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Recent Progress in Molecular Biology of RNA 2.0
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Recent Progress in Molecular Biology of RNA 2.0

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 2394

Special Issue Editor

Dr. Anne-Catherine Prats

E-Mail Website
Guest Editor
UMR 1297-I2MC, Université de Toulouse, Inserm, UT3, FHU IMPACT, 31432 Toulouse, France
Interests: translation control; RNA; IRES; hypoxia; angiogenesis; cardiovascular disease; cancer; gene therapy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

When it was demonstrated in 1961 that the genetic information contained in DNA was provided into the locus to be translated into protein via an intermediary, the messenger RNA, RNA turned out to be the key in genome expression. RNA implication in cell biology rapidly extended to non-coding RNAs, whose function in translational machinery and splicing was shown as essential. A major milestone demonstrating the importance of RNA appeared in the beginning of the 21st century with the discovery that only 2% of the human genome codes proteins while 75% is transcribed, revealing the existence of numerous non-coding RNAs. Then, several families of non-coding RNAs were discovered, including microRNAs, long non-coding RNAs, circular RNAs, etc., which are fully involved in the epigenetics landscape. All this fundamental knowledge on RNA associated with the strong technological advances of these last few years provided by cutting-edge technologies in molecular biology led to biotechnological and medical applications of RNA. Technologies such as RNA interference and genome edition with the CRISPR Cas9, based on guide RNAs, have provided powerful tools to control gene expression. More recently, the mRNA vaccine against SARS-COV-2 has opened the way toward a new generation of RNA-based therapeutics. This Special Issue aims to update the state of art in this fascinating RNA world, on both basic and applied research aspects.

Potential topics include (but are not limited to):

  • Molecular mechanisms involving RNA
  • mRNA translational control
  • RNA maturation and metabolism
  • Non-coding RNAs
  • Circular RNAs
  • RNA–protein complexes
  • RNA in biotechnology
  • RNA and diseases
  • RNA-based therapeutics

Dr. Anne-Catherine Prats
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

  • mRNA
  • ncRNA
  • circRNA
  • translation
  • RNA-binding proteins
  • genome edition
  • diseases
  • therapeutics

Published Papers (4 papers)

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Research

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14 pages, 6176 KiB  
Article
Poly (I:C)-Induced microRNA-30b-5p Negatively Regulates the JAK/STAT Signaling Pathway to Mediate the Antiviral Immune Response in Silver Carp (Hypophthalmichthys molitrix) via Targeting CRFB5
by Meng Liu, Huan Tang, Kun Gao, Xiqing Zhang, Zhenhua Ma, Yunna Jia, Zihan Yang, Muhammad Inam, Yunhang Gao, Guiqin Wang and Xiaofeng Shan
Int. J. Mol. Sci. 2024, 25(11), 5712; https://doi.org/10.3390/ijms25115712 - 24 May 2024
Viewed by 194
Abstract
In aquaculture, viral diseases pose a significant threat and can lead to substantial economic losses. The primary defense against viral invasion is the innate immune system, with interferons (IFNs) playing a crucial role in mediating the immune response. With advancements in molecular biology, [...] Read more.
In aquaculture, viral diseases pose a significant threat and can lead to substantial economic losses. The primary defense against viral invasion is the innate immune system, with interferons (IFNs) playing a crucial role in mediating the immune response. With advancements in molecular biology, the role of non-coding RNA (ncRNA), particularly microRNAs (miRNAs), in gene expression has gained increasing attention. While the function of miRNAs in regulating the host immune response has been extensively studied, research on their immunomodulatory effects in teleost fish, including silver carp (Hyphthalmichthys molitrix), is limited. Therefore, this research aimed to investigate the immunomodulatory role of microRNA-30b-5p (miR-30b-5p) in the antiviral immune response of silver carp (Hypophthalmichthys molitrix) by targeting cytokine receptor family B5 (CRFB5) via the JAK/STAT signaling pathway. In this study, silver carp were stimulated with polyinosinic-polycytidylic acid (poly (I:C)), resulting in the identification of an up-regulated miRNA (miR-30b-5p). Through a dual luciferase assay, it was demonstrated that CRFB5, a receptor shared by fish type I interferon, is a novel target of miR-30b-5p. Furthermore, it was found that miR-30b-5p can suppress post-transcriptional CRFB5 expression. Importantly, this study revealed for the first time that miR-30b-5p negatively regulates the JAK/STAT signaling pathway, thereby mediating the antiviral immune response in silver carp by targeting CRFB5 and maintaining immune system stability. These findings not only contribute to the understanding of how miRNAs act as negative feedback regulators in teleost fish antiviral immunity but also suggest their potential therapeutic measures to prevent an excessive immune response. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Biology of RNA 2.0)
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26 pages, 5548 KiB  
Article
Mitochondrial Ribosomal Protein MRPS15 Is a Component of Cytosolic Ribosomes and Regulates Translation in Stressed Cardiomyocytes
by Florian David, Emilie Roussel, Carine Froment, Tangra Draia-Nicolau, Françoise Pujol, Odile Burlet-Schiltz, Anthony K. Henras, Eric Lacazette, Florent Morfoisse, Florence Tatin, Jean-Jacques Diaz, Frédéric Catez, Barbara Garmy-Susini and Anne-Catherine Prats
Int. J. Mol. Sci. 2024, 25(6), 3250; https://doi.org/10.3390/ijms25063250 - 13 Mar 2024
Viewed by 923
Abstract
Regulation of mRNA translation is a crucial step in controlling gene expression in stressed cells, impacting many pathologies, including heart ischemia. In recent years, ribosome heterogeneity has emerged as a key control mechanism driving the translation of subsets of mRNAs. In this study, [...] Read more.
Regulation of mRNA translation is a crucial step in controlling gene expression in stressed cells, impacting many pathologies, including heart ischemia. In recent years, ribosome heterogeneity has emerged as a key control mechanism driving the translation of subsets of mRNAs. In this study, we investigated variations in ribosome composition in human cardiomyocytes subjected to endoplasmic reticulum stress induced by tunicamycin treatment. Our findings demonstrate that this stress inhibits global translation in cardiomyocytes while activating internal ribosome entry site (IRES)-dependent translation. Analysis of translating ribosome composition in stressed and unstressed cardiomyocytes was conducted using mass spectrometry. We observed no significant changes in ribosomal protein composition, but several mitochondrial ribosomal proteins (MRPs) were identified in cytosolic polysomes, showing drastic variations between stressed and unstressed cells. The most notable increase in polysomes of stressed cells was observed in MRPS15. Its interaction with ribosomal proteins was confirmed by proximity ligation assay (PLA) and immunoprecipitation, suggesting its intrinsic role as a ribosomal component during stress. Knock-down or overexpression experiments of MRPS15 revealed its role as an activator of IRES-dependent translation. Furthermore, polysome profiling after immunoprecipitation with anti-MRPS15 antibody revealed that the “MRPS15 ribosome” is specialized in translating mRNAs involved in the unfolded protein response. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Biology of RNA 2.0)
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Review

