RNA Epigenetics: RNA Modification and Epitranscriptome Analysis—2nd Edition

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "RNA".

Deadline for manuscript submissions: closed (25 May 2025) | Viewed by 2749

Special Issue Editors

Department of Public Health, Nanjing University of Chinese Medicine, Nanjing 210023, China
Interests: RNA modification; bioinformatics; epitranscriptomics; data mining
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Guest Editor
College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
Interests: RNA acetylation; plant; modified nucleosides

Special Issue Information

Dear Colleagues,

We would like to invite you to participate in this Special Issue, “RNA Epigenetics: RNA Modification and Epitranscriptome Analysis—2nd Edition”.

RNA modifications are essential biological mechanisms that alter the structure and function of RNA molecules, affecting a myriad of vital processes in different species, including animals, plants, and microorganisms. These modifications occur naturally in various types of RNA, such as mRNA, lncRNA, rRNA, tRNA, snRNA, snoRNA, and circRNA, and are crucial in the regulation of RNA activity. In essence, RNA modifications help regulate the stability, localization, and translation of RNA, which are key factors in gene expression. In addition, RNA modifications play a significant role in the onset and progression of various diseases, including cancer. The process of modifying RNA is a highly regulated one, and any disruption or dysregulation in this can lead to disease.

In this Special Issue, we aim to gather articles from all aspects of RNA epitranscriptomics on any life form (e.g., mammal, vertebrate, plant, and virus). Topics for consideration include, but are not limited to, new wet experimental results/biomolecular mechanisms, new computational and experimental combined analysis, novel bioinformatics software/pipelines for analysis epigenetics data, new/updated RNA modification knowledge base, new web-server tools, and review article for publication.

Dr. Bowen Song
Dr. Mingjia Chen
Guest Editors

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Keywords

  • RNA modification
  • epitranscriptomics
  • RNA editing
  • RNA epigenetics
  • computational biology

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Published Papers (1 paper)

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Review

24 pages, 1962 KB  
Review
Uncovering the Epitranscriptome: A Review on mRNA Modifications and Emerging Frontiers
by Douglas M. Ruden
Genes 2025, 16(8), 951; https://doi.org/10.3390/genes16080951 - 12 Aug 2025
Viewed by 2100
Abstract
Background/Objectives: Messenger RNA (mRNA) modifications regulate key steps in gene expression, including splicing, translation, and stability. Despite over 300 known RNA modifications, the relatively small subset occurring in mRNA remains understudied compared with tRNA and rRNA. This review aims to systematically evaluate 15 [...] Read more.
Background/Objectives: Messenger RNA (mRNA) modifications regulate key steps in gene expression, including splicing, translation, and stability. Despite over 300 known RNA modifications, the relatively small subset occurring in mRNA remains understudied compared with tRNA and rRNA. This review aims to systematically evaluate 15 known naturally occurring mRNA-specific modifications, rank them by publication frequency, and highlight emerging frontiers in epitranscriptomics, including discovering new naturally occurring mRNA modifications and environmental RNA (eRNA) epitranscriptomics. Methods: We conducted a structured literature review of PubMed-indexed publications to rank mRNA modifications by citation prevalence. Key modifications such as m6A, m5C, Ψ, and m1A were analyzed in terms of enzymatic machinery (“writers,” “erasers,” and “readers”), molecular functions, and physiological relevance. We also reviewed technological advances, with a focus on nanopore sequencing for detection of RNA modifications in native and environmental contexts. Results: The modification m6A was identified as the most studied mRNA modification, followed by Ψ, m5C, and A-to-I editing (inosine). These modifications influence diverse mRNA processes, including translation efficiency, localization, and immune evasion. Cap-specific modifications such as Cap0, Cap1, and Cap2 were also described, highlighting their role in transcript stability and innate immune regulation. Advances in nanopore sequencing have enabled direct detection of RNA modifications and offer promise for eRNA (environmental RNA) surveys. The potential for nanopore sequencing of many other of the 335 known RNA modifications in the MODOMICS database using existing nanopore technologies is also discussed. Conclusions: mRNA modifications represent a critical, yet incompletely mapped, layer of gene regulation. Continued research—especially using nanopore and machine learning technologies—will help uncover their full biological significance. Exploration of eRNA and identifying new mRNA modifications will redefine our understanding of RNA biology. Full article
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