390/ijms24097921 - 27 Apr 2023

Viewed by 1078

Abstract

Long-term high-energy intake has detrimental effects on pig health and elevates the risk of metabolic disease. RNA editing modifying RNA bases in a post-transcriptional process has been extensively studied for model animals. However, less evidence is available that RNA editing plays a role in the development of metabolic disorders. Here, we profiled the A-to-I editing in three tissues and six gut segments and characterized the functional aspect of editing sites in model pigs for metabolic disorders. We detected 64,367 non-redundant A-to-I editing sites across the pig genome, and 20.1% correlated with their located genes’ expression. The largest number of A-to-I sites was found in the abdominal aorta with the highest editing levels. The significant difference in editing levels between high-energy induced and control pigs was detected in the abdominal aorta, testis, duodenum, ileum, colon, and cecum. We next focused on 6041 functional A-to-I sites that detected differences or specificity between treatments. We found functional A-to-I sites specifically involved in a tissue-specific manner. Two of them, located in gene SLA-DQB1 and near gene B4GALT5 were found to be shared by three tissues and six gut segments. Although we did not find them enriched in each of the gene features, in correlation analysis, we noticed that functional A-to-I sites were significantly enriched in gene 3′-UTRs. This result indicates, in general, A-to-I editing has the largest potential in the regulation of gene expression through changing the 3′-UTRs’ sequence, which is functionally involved in pigs under a long-term high-energy diet. Our work provides valuable knowledge of A-to-I editing sites functionally involved in the development of the metabolic disorder. Full article

(This article belongs to the Special Issue RNA Modifications and Epitranscriptomics in Human Disease)

► Show Figures

Figure 1

18 pages, 5435 KiB

Open AccessArticle

The Profiles and Functions of RNA Editing Sites Associated with High-Altitude Adaptation in Goats

by Li Li, Xiaoli Xu, Miao Xiao, Chunhua Huang, Jiaxue Cao, Siyuan Zhan, Jiazhong Guo, Tao Zhong, Linjie Wang, Liu Yang and Hongping Zhang

Int. J. Mol. Sci. 2023, 24(4), 3115; https://doi.org/10.3390/ijms24043115 - 4 Feb 2023

Cited by 3 | Viewed by 1797

Abstract

High-altitude environments dramatically influenced the genetic evolution of vertebrates. However, little is known about the role of RNA editing on high-altitude adaptation in non-model species. Here, we profiled the RNA editing sites (RESs) of heart, lung, kidney, and longissimus dorsi muscle from Tibetan cashmere goats (TBG, 4500 m) and Inner Mongolia cashmere goats (IMG, 1200 m) to reveal RNA editing-related functions of high-altitude adaptation in goats. We identified 84,132 high-quality RESs that were unevenly distributed across the autosomes in TBG and IMG, and more than half of the 10,842 non-redundant editing sites were clustered. The majority (62.61%) were adenosine-to-inosine (A-to-I) sites, followed by cytidine-to-uridine (C-to-U) sites (19.26%), and 32.5% of them had a significant correlation with the expression of catalytic genes. Moreover, A-to-I and C-to-U RNA editing sites had different flanking sequences, amino acid mutations, and alternative splicing activity. TBG had higher editing levels of A-to-I and C-to-U than IMG in the kidney, whereas a lower level was found in the longissimus dorsi muscle. Furthermore, we identified 29 IMG and 41 TBG population-specific editing sites (pSESs) and 53 population-differential editing sites (pDESs) that were functionally involved in altering RNA splicing or recoding protein products. It is worth noting that 73.3% population-differential, 73.2% TBG-specific, and 80% IMG-specific A-to-I sites were nonsynonymous sites. Moreover, the pSESs and pDESs editing-related genes play critical functions in energy metabolisms such as ATP binding molecular function, translation, and adaptive immune response, which may be linked to goat high-altitude adaptation. Our results provide valuable information for understanding the adaptive evolution of goats and studying plateau-related diseases. Full article

