Non-Coding RNA

33 pages, 1562 KiB

Open AccessReview

Role of ncRNAs in the Development of Chronic Pain

by Mario García-Domínguez

Non-Coding RNA 2025, 11(4), 51; https://doi.org/10.3390/ncrna11040051 - 3 Jul 2025

Chronic pain is a multifactorial and complex condition that significantly affects individuals’ quality of life. The underlying mechanisms of chronic pain involve complex alterations in neural circuits, gene expression, and cellular signaling pathways. Recently, ncRNAs, such as miRNAs, lncRNAs, circRNAs, and siRNAs, have [...] Read more.

Chronic pain is a multifactorial and complex condition that significantly affects individuals’ quality of life. The underlying mechanisms of chronic pain involve complex alterations in neural circuits, gene expression, and cellular signaling pathways. Recently, ncRNAs, such as miRNAs, lncRNAs, circRNAs, and siRNAs, have been identified as crucial regulators in the pathophysiology of chronic pain. These ncRNAs modulate gene expression at both the transcriptional and post-transcriptional levels, affecting pain-related pathways like inflammation, neuronal plasticity, and sensory processing. miRNAs have been shown to control genes involved in pain perception and nociceptive signaling, while lncRNAs interact with chromatin remodeling factors and transcription factors to modify pain-related gene expression. CircRNAs act as sponges for miRNAs, thereby influencing pain mechanisms. siRNAs, recognized for their gene-silencing capabilities, also participate in regulating the expression of pain-related genes. This review examines the diverse roles of ncRNAs in chronic pain, emphasizing their potential as biomarkers for pain assessment and as targets for novel therapeutic strategies. A profound understanding of the ncRNA-mediated regulatory networks involved in chronic pain could result in more effective and personalized pain management solutions. Full article

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3 pages, 134 KiB

Open AccessCorrection

Correction: Piergentili et al. miR-125 in Breast Cancer Etiopathogenesis: An Emerging Role as a Biomarker in Differential Diagnosis, Regenerative Medicine, and the Challenges of Personalized Medicine. Non-Coding RNA 2024, 10, 16

by Roberto Piergentili, Enrico Marinelli, Gaspare Cucinella, Alessandra Lopez, Gabriele Napoletano, Giuseppe Gullo and Simona Zaami

Non-Coding RNA 2025, 11(4), 50; https://doi.org/10.3390/ncrna11040050 - 25 Jun 2025

Abstract

There was an error in the original publication [...] Full article

25 pages, 1699 KiB

Open AccessArticle

LncRNA Subcellular Localization Across Diverse Cell Lines: An Exploration Using Deep Learning with Inexact q-mers

by Weijun Yi, Jason R. Miller, Gangqing Hu and Donald A. Adjeroh

Non-Coding RNA 2025, 11(4), 49; https://doi.org/10.3390/ncrna11040049 - 25 Jun 2025

Abstract

Background: Long non-coding Ribonucleic Acids (lncRNAs) can be localized to different cellular compartments, such as the nuclear and the cytoplasmic regions. Their biological functions are influenced by the region of the cell where they are located. Compared to the vast number of lncRNAs, [...] Read more.

Background: Long non-coding Ribonucleic Acids (lncRNAs) can be localized to different cellular compartments, such as the nuclear and the cytoplasmic regions. Their biological functions are influenced by the region of the cell where they are located. Compared to the vast number of lncRNAs, only a relatively small proportion have annotations regarding their subcellular localization. It would be helpful if those few annotated lncRNAs could be leveraged to develop predictive models for localization of other lncRNAs. Methods: Conventional computational methods use q-mer profiles from lncRNA sequences and train machine learning models such as support vector machines and logistic regression with the profiles. These methods focus on the exact q-mer. Given possible sequence mutations and other uncertainties in genomic sequences and their role in biological function, a consideration of these variabilities might improve our ability to model lncRNAs and their localization. Thus, we build on inexact q-mers and use machine learning/deep learning techniques to study three specific problems in lncRNA subcellular localization, namely, prediction of lncRNA localization using inexact q-mers, the issue of whether lncRNA localization is cell-type-specific, and the notion of switching (lncRNA) genes. Results: We performed our analysis using data on lncRNA localization across 15 cell lines. Our results showed that using inexact q-mers (with q = 6) can improve the lncRNA localization prediction performance compared to using exact q-mers. Further, we showed that lncRNA localization, in general, is not cell-line-specific. We also identified a category of LncRNAs which switch cellular compartments between different cell lines (we call them switching lncRNAs). These switching lncRNAs complicate the problem of predicting lncRNA localization using machine learning models, showing that lncRNA localization is still a major challenge. Full article

