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Cells
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Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs
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Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Nuclei: Function, Transport and Receptors".

Deadline for manuscript submissions: 15 July 2025 | Viewed by 4785

Special Issue Editor

Dr. Xinguo Chen

E-Mail Website
Guest Editor
National Cancer Institute, Frederick, MD, USA
Interests: noncoding RNA biogenesis and function; RNA-protein interactions; exo- and endoribonucleases; RNA processing and decay; RNA damage response

Special Issue Information

 Dear Colleagues,

Large class of noncoding RNAs (ncRNAs) play important regulatory roles in diverse biological processes, such as gene expression, cell differentiation, development, metabolism, and disease. In past years, discoveries of new ncRNAs have rapidly increased via revolutionized high-throughput sequencing, including RNA-seq technologies that can analyze single-cell transcriptomes and access secondary structures. Extraordinary efforts and progress have been made to understand the roles of some of the noncoding RNAs in post-transcriptional regulation (miRNAs), scaffolding (NEAT 1, 7SL), chromatin regulation (HOTTIP, HOTAIR), transcriptional silencing (XIST), and activation (eRNAs). In addition, some emerging ncRNAs have been demonstrated to function in complex processes; for example, tRNA-derived fragments (tRFs) are proposed to regulate translation inhibition, apoptosis, epigenetic inheritance, and cancer, whilst circular RNAs (circRNAs) have been shown to sponge miRNA, sponge proteins, modulate transcription, and regulate splicing. However, many ncRNAs remain uncharacterized, and their biogenesis as well as regulatory roles are yet to be elucidated.

This Special Issue aims to publish research articles, communications, and reviews covering any aspects of the biogenesis, biology, and function of ncRNAs.

Dr. Xinguo Chen
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. Cells is an international peer-reviewed open access semimonthly 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 2700 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

  • noncoding RNA biogenesis
  • long noncoding RNA (lncRNAs)
  • circular RNA (circRNAs)
  • enhancer RNA (eRNAs)
  • microRNA (miRNAs)
  • PIWI-interacting RNAs (pi-RNAs)
  • tRNA-derived fragments (tRFs)

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Published Papers (4 papers)