(This article belongs to the Special Issue RNA Modifications and Epitranscriptomics in Human Disease)

► Show Figures

Figure 1

Review

Jump to: Research

13 pages, 752 KiB

Open AccessReview

The Role of m⁶A Modifications in B-Cell Development and B-Cell-Related Diseases

by Shuqi Wang, Huanxiang Li, Zhengxing Lian and Shoulong Deng

Int. J. Mol. Sci. 2023, 24(5), 4721; https://doi.org/10.3390/ijms24054721 - 1 Mar 2023

Cited by 1 | Viewed by 1816

Abstract

B cells are a class of professional antigen-presenting cells that produce antibodies to mediate humoral immune response and participate in immune regulation. m⁶A modification is the most common RNA modification in mRNA; it involves almost all aspects of RNA metabolism and can affect RNA splicing, translation, stability, etc. This review focuses on the B-cell maturation process as well as the role of three m⁶A modification-related regulators—writer, eraser, and reader—in B-cell development and B-cell-related diseases. The identification of genes and modifiers that contribute to immune deficiency may shed light on regulatory requirements for normal B-cell development and the underlying mechanism of some common diseases. Full article

(This article belongs to the Special Issue RNA Modifications and Epitranscriptomics in Human Disease)

► Show Figures

Figure 1

18 pages, 856 KiB

Open AccessReview

The Role of RNA Modification in HIV-1 Infection

by Shuqi Wang, Huanxiang Li, Zhengxing Lian and Shoulong Deng

Int. J. Mol. Sci. 2022, 23(14), 7571; https://doi.org/10.3390/ijms23147571 - 8 Jul 2022

Cited by 8 | Viewed by 3301

Abstract

RNA plays an important role in biology, and more than 170 RNA modifications have been identified so far. Post-transcriptional modification of RNA in cells plays a crucial role in the regulation of its stability, transport, processing, and gene expression. So far, the research on RNA modification and the exact role of its enzymes is becoming more and more comprehensive. Human immunodeficiency virus 1 (HIV-1) is an RNA virus and the causative agent of acquired immunodeficiency syndrome (AIDS), which is one of the most devastating viral pandemics in history. More and more studies have shown that HIV has RNA modifications and regulation of its gene expression during infection and replication. This review focuses on several RNA modifications and their regulatory roles as well as the roles that different RNA modifications play during HIV-1 infection, in order to find new approaches for the development of anti-HIV-1 therapeutics. Full article

(This article belongs to the Special Issue RNA Modifications and Epitranscriptomics in Human Disease)

► Show Figures

Figure 1

18 pages, 1832 KiB

Open AccessReview

The Progression of N6-methyladenosine Study and Its Role in Neuropsychiatric Disorders

by Chunguang Lei and Qingzhong Wang

Int. J. Mol. Sci. 2022, 23(11), 5922; https://doi.org/10.3390/ijms23115922 - 25 May 2022

Cited by 9 | Viewed by 2680

Abstract

Epitranscriptomic modifications can affect every aspect of RNA biology, including stability, transport, splicing, and translation, participate in global intracellular mRNA metabolism, and regulate gene expression and a variety of biological processes. N6-methyladenosine (m6A) as the most prevalent modification contributes to normal embryonic brain development and memory formation. However, changes in the level of m6A modification and the expression of its related proteins cause abnormal nervous system functions, including brain tissue development retardation, axon regeneration disorders, memory changes, and neural stem cell renewal and differentiation disorders. Recent studies have revealed that m6A modification and its related proteins play key roles in the development of various neuropsychiatric disorders, such as depression, Alzheimer’s disease, and Parkinson’s disease. In this review, we summarize the research progresses of the m6A modification regulation mechanism in the central nervous system and discuss the effects of gene expression regulation mediated by m6A modification on the biological functions of the neuropsychiatric disorders, thereby providing some insight into new research targets and treatment directions for human diseases. Full article

(This article belongs to the Special Issue RNA Modifications and Epitranscriptomics in Human Disease)

► Show Figures