(This article belongs to the Section Long Non-Coding RNA)

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11 pages, 718 KiB

Open AccessBrief Report

Insights into miRNAs of the Stingless Bee Melipona quadrifasciata

by Dalliane Oliveira Soares, Lucas Yago Melo Ferreira, Gabriel Victor Pina Rodrigues, João Pedro Nunes Santos, Ícaro Santos Lopes, Lucas Barbosa de Amorim Conceição, Tatyana Chagas Moura, Isaque João da Silva de Faria, Roenick Proveti Olmo, Weyder Cristiano Santana, Marco Antônio Costa and Eric Roberto Guimarães Rocha Aguiar

Non-Coding RNA 2025, 11(3), 48; https://doi.org/10.3390/ncrna11030048 - 19 Jun 2025

Abstract

MicroRNAs (miRNAs) are key post-transcriptional regulators involved in a wide range of biological processes in insects, yet little is known about their roles in stingless bees. Here, we present the first characterization of miRNAs in Melipona quadrifasciata using small RNAs (sRNAs) deep sequencing. [...] Read more.

MicroRNAs (miRNAs) are key post-transcriptional regulators involved in a wide range of biological processes in insects, yet little is known about their roles in stingless bees. Here, we present the first characterization of miRNAs in Melipona quadrifasciata using small RNAs (sRNAs) deep sequencing. A total of 193 high-confidence mature miRNAs were identified, including 106 M. quadrifasciata-exclusive sequences. Expression profiling revealed that mqu-miR-1 and mqu-miR-276 together accounted for over 70% of all miRNA reads, suggesting their central roles in development and reproduction. Comparative analyses showed a higher conservation of M. quadrifasciata miRNAs with other Hymenopterans, especially Apis mellifera and Bombus spp. Putative target genes were predicted using a consensus approach, and functional annotation indicated their involvement in diverse biological regulatory pathways. This work represents the first comprehensive identification of the miRNA repertoire in stingless bees using sRNAs and provides a valuable foundation for understanding miRNA-mediated gene regulation in this ecologically and economically important pollinator. Full article

(This article belongs to the Section Small Non-Coding RNA)

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23 pages, 5199 KiB

Open AccessArticle

Diagnostic Potential of Exosomal and Non-Exosomal Biomarkers in Lung Cancer: A Comparative Analysis Using a Rat Model of Lung Carcinogenesis

by Sherien M. El-Daly, Sahar S. Abdelrahman, Amira Mohamed Abd El-Jawad, Mahmoud A. Abdel-Monem and Gamila S. M. El-Saeed

Non-Coding RNA 2025, 11(3), 47; https://doi.org/10.3390/ncrna11030047 - 16 Jun 2025

Abstract

Background: Identifying liquid biopsy biomarkers with high efficacy is crucial for cancer diagnosis. Exosomal cargo, including miRNAs and proteins, offers enhanced stability in biofluids compared with their free circulating forms, but direct comparisons of their diagnostic performance remain limited. This study evaluates and [...] Read more.

Background: Identifying liquid biopsy biomarkers with high efficacy is crucial for cancer diagnosis. Exosomal cargo, including miRNAs and proteins, offers enhanced stability in biofluids compared with their free circulating forms, but direct comparisons of their diagnostic performance remain limited. This study evaluates and compares the diagnostic value of selected miRNAs and protein markers in exosomal versus non-exosomal fractions across stages of lung carcinogenesis in a rat model. Methods: Lung cancer was induced in rats, and blood and lung tissue samples were collected at consecutive stages of tumor induction. We investigated the expression patterns of key miRNAs (miR-19b, miR-21, and miR-145) in exosomes, serum, and tissue and quantified levels of tumor biomarkers CEA and CYFRA 21-1 in exosomal and serum fractions. Results: Our results revealed distinct expression patterns of the evaluated miRNAs across exosomes, serum, and tissue, throughout different stages of tumor induction. The expression of exosomal miRNAs dynamically changed in parallel with the tumor induction process, demonstrating high diagnostic efficacy. Specifically, exosomal miR-19b and miR-21 were significantly upregulated from an early induction stage, whereas their serum and tissue forms increased only during the late stages of induction. On the other hand, miR-145 was consistently downregulated across all fractions at every stage. Both exosomal and serum CEA levels increased significantly during tumor induction, while serum CYFRA 21-1 outperformed its exosomal counterpart. Strong positive correlations linked exosomal miR-19b and miR-145 with their non-exosomal counterparts, while moderate correlations were seen for miR-21 and the protein markers. Conclusions: Our findings underscore the value of integrating exosomal biomarkers in liquid biopsies, highlighting their potential to improve early detection and monitoring of lung cancer development. Full article

