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Feature Papers: RNA
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Feature Papers: RNA

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

Deadline for manuscript submissions: closed (20 March 2025) | Viewed by 3295

Special Issue Editor

Dr. Christiane Branlant

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Guest Editor
Christiane Branlant DRE CNRS, IMoPA CNRS-UL Laboratory UMR7365, Biopôle, Campus Brabois-Santé, Avenue de la Forêt de Haye, 54500 Vandoeuvre les Nancy, France
Interests: RNA structure and function; ribosome biogenesis; RNA splicing; RNA and diseases; non-coding RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the last 20 years, the RNA field has exploded with the finding of a huge number of new regulatory non-coding RNAs that play crucial roles in most biological processes. This Special Issue "Feature papers in the RNA field" aims to collect high-quality research articles, original review articles, and communications on recent advances in the RNA research field.

We encourage Editorial Board Members working in the RNA field to contribute feature papers reflecting the latest progresses in their exciting research field, or to invite relevant senior experts and high-level young colleagues to make original contributions to this Special Issue.

Topics include, but are not limited to, the following:

 

  • modified nucleotides in RNA
  • In vitro synthesis of RNA and its applications
  • viral RNAs and diseases
  • ribosomes and translation regulations
  • RNA splicing mechanisms and regulations
  • small and long non-coding RNAs
  • RNA transport mechanisms
  • RNAs and cancer
  • RNA–protein interactions

Dr. Christiane Branlant
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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • non-coding RNA
  • miRNAs
  • RNAs and chromatin structure
  • viral RNAs
  • synthetic RNAs

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

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15 pages, 6950 KiB  
Article
Cell Cycle-Based Molecular Features via Synthetic Lethality and Non-Coding RNA Interactions in Cancer
by Shizheng Xiong, Jiaming Jin, Xinmiao Zhao, Yang Zhao, Zhiheng He, Haochuan Guo, Chengjun Gong, Jiafeng Yu, Li Guo and Tingming Liang
Genes 2025, 16(3), 310; https://doi.org/10.3390/genes16030310 - 5 Mar 2025
Viewed by 728
Abstract
Background: The cell cycle, a critical and intricate biological process, comprises various phases, and its dysregulation plays a pivotal role in tumorigenesis and metastasis. The exploration of cell cycle-based molecular subtypes across pan-cancers, along with the application of synthetic lethality concepts, holds promise [...] Read more.
Background: The cell cycle, a critical and intricate biological process, comprises various phases, and its dysregulation plays a pivotal role in tumorigenesis and metastasis. The exploration of cell cycle-based molecular subtypes across pan-cancers, along with the application of synthetic lethality concepts, holds promise for advancing cancer therapies. Methods: A pan-cancer analysis was conducted to assess the cell cycle serves as a reliable signature for classifying molecular subtypes and to understand the potential clinical application of genes as potential drug targets based on synthetic lethality. Results: Molecular subtypes derived from cell cycle features in certain cancers, particularly kidney-related malignancies, exhibited distinct immune characteristics. Synthetic lethal interactions within the cell cycle pathway were common, with significant genetic interactions further identifying potential drug targets through the exploitation of genetic relationships with key driver genes. Additionally, miRNAs and lncRNAs may influence the cell cycle through miRNA:mRNA interactions and ceRNA networks, thereby enriching the genetic interaction landscape. Conclusions: These findings suggest that the cell cycle pathway could serve as a promising molecular subtype signature to enhance cancer prognostication and offer potential targets for anticancer drug development through synthetic lethality. Full article
(This article belongs to the Special Issue Feature Papers: RNA)
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Review

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18 pages, 1683 KiB  
Review
Detection of mRNA Transcript Variants
by Kevin Vo, Sharmin Shila, Yashica Sharma, Grace J. Pei, Cinthia Y. Rosales, Vinesh Dahiya, Patrick E. Fields and M. A. Karim Rumi
Genes 2025, 16(3), 343; https://doi.org/10.3390/genes16030343 - 16 Mar 2025
Viewed by 748
Abstract
Most eukaryotic genes express more than one mature mRNA, defined as transcript variants. This complex phenomenon arises from various mechanisms, such as using alternative transcription start sites and alternative post-transcriptional processing events. The resulting transcript variants can lead to synthesizing proteins that possess [...] Read more.
Most eukaryotic genes express more than one mature mRNA, defined as transcript variants. This complex phenomenon arises from various mechanisms, such as using alternative transcription start sites and alternative post-transcriptional processing events. The resulting transcript variants can lead to synthesizing proteins that possess distinct functional domains or may even generate noncoding RNAs, each with unique roles in cellular processes. The generation of these transcript variants is not merely a random occurrence; it is cell-type specific and varies with developmental stages, aging processes, or pathogenesis of diseases. This highlights the biological significance of transcript variants in regulating gene expression and their potential impact on cellular functionality. Despite the biological importance, investigating transcript variants has been hampered by challenges associated with detecting their expression. This review article addresses the advancements in molecular techniques in detecting transcript variants. Traditional methods such as RT-PCR and RT-qPCR can easily detect known transcript variants using primers that target unique exons associated with the variants. Other techniques like RACE-PCR and hybridization-based methods, including Northern blotting, RNase protection assays, and microarrays, have also been utilized to detect transcript variants. Nevertheless, RNA sequencing (RNA-Seq) has emerged as a powerful technique for identifying transcript variants, especially those with previously unknown sequences. The effectiveness of RNA sequencing in transcript variant detection depends on the specific sequencing approach and the precision of data analysis. By understanding the strengths and weaknesses of each laboratory technique, researchers can develop more effective strategies for detecting mRNA transcript variants. This ability will be crucial for our comprehensive understanding of gene regulation and the implications of transcript diversity in various biological contexts. Full article
(This article belongs to the Special Issue Feature Papers: RNA)
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22 pages, 1471 KiB  
Review
The Plethora of RNA–Protein Interactions Model a Basis for RNA Therapies
by Stephen J. Dansereau, Hua Cui, Ricky P. Dartawan and Jia Sheng
Genes 2025, 16(1), 48; https://doi.org/10.3390/genes16010048 - 2 Jan 2025
Viewed by 1471
Abstract
The notion of RNA-based therapeutics has gained wide attractions in both academic and commercial institutions. RNA is a polymer of nucleic acids that has been proven to be impressively versatile, dating to its hypothesized RNA World origins, evidenced by its enzymatic roles in [...] Read more.
The notion of RNA-based therapeutics has gained wide attractions in both academic and commercial institutions. RNA is a polymer of nucleic acids that has been proven to be impressively versatile, dating to its hypothesized RNA World origins, evidenced by its enzymatic roles in facilitating DNA replication, mRNA decay, and protein synthesis. This is underscored through the activities of riboswitches, spliceosomes, ribosomes, and telomerases. Given its broad range of interactions within the cell, RNA can be targeted by a therapeutic or modified as a pharmacologic scaffold for diseases such as nucleotide repeat disorders, infectious diseases, and cancer. RNA therapeutic techniques that have been researched include, but are not limited to, CRISPR/Cas gene editing, anti-sense oligonucleotides (ASOs), siRNA, small molecule treatments, and RNA aptamers. The knowledge gleaned from studying RNA-centric mechanisms will inevitably improve the design of RNA-based therapeutics. Building on this understanding, we explore the physiological diversity of RNA functions, examine specific dysfunctions, such as splicing errors and viral interactions, and discuss their therapeutic implications. Full article
(This article belongs to the Special Issue Feature Papers: RNA)
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