Regulation of Gene Expression: RNA Modification of Genes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 6085

Special Issue Editors


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Guest Editor
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
Interests: RNA modification; RNA processing; RNA binding proteins; transcriptional regulation; functional genomics
Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou 310058, China
Interests: RNA modificaiton, sequencing technologies, RNA biology, tRNA-derived small RNA, noncoding RNA

Special Issue Information

Dear Colleagues,

More than 100 types of RNA modifications have been identified in both mRNA and non-coding RNAs, including adenosine-to-inosine RNA editing, N6-methyladenosine (m6A), and 5-methycytosine (m5C), to name just a few. With the development of various genome-wide sequencing technologies for detecting RNA modifications and the discovery of writers, erasers and readers in the last decade, RNA modifications have been increasingly appreciated as key players in regulating gene expression programs. In response to both internal and external stimuli, RNA modifications confer cell a tunable mechanism to regulate transcription, RNA metabolism and translation. However, our understanding of the regulatory mechanisms remains incomplete. Extensive efforts are needed to develop novel tools for detecting RNA modifications at a single-base resolution and in a quantitative manner, to characterize key binding proteins of RNA modifications for elucidating the regulatory network, and to understand how the dysregulation of RNA modifications might contribute to disorders and diseases.

The present Special Issue is expected to present technical advances and mechanistic studies towards a better understanding of gene expression regulation by RNA modifications. We welcome both reviews and original research articles. For further information about the scope of this Special Issue and preferred manuscript topics, please feel free to contact the Guest Editors.

Dr. Jia-Yu Chen
Dr. Xiaoyu Li
Guest Editors

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Published Papers (2 papers)

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Research

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15 pages, 2140 KiB  
Article
Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
by Madeline E. Melzer, Jonathan V. Sweedler and Kevin D. Clark
Genes 2022, 13(6), 1008; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061008 - 02 Jun 2022
Cited by 1 | Viewed by 1870
Abstract
The reversible and substoichiometric modification of RNA has recently emerged as an additional layer of translational regulation in normal biological function and disease. Modifications are often enzymatically deposited in and removed from short (~5 nt) consensus motif sequences to carefully control the translational [...] Read more.
The reversible and substoichiometric modification of RNA has recently emerged as an additional layer of translational regulation in normal biological function and disease. Modifications are often enzymatically deposited in and removed from short (~5 nt) consensus motif sequences to carefully control the translational output of the cell. Although characterization of modification occupancy at consensus motifs can be accomplished using RNA sequencing methods, these approaches are generally time-consuming and do not directly detect post-transcriptional modifications. Here, we present a nuclease protection assay coupled with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to rapidly characterize modifications in consensus motifs, such as GGACU, which frequently harbor N6-methyladenosine (m6A). While conventional nuclease protection methods rely on long (~30 nt) oligonucleotide probes that preclude the global assessment of consensus motif modification stoichiometry, we investigated a series of ion-tagged oligonucleotide (ITO) probes and found that a benzylimidazolium-functionalized ITO (ABzIM-ITO) conferred significantly improved nuclease resistance for GGACU targets. After optimizing the conditions of the nuclease protection assay, we applied the ITO and MALDI-MS-based method for determining the stoichiometry of GG(m6A)CU and GGACU in RNA mixtures. Overall, the ITO-based nuclease protection and MALDI-MS method constitutes a rapid and promising approach for determining modification stoichiometries of consensus motifs. Full article
(This article belongs to the Special Issue Regulation of Gene Expression: RNA Modification of Genes)
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10 pages, 2329 KiB  
Review
m1A RNA Modification in Gene Expression Regulation
by Hao Jin, Chunxiao Huo, Tianhua Zhou and Shanshan Xie
Genes 2022, 13(5), 910; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050910 - 19 May 2022
Cited by 25 | Viewed by 3603
Abstract
N1-methyladenosine (m1A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m1A RNA [...] Read more.
N1-methyladenosine (m1A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m1A RNA modification in gene regulation and biological processes. In this review, we focus on progress in the study of m1A methyltransferases, m1A demethylases and m1A-dependent RNA-binding proteins and highlight the biological mechanisms and functions of m1A RNA modification, as well as its association with human disease. We also summarize the current understanding of detection approaches for m1A RNA modification. Full article
(This article belongs to the Special Issue Regulation of Gene Expression: RNA Modification of Genes)
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