(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)

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20 pages, 2048 KiB

Open AccessArticle

Patterns of Circulating piRNAs in the Context of a Single Bout of Exercise: Potential Biomarkers of Exercise-Induced Adaptation?

by Caroline Eva Riedel, Javier Ibáñez, Annunziata Fragasso, Angelika Schmitt, Manuel Widmann, Felipe Mattioni Maturana, Andreas M. Niess and Barbara Munz

Non-Coding RNA 2025, 11(3), 46; https://doi.org/10.3390/ncrna11030046 - 16 Jun 2025

Abstract

Background: Physical activity induces a range of physiological and molecular adaptations, particularly affecting skeletal muscle and the cardiovascular system, regulating both tissue architecture and metabolic pathways. Emerging evidence suggests that PIWI-interacting RNAs (piRNAs) may serve as potential biomarkers for these adaptations. Here, we [...] Read more.

Background: Physical activity induces a range of physiological and molecular adaptations, particularly affecting skeletal muscle and the cardiovascular system, regulating both tissue architecture and metabolic pathways. Emerging evidence suggests that PIWI-interacting RNAs (piRNAs) may serve as potential biomarkers for these adaptations. Here, we analyzed piRNA patterns in the context of exercise. Methods: This study selected eight participants of the iReAct study (DRKS00017446) for piRNA analysis. Baseline assessments included demographic profiling and fitness evaluation, particularly maximal oxygen uptake (V̇O2max) assessment. In addition, blood samples were collected pre- and (for six of the eight participants) post- standard reference training sessions. Subsequently, subjects underwent 6-week training protocols, employing standardized high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) regimens. Next, RNA sequencing was conducted to identify differentially expressed piRNAs, and correlation analyses were performed between piRNA expression patterns and training-associated changes in V̇O2max. Finally, to identify piRNAs potentially of interest in the context of exercise, different screening procedures were applied. Results: There were unique and specific changes in individual piRNA expression levels in response to exercise. In addition, we could define correlations of piRNA expression patterns, namely of piR-32886, piR-33151, piR-12547, and piR-33074, with changes in V̇O2max. These correlations did not reach significance in the small sample size of this pilot study, but might be verified in larger, confirming studies. Conclusions: This hypothesis-generating study identifies characteristic piRNA patterns in the context of exercise. Their significance as biomarkers is yet to be determined. Full article

(This article belongs to the Section Detection and Biomarkers of Non-Coding RNA)

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15 pages, 2877 KiB

Open AccessArticle

Role of Compensatory miRNA Networks in Cognitive Recovery from Heart Failure

by Verena Gisa, Md Rezaul Islam, Dawid Lbik, Raoul Maximilian Hofmann, Tonatiuh Pena, Dennis Manfred Krüger, Susanne Burkhardt, Anna-Lena Schütz, Farahnaz Sananbenesi, Karl Toischer and Andre Fischer

Non-Coding RNA 2025, 11(3), 45; https://doi.org/10.3390/ncrna11030045 - 12 Jun 2025

Abstract

Background: Heart failure (HF) is associated with an increased risk of cognitive impairment and hippocampal dysfunction, yet the underlying molecular mechanisms remain poorly understood. This study aims to investigate the role of microRNA (miRNA) networks in hippocampus-dependent memory recovery in a mouse model [...] Read more.

Background: Heart failure (HF) is associated with an increased risk of cognitive impairment and hippocampal dysfunction, yet the underlying molecular mechanisms remain poorly understood. This study aims to investigate the role of microRNA (miRNA) networks in hippocampus-dependent memory recovery in a mouse model of HF. Methods: CaMKIIδC transgenic (TG) mice, a model for HF, were used to assess hippocampal function at 3 and 6 months of age. Memory performance was evaluated using hippocampus-dependent behavioral tasks. Small RNA sequencing was performed to analyze hippocampal miRNA expression profiles across both time points. Bioinformatic analyses identified miRNAs that potentially regulate genes previously implicated in HF-induced cognitive impairment. Results: We have previously shown that at 3 months of age, CaMKIIδC TG mice exhibited significant memory deficits associated with dysregulated hippocampal gene expression. In this study, we showed that these impairments, memory impairment and hippocampal gene expression, were no longer detectable at 6 months, despite persistent cardiac dysfunction. However, small RNA sequencing revealed a dynamic shift in hippocampal miRNA expression, identifying 27 miRNAs as “compensatory miRs” that targeted 73% of the transcripts dysregulated at 3 months but reinstated by 6 months. Notably, miR-181a-5p emerged as a central regulatory hub, with its downregulation coinciding with restored memory function. Conclusions: These findings suggest that miRNA networks contribute to the restoration of hippocampal function in HF despite continued cardiac pathology and provide an important compensatory mechanism towards memory impairment. A better understanding of these compensatory miRNA mechanisms may provide novel therapeutic targets for managing HF-related cognitive dysfunction. Full article