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Research

Jump to: Review

17 pages, 6822 KiB  
Article
LUCAT1-Mediated Competing Endogenous RNA (ceRNA) Network in Triple-Negative Breast Cancer
by Deepak Verma, Sumit Siddharth, Ashutosh S. Yende, Qitong Wu and Dipali Sharma
Cells 2024, 13(22), 1918; https://doi.org/10.3390/cells13221918 - 19 Nov 2024
Viewed by 428
Abstract
Breast cancer is a heterogeneous disease comprising multiple molecularly distinct subtypes with varied prevalence, prognostics, and treatment strategies. Among them, triple-negative breast cancer, though the least prevalent, is the most aggressive subtype, with limited therapeutic options. Recent emergence of competing endogenous RNA (ceRNA) [...] Read more.
Breast cancer is a heterogeneous disease comprising multiple molecularly distinct subtypes with varied prevalence, prognostics, and treatment strategies. Among them, triple-negative breast cancer, though the least prevalent, is the most aggressive subtype, with limited therapeutic options. Recent emergence of competing endogenous RNA (ceRNA) networks has highlighted how long noncoding RNAs (lncRNAs), microRNAs (miRs), and mRNA orchestrate a complex interplay meticulously modulating mRNA functionality. Focusing on TNBC, this study aimed to construct a ceRNA network using differentially expressed lncRNAs, miRs, and mRNAs. We queried the differentially expressed lncRNAs (DElncRNAs) between TNBC and luminal samples and found 389 upregulated and 386 downregulated lncRNAs, including novel transcripts in TNBC. DElncRNAs were further evaluated for their clinical, functional, and mechanistic relevance to TNBCs using the lnc2cancer 3.0 database, which presented LUCAT1 (lung cancer-associated transcript 1) as a putative node. Next, the ceRNA network (lncRNA–miRNA–mRNA) of LUCAT1 was established. Several miRNA–mRNA connections of LUCAT1 implicated in regulating stemness (LUCAT1-miR-375-Yap1, LUCAT1-miR181-5p-Wnt, LUCAT1-miR-199a-5p-ZEB1), apoptosis (LUCAT1-miR-181c-5p-Bcl2), drug efflux (LUCAT1-miR-200c-ABCB1, LRP1, MRP5, MDR1), and sheddase activities (LUCAT1-miR-493-5p-ADAM10) were identified, indicating an intricate regulatory mechanism of LUCAT1 in TNBC. Indeed, LUCAT1 silencing led to mitigated cell growth, migration, and stem-like features in TNBC. This work sheds light on the LUCAT1 ceRNA network in TNBC and implies its involvement in TNBC growth and progression. Full article
(This article belongs to the Special Issue Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs)
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22 pages, 5573 KiB  
Article
Circular RNA hsa_circ_0008726 Targets the hsa-miR-206-3p/KLF4 Axis to Modulate 4,4′-Methylene Diphenyl Diisocyanate-Glutathione Conjugate-Induced Chemokine Transcription in Macrophages
by Chen-Chung Lin, Brandon F. Law and Justin M. Hettick
Cells 2024, 13(20), 1725; https://doi.org/10.3390/cells13201725 - 18 Oct 2024
Viewed by 850
Abstract
Exposure to 4,4′-methylene diphenyl diisocyanate (MDI) in the workplace may lead to the development of occupational asthma (OA). However, the specific mechanism(s) by which MDI induces OA are poorly understood. Previous reports have demonstrated that MDI and MDI-glutathione (GSH) conjugate exposure downregulates endogenous [...] Read more.
Exposure to 4,4′-methylene diphenyl diisocyanate (MDI) in the workplace may lead to the development of occupational asthma (OA). However, the specific mechanism(s) by which MDI induces OA are poorly understood. Previous reports have demonstrated that MDI and MDI-glutathione (GSH) conjugate exposure downregulates endogenous human/murine (hsa/mmu)-microRNA(miR)-206-3p, resulting in the activation of mmu/hsa-miR-206-3p-regulated signaling pathways in macrophages. Circular RNAs (circRNAs) regulate many important biological processes by targeting endogenous miRs; however, whether MDI/MDI-GSH exposure may influence circRNA expressions is unknown. Several circRNAs have been identified that regulate hsa-miR-206-3p. We hypothesize that MDI-GSH conjugate exposure induces endogenous circRNA(s) to regulate hsa-miR-206-3p in macrophages. The expression of candidate hsa-miR-206-3p-binding circRNAs was determined from MDI-GSH conjugate-treated differentiated THP-1 macrophages using RT-qPCR. MDI-GSH exposures induced hsa_circ_0008726 and its host gene transcript DNAJB6, whereas other circRNA(s) examined were either not detected or unchanged. RNA-induced silencing complex-immunoprecipitation (RISC-IP) experiments confirm that hsa-miR-206-3p can bind to hsa_circ_0008726. The expressions of endogenous hsa-miR-206-3p, hsa-miR-206-3p-regulated KLF4, and KLF4-activated M2 macrophage-associated markers and chemokines were up-/down-regulated by transfection of hsa_circ_0008726 siRNAs or hsa_circ_0008726 overexpression plasmid in macrophages, respectively. These results suggest MDI-GSH exposure downregulates hsa-miR-206-3p via induction of endogenous hsa_circ_0008726/DNAJB6, resulting in the upregulation of hsa-miR-206-3p-mediated regulations in macrophages. Full article
(This article belongs to the Special Issue Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs)
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15 pages, 4785 KiB  
Article
LncRNA NEAT1/miR-146a-5p Axis Restores Normal Angiogenesis in Diabetic Foot Ulcers by Targeting mafG
by TCA Architha, George Raj Juanitaa, Ramanarayanan Vijayalalitha, Ravichandran Jayasuriya, Gopinathan Athira, Ramachandran Balamurugan, Kumar Ganesan and Kunka Mohanram Ramkumar
Cells 2024, 13(5), 456; https://doi.org/10.3390/cells13050456 - 5 Mar 2024
Viewed by 1464
Abstract
Non-healing lesions in diabetic foot ulcers are a significant effect of poor angiogenesis. Epigenetic regulators, mainly lncRNA and miRNA, are recognized for their important roles in disease progression. We deciphered the regulation of lncRNA NEAT1 through the miR-146a-5p/mafG axis in the progression of [...] Read more.
Non-healing lesions in diabetic foot ulcers are a significant effect of poor angiogenesis. Epigenetic regulators, mainly lncRNA and miRNA, are recognized for their important roles in disease progression. We deciphered the regulation of lncRNA NEAT1 through the miR-146a-5p/mafG axis in the progression of DFU. A lowered expression of lncRNA NEAT1 was associated with dysregulated angiogenesis through the reduced expression of mafG, SDF-1α, and VEGF in chronic ulcer subjects compared to acute DFU. This was validated by silencing NEAT1 by SiRNA in the endothelial cells which resulted in the transcriptional repression of target genes. Our in silico analysis identified miR-146a-5p as a potential target of lncRNA NEAT1. Further, silencing NEAT1 led to an increase in the levels of miR-146a-5p in chronic DFU subjects. This research presents the role of the lncRNA NEAT1/miR-146a-5p/mafG axis in enhancing angiogenesis in DFU. Full article
(This article belongs to the Special Issue Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs)
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Review

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22 pages, 2308 KiB  
Review
A Comprehensive Insight and In Silico Analysis of CircRNAs in Hepatocellular Carcinoma: A Step toward ncRNA-Based Precision Medicine
by Rana A. Youness, Hossam A. Hassan, Tasneem Abaza, Ahmed A. Hady, Hekmat M. El Magdoub, Mohamed Ali, Johannes Vogel, Markus Thiersch, Max Gassmann, Nadia M. Hamdy and Mostafa A. Aboouf
Cells 2024, 13(15), 1245; https://doi.org/10.3390/cells13151245 - 24 Jul 2024
Viewed by 1166
Abstract
Circular RNAs (circRNAs) are cardinal players in numerous physiological and pathological processes. CircRNAs play dual roles as tumor suppressors and oncogenes in different oncological contexts, including hepatocellular carcinoma (HCC). Their roles significantly impact the disease at all stages, including initiation, development, progression, invasion, [...] Read more.
Circular RNAs (circRNAs) are cardinal players in numerous physiological and pathological processes. CircRNAs play dual roles as tumor suppressors and oncogenes in different oncological contexts, including hepatocellular carcinoma (HCC). Their roles significantly impact the disease at all stages, including initiation, development, progression, invasion, and metastasis, in addition to the response to treatment. In this review, we discuss the biogenesis and regulatory functional roles of circRNAs, as well as circRNA–protein–mRNA ternary complex formation, elucidating the intricate pathways tuned by circRNAs to modulate gene expression and cellular processes through a comprehensive literature search, in silico search, and bioinformatics analysis. With a particular focus on the interplay between circRNAs, epigenetics, and HCC pathology, the article sets the stage for further exploration of circRNAs as novel investigational theranostic agents in the dynamic realm of HCC. Full article
(This article belongs to the Special Issue Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs)
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