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37 pages, 3068 KiB  
Review
Circular RNAs in Cell Cycle Regulation of Cancers
by Pannathon Thamjamrassri and Chaiyaboot Ariyachet
Int. J. Mol. Sci. 2024, 25(11), 6094; https://doi.org/10.3390/ijms25116094 (registering DOI) - 31 May 2024
Abstract
Cancer has been one of the most problematic health issues globally. Typically, all cancers share a common characteristic or cancer hallmark, such as sustaining cell proliferation, evading growth suppressors, and enabling replicative immortality. Indeed, cell cycle regulation in cancer is often found to [...] Read more.
Cancer has been one of the most problematic health issues globally. Typically, all cancers share a common characteristic or cancer hallmark, such as sustaining cell proliferation, evading growth suppressors, and enabling replicative immortality. Indeed, cell cycle regulation in cancer is often found to be dysregulated, leading to an increase in aggressiveness. These dysregulations are partly due to the aberrant cellular signaling pathway. In recent years, circular RNAs (circRNAs) have been widely studied and classified as one of the regulators in various cancers. Numerous studies have reported that circRNAs antagonize or promote cancer progression through the modulation of cell cycle regulators or their associated signaling pathways, directly or indirectly. Mostly, circRNAs are known to act as microRNA (miRNA) sponges. However, they also hold additional mechanisms for regulating cellular activity, including protein binding, RNA-binding protein (RBP) recruitment, and protein translation. This review will discuss the current knowledge of how circRNAs regulate cell cycle-related proteins through the abovementioned mechanisms in different cancers. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Biology of RNA 2.0)
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Other

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10 pages, 981 KiB  
Brief Report
Quantitative Investigation of FAD2 Cosuppression Reveals RDR6-Dependent and RDR6-Independent Gene Silencing Pathways
by Yangyang Chen, Hangkai Ku, Yingdong Zhao, Chang Du and Meng Zhang
Int. J. Mol. Sci. 2023, 24(24), 17165; https://doi.org/10.3390/ijms242417165 - 6 Dec 2023
Viewed by 950
Abstract
The frequency and extent of transgene-mediated cosuppression varies substantially among plant genes. However, the underlying mechanisms leading to strong cosuppression have received little attention. In previous studies, we showed that the expression of FAD2 in the seeds of Arabidopsis results in strong RDR6-mediated [...] Read more.
The frequency and extent of transgene-mediated cosuppression varies substantially among plant genes. However, the underlying mechanisms leading to strong cosuppression have received little attention. In previous studies, we showed that the expression of FAD2 in the seeds of Arabidopsis results in strong RDR6-mediated cosuppression, where both endogenous and transgenic FAD2 were silenced. Here, the FAD2 strong cosuppression system was quantitatively investigated to identify the genetic factors by the expression of FAD2 in their mutants. The involvement of DCL2, DCL4, AGO1, and EIN5 was first confirmed in FAD2 cosuppression. SKI2, a remover of 3′ end aberrant RNAs, was newly identified as being involved in the cosuppression, while DCL3 was identified as antagonistic to DCL2 and DCL3. FAD2 cosuppression was markedly reduced in dcl2, dcl4, and ago1. The existence of an RDR6-independent cosuppression was revealed for the first time, which was demonstrated by weak gene silencing in rdr6 ein5 ski2. Further investigation of FAD2 cosuppression may unveil unknown genetic factor(s). Full article
(This article belongs to the Special Issue Recent Progress in Molecular Biology of RNA 2.0)
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