(This article belongs to the Section Clinical Applications of Non-Coding RNA)

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17 pages, 2165 KiB

Open AccessReview

The Multifaceted Roles of CHROMR in Innate Immunity, Cancer, and Cholesterol Homeostasis

by Emma R. Blaustein and Coen van Solingen

Non-Coding RNA 2025, 11(3), 44; https://doi.org/10.3390/ncrna11030044 - 10 Jun 2025

Abstract

CHROMR is a primate-specific long noncoding RNA with emerging roles in homeostasis and pathophysiology. Elevated blood levels of CHROMR have been observed in patients with cardiovascular disease and several cancers, where it is correlated with poor clinical outcomes. Like many lncRNAs, CHROMR accumulates [...] Read more.

CHROMR is a primate-specific long noncoding RNA with emerging roles in homeostasis and pathophysiology. Elevated blood levels of CHROMR have been observed in patients with cardiovascular disease and several cancers, where it is correlated with poor clinical outcomes. Like many lncRNAs, CHROMR accumulates in both the nucleus and the cytoplasm, and it assumes distinct functions in each of these cellular compartments. In the nucleus, CHROMR sequesters a transcriptional repressor complex to activate interferon-stimulated gene expression and antiviral immunity. In the cytoplasm, CHROMR competitively inhibits microRNAs involved in cholesterol efflux and cell cycle regulation, thereby impacting gene pathways involved in reverse cholesterol transport, HDL biogenesis, and tumor growth. In this review, we detail the multifaceted functions of CHROMR in cholesterol metabolism, innate immunity, and cancer progression. We also explore the potential molecular mechanisms that govern its expression and dynamic subcellular localization, which may be key to its functional versatility. Advancing our understanding of the regulatory networks and cellular environments that shape CHROMR activity will be critical for assessing its promise as a therapeutic target and diagnostic biomarker. Full article

(This article belongs to the Section Long Non-Coding RNA)

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21 pages, 2183 KiB

Open AccessArticle

Human Papillomavirus-Encoded microRNAs as Regulators of Human Gene Expression in Anal Squamous Cell Carcinoma: A Meta-Transcriptomics Study

by Daniel J. García, Marco A. Pulpillo-Berrocal, José L. Ruiz, Eduardo Andrés-León and Laura C. Terrón-Camero

Non-Coding RNA 2025, 11(3), 43; https://doi.org/10.3390/ncrna11030043 - 9 Jun 2025

Abstract

Introduction: Anal squamous cell carcinoma (ASCC) is a rare but increasingly common gastrointestinal malignancy, mainly associated with oncogenic human papillomaviruses (HPVs). The role of non-coding RNAs (ncRNAs) in tumorigenesis is recognized, but the impact of viral ncRNAs on host gene expression remains unclear. [...] Read more.

Introduction: Anal squamous cell carcinoma (ASCC) is a rare but increasingly common gastrointestinal malignancy, mainly associated with oncogenic human papillomaviruses (HPVs). The role of non-coding RNAs (ncRNAs) in tumorigenesis is recognized, but the impact of viral ncRNAs on host gene expression remains unclear. Methods: We re-analyzed total RNA-Seq data from 70 anal biopsies: 31 low-grade squamous intraepithelial lesions (LGSIL), 16 high-grade SIL (HGSIL), and 23 ASCC cases. Microbial composition was assessed taxonomically. Novel viral miRNAs were predicted using vsRNAfinder and linked to host targets using TargetScan and expression correlation analyses. Results: Microbial profiling revealed significant differences in abundance, with Alphapapillomaviruses types 9, 10, and 14 enriched across lesion grades. We identified 90 novel viral miRNAs and 177 significant anti-correlated miRNA–mRNA interactions. Target genes were enriched in pathways related to cell cycle, epithelial–mesenchymal transition, lipid metabolism, immune modulation, and viral replication. Discussion: Our findings suggest that HPV-derived miRNAs, including those from low-risk types, may contribute to neoplastic transformation by modulating host regulatory networks. Conclusion: This study highlights viral miRNAs as potential drivers of HPV-related anal cancer and supports their utility as early biomarkers and therapeutic targets in ASCC. Full article

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27 pages, 1665 KiB

Open AccessReview

An Emphasis on the Role of Long Non-Coding RNAs in Viral Gene Expression, Pathogenesis, and Innate Immunity in Viral Chicken Diseases

by Anindita Sarma, Parul Suri, Megan Justice, Raja Angamuthu and Samuel Pushparaj

Non-Coding RNA 2025, 11(3), 42; https://doi.org/10.3390/ncrna11030042 - 26 May 2025

Abstract

The poultry farming industry encounters considerable obstacles stemming from viral diseases, resulting in elevated mortality rates and substantial economic losses. Current research highlights the significant involvement of long non-coding RNAs (lncRNAs) in the interactions between hosts and pathogens by enhancing antiviral responses at [...] Read more.

The poultry farming industry encounters considerable obstacles stemming from viral diseases, resulting in elevated mortality rates and substantial economic losses. Current research highlights the significant involvement of long non-coding RNAs (lncRNAs) in the interactions between hosts and pathogens by enhancing antiviral responses at different levels, such as the activation of pathogen recognition receptors, as well as through epigenetic, transcriptional, and post-transcriptional modifications. Specific long non-coding RNAs (lncRNAs), including ERL lncRNA, linc-GALMD3, and loc107051710, have been recognized as significant contributors to the antiviral immune response to multiple avian viral pathogens. Understanding the mechanisms by which long non-coding RNAs (lncRNAs) act offers valuable insights into prospective diagnostic and therapeutic approaches aimed at improving disease resistance in poultry. Differentially expressed lncRNAs may also be utilized as biomarkers for both prognosis and diagnosis of avian viral diseases. This review delves into the various roles of long non-coding RNAs (lncRNAs) in the context of viral diseases in chickens, such as avian leukosis, Marek’s disease, infectious bursal disease, avian influenza, infectious bronchitis, and Newcastle disease. It highlights the pivotal role of lncRNAs in the complex dynamics between the host and viral pathogens, particularly their interactions with specific viral proteins. Understanding these interactions may provide valuable insights into the spatial and temporal regulation of lncRNAs, aid in the identification of potential drug targets, and reveal the expression patterns of lncRNA and coding gene transcripts in response to different viral infections in avian species. Full article

(This article belongs to the Section Long Non-Coding RNA)

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25 pages, 1142 KiB

Open AccessArticle

Polychlorinated Biphenyl Exposure Alters tRNA Transcriptome in High-Fat Diet-Fed Mouse Liver

by Carolyn M. Klinge, Julia H. Chariker, Kellianne M. Piell, Belinda J. Petri, Eric C. Rouchka and Matthew C. Cave

Non-Coding RNA 2025, 11(3), 41; https://doi.org/10.3390/ncrna11030041 - 22 May 2025

Abstract

Background/Objectives: Exposure of high-fat diet (HFD)-fed mice to polychlorinated biphenyls (PCBs) results in metabolic dysfunction-associated steatotic liver disease (MASLD) and progression to metabolic dysfunction-associated steatohepatitis (MASH). The mechanisms by which HFD diet and PCBs increase MASLD are unclear. Previously, we identified differences in [...] Read more.

Background/Objectives: Exposure of high-fat diet (HFD)-fed mice to polychlorinated biphenyls (PCBs) results in metabolic dysfunction-associated steatotic liver disease (MASLD) and progression to metabolic dysfunction-associated steatohepatitis (MASH). The mechanisms by which HFD diet and PCBs increase MASLD are unclear. Previously, we identified differences in HFD-fed mouse liver tRNA modifications with single oral exposures to the dioxin-like PCB126, the non-dioxin-like PCB mixture Aroclor 1260 (Ar1260), or the combination of Ar1260 + PCB126. Methods: Here, we used small RNA sequencing and the tRNA analysis of expression (tRAX) pipeline to examine if PCB exposures alter the tRNA transcriptome, including tRNA-derived fragments (tRFs), in the livers of the PCB-exposed mice. Results: Each PCB exposure produced distinct hepatic tRNA transcriptomes with more tRNAs decreased than increased. Only tRNA-Glu-TTC-1 was reduced with all three PCB exposures. More changes in tRFs were identified with Ar1260 alone or in combination with PCB126 than with PCB126 alone. Four tRF-3s were upregulated in both PCB126 and Ar1260 + PCB126 co-exposed mice, suggesting PCB126 as responsible for this increase. We previously reported that PCB126 exposure increased hepatic Angiogenin (ANG) protein which generates tRF-3s. Four previously reported tRNA modifications corresponded to positions of PCB-associated tRNA modifications identified by tRAX: m1A, m6A, ms2t6A, and Ψ. Conclusions: Overall, the differences in hepatic tRNAs and tRFs with three different PCB exposures suggest that PCB exposures play an unexplored role in regulating translation in mouse liver. Full article

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1 pages, 129 KiB

Open AccessCorrection

Correction: Schlösser et al. Anti-HIV-1 Effect of the Fluoroquinolone Enoxacin and Modulation of Pro-Viral hsa-miR-132 Processing in CEM-SS Cells. Non-Coding RNA 2025, 11, 8

by Verena Schlösser, Helen Louise Lightfoot, Christine Leemann, Seyedeh Elnaz Banijamali, Aathma Merin Bejoy, Shashank Tiwari, Jeffrey L. Schloßhauer, Valentina Vongrad, Andreas Brunschweiger, Jonathan Hall, Karin J. Metzner and Jochen Imig

Non-Coding RNA 2025, 11(3), 40; https://doi.org/10.3390/ncrna11030040 - 16 May 2025

Abstract

Seyedeh Elnaz Banijamali was not included as an author in the original publication [...] Full article

23 pages, 2452 KiB

Open AccessArticle

Analysis of RNA Transcribed by RNA Polymerase III from B2 SINEs in Mouse Cells

by Olga R. Borodulina, Sergey A. Kosushkin, Ilia G. Ustyantsev, Nikita S. Vassetzky and Dmitri A. Kramerov

Non-Coding RNA 2025, 11(3), 39; https://doi.org/10.3390/ncrna11030039 - 14 May 2025

Abstract

Background/Objectives: SINEs (short interspersed elements) are eukaryotic non-autonomous retrotransposons. They are transcribed by RNA polymerase III (pol III) and generate non-coding RNAs. The 3′ end of many mammalian SINEs contains a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail. [...] Read more.

Background/Objectives: SINEs (short interspersed elements) are eukaryotic non-autonomous retrotransposons. They are transcribed by RNA polymerase III (pol III) and generate non-coding RNAs. The 3′ end of many mammalian SINEs contains a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail. Studies have shown that, in human HeLa cells that have been transiently transfected with such SINEs, short pol III-generated SINE transcripts undergo polyadenylation, resulting in the addition of a long poly(A)-tail. Notably, this AAUAAA-dependent polyadenylation is not characteristic of any other transcripts synthesized by pol III. B2 SINEs, found in the genomes of mouse-like rodents, exemplify all these features. Methods: In this study, we implemented a novel approach to sequencing pol III-generated B2 transcripts from mouse cell cultures (L929 and 4T1) and organs (brain and testis). Results: Transcription occurred in 16,000–20,000 B2 copies in each cell type, 51–62% of which were transcribed in all four cell types. Effective transcription terminators (e.g., TCT_>3 and T_≥4) were found in approximately 40% of the transcribed B2 copies. The transcripts of these B2 copies contained a truncated terminator sequence, as pol III transcriptional arrest is known to occur within the terminator, with a poly(A)-tail immediately downstream. Such a tail could only have formed through RNA polyadenylation. Conclusions: These results demonstrate that B2 transcripts synthesized by pol III are capable of polyadenylation in mouse cells. We discuss the transcription of B2 copies with and without moderately efficient pol III terminators (TCTTT) and provide examples of the polyadenylation of such transcripts. Full article

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15 pages, 4295 KiB

Open AccessFeature PaperArticle

Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer

by Mafalda Antunes-Ferreira, Ilias Glogovitis, Diogo Fortunato, Silvia D’Ambrosi, Mariona Colom Saborit, Galina Yahubyan, Vesselin Baev, Michael Hackenberg, Natasa Zarovni, Thomas Wurdinger and Danijela Koppers-Lalic

Non-Coding RNA 2025, 11(3), 38; https://doi.org/10.3390/ncrna11030038 - 7 May 2025

Abstract

Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in [...] Read more.

Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in patients with non-small-cell lung cancer (NSCLC), focusing on their small RNA signatures and diagnostic potential. Methods: The EVs were isolated directly from the plasma of healthy donors and patients with NSCLC using the surface markers CD9, CD63, CD81 (overall EVs), and CD61 (PD). Small RNA sequencing was then performed to comprehensively profile the miRNAs. Results: Our analysis revealed distinct small RNA profiles in the EVs and the PD from the patients with NSCLC. The EVs (CD9-, CD63-, and CD81-positive) showed the enrichment of four miRNAs and the depletion of ten miRNAs, while the PD (CD61-positive) exhibited a more complex profile, with nineteen miRNAs enriched and nine miRNAs depleted in the patients with NSCLC compared to those of the healthy controls. Conclusions: This exploratory study enhances our understanding of miRNA composition within different plasma vesicle populations, shedding light on the biology of plasma vesicles and their contents. Furthermore, utilizing an extracellular vesicle isolation method with potential clinical applicability offers the prospect of improved cancer characterization and detection by selecting the most informative subpopulation of plasma vesicles. Full article

(This article belongs to the Special Issue Extracellular Vesicles and ncRNA)

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14 pages, 364 KiB

Open AccessSystematic Review

Expression of miRNAs in the Relationship Between Periodontitis and Cardiovascular Diseases: A Systematic Review

by Montiel Guerrero-Sabater, María Cosín-Villanueva, Pedro Almiñana-Pastor and Andrés López-Roldán

Non-Coding RNA 2025, 11(3), 37; https://doi.org/10.3390/ncrna11030037 - 6 May 2025

Abstract

Objectives: Periodontitis is a chronic inflammatory disease that could influence the pathophysiology of cardiovascular diseases through immunoinflammatory and epigenetic mechanisms. MicroRNAs (miRNAs) could be key mediators in this interaction, regulating gene expression and the synthesis of inflammatory molecules. The objective of this systematic [...] Read more.

Objectives: Periodontitis is a chronic inflammatory disease that could influence the pathophysiology of cardiovascular diseases through immunoinflammatory and epigenetic mechanisms. MicroRNAs (miRNAs) could be key mediators in this interaction, regulating gene expression and the synthesis of inflammatory molecules. The objective of this systematic review was to evaluate the relationship between periodontitis and cardiovascular diseases by analyzing the expression of miRNAs involved in both pathologies. Methods: A systematic search was performed in the PubMed, Scopus, Embase, and Web of Science databases following the PRISMA guidelines. A total of 320 studies were identified, of which seven were included after applying eligibility criteria. Data on study design, sample characteristics, periodontal and cardiovascular diagnostic methodology, and the analyzed miRNAs were extracted. Results: The included studies were observational case-control studies in humans (n = 5) and experimental studies in animal models (n = 3). The miRNAs selected by the studies to link both pathologies were miR-155, miR-155-5p, miR-146a, miR-143, miR-145, and miR-23b. Most studies observed the overexpression of these miRNAs in patients with periodontitis and cardiovascular disease, with miR-146a being the most frequently associated. Conclusions: The findings suggest that certain miRNAs, particularly miR-146a, may play a key role in the connection between periodontitis and cardiovascular disease. Its overexpression in patients with both pathologies reinforces the hypothesis of its involvement in the inflammatory processes associated with both conditions. It would be interesting to conduct studies to validate their clinical applicability as biomarkers of susceptibility to cardiovascular disease. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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45 pages, 2779 KiB

Open AccessReview

Tiny but Mighty: Small RNAs—The Micromanagers of Bacterial Survival, Virulence, and Host–Pathogen Interactions

by Rajdeep Banerjee

Non-Coding RNA 2025, 11(3), 36; https://doi.org/10.3390/ncrna11030036 - 5 May 2025

Abstract

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These [...] Read more.

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These sRNAs function as posttranscriptional regulators that fine-tune gene expression, enabling bacteria to adapt rapidly to challenging environments. This review explores the multifaceted roles of bacterial sRNAs in host–pathogen interactions. Firstly, it examines how sRNAs regulate pathogenicity by modulating the expression of key virulence factors, including fimbriae, toxins, and secretion systems, followed by discussing the role of sRNAs in bacterial stress response mechanisms that counteract host immune defenses, such as oxidative and envelope stress. Additionally, this review investigates the involvement of sRNAs in antibiotic resistance by regulating efflux pumps, biofilm formation, and membrane modifications, which contribute to multi-drug resistance phenotypes. Lastly, this review highlights how sRNAs contribute to intra- and interspecies communication through quorum sensing, thereby coordinating bacterial behavior in response to environmental cues. Understanding these regulatory networks governed by sRNAs is essential for the development of innovative antimicrobial strategies. This review highlights the growing significance of sRNAs in bacterial pathogenicity and explores their potential as therapeutic targets for the treatment of bacterial infections. Full article

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15 pages, 7171 KiB

Open AccessReview

Human XIST: Origin and Divergence of a cis-Acting Silencing RNA

by Maria Jose Navarro-Cobos and Carolyn J. Brown

Non-Coding RNA 2025, 11(3), 35; https://doi.org/10.3390/ncrna11030035 - 1 May 2025

Abstract

Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST originated from the ancestral protein-coding Lnx3 gene with [...] Read more.

Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST originated from the ancestral protein-coding Lnx3 gene with contributions from various mobile elements that contributed to the striking domains of tandem repeats within the first and sixth exons. Modular domains of XIST are now involved in recruiting heterochromatic marks and proteins essential for XCI initiation and maintenance. This review presents a comparative analysis of human XIST with five other eutherian mammals—chimpanzees, cats, pigs, sheep, and mice—examining conservation across exons as well as the tandem repeats. Notably, repeats exhibited higher conservation than exons, underscoring their functional importance. Additionally, a species-specific G repeat, previously described in pigs, was also identified in sheep and cats. These findings provide insights into the domains of XIST, a cis-acting silencer that has been used to proposed to alleviate the impact of a supernumerary chromosome in Down syndrome. Full article

(This article belongs to the Special Issue Evolution of Regulatory ncRNAs and ncRNA Genes)

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30 pages, 2375 KiB

Open AccessSystematic Review

Building a Hand-Curated ceRNET for Endometrial Cancer, Striving for Clinical as Well as Medicolegal Soundness: A Systematic Review

by Roberto Piergentili, Stefano Sechi, Lina De Paola, Simona Zaami and Enrico Marinelli

Non-Coding RNA 2025, 11(3), 34; https://doi.org/10.3390/ncrna11030034 - 30 Apr 2025

Abstract

Background/Objectives: Competing endogenous RNAs (ceRNA) are molecules that compete for the binding to a microRNA (miR). Usually, there are two ceRNA, one of which is a protein-coding RNA (mRNA), with the other being a long non-coding RNA (lncRNA). The miR role is to [...] Read more.

Background/Objectives: Competing endogenous RNAs (ceRNA) are molecules that compete for the binding to a microRNA (miR). Usually, there are two ceRNA, one of which is a protein-coding RNA (mRNA), with the other being a long non-coding RNA (lncRNA). The miR role is to inhibit mRNA expression, either promoting its degradation or impairing its translation. The lncRNA can “sponge” the miR, thus impeding its inhibitory action on the mRNA. In their easier configuration, these three molecules constitute a regulatory axis for protein expression. However, each RNA can interact with multiple targets, creating branched and intersected axes that, all together, constitute what is known as a competing endogenous RNA network (ceRNET). Methods: In this systematic review, we collected all available data from PubMed about experimentally verified (by luciferase assay) regulatory axes in endometrial cancer (EC), excluding works not using this test; Results: This search allowed the selection of 172 bibliographic sources, and manually building a series of ceRNETs of variable complexity showed the known axes and the deduced intersections. The main limitation of this search is the highly stringent selection criteria, possibly leading to an underestimation of the complexity of the networks identified. However, this work allows us not only to hypothesize possible gap fillings but also to set the basis to instruct artificial intelligence, using adequate prompts, to expand the EC ceRNET by comparing it with ceRNETs of other cancers. Moreover, these networks can be used to inform and guide research toward specific, though still unidentified, axes in EC, to complete parts of the network that are only partially described, or even to integrate low complexity subnetworks into larger more complex ones. Filling the gaps among the existing EC ceRNET will allow physicians to hypothesize new therapeutic strategies that may either potentiate or substitute existing ones. Conclusions: These ceRNETs allow us to easily visualize long-distance interactions, thus helping to select the best treatment, depending on the molecular profile of each patient, for personalized medicine. This would yield higher efficiency rates and lower toxicity levels, both of which are extremely relevant factors not only for patients’ wellbeing, but also for the legal, regulatory, and ethical aspects of miR-based innovative treatments and personalized medicine as a whole. This systematic review has been registered in PROSPERO (ID: PROSPERO 2025 CRD420251035222). Full article

(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)

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24 pages, 4722 KiB

Open AccessArticle

Bromodomain and Extra-Terminal Family Proteins BRD2, BRD3, and BRD4 Contribute to H19-Dependent Transcriptional Regulation of Cell Adhesion Molecules, Modulating Metastatic Dissemination Program in Prostate Cancer

by Valeria Pecci, Melissa Borsa, Aurora Aiello, Sara De Martino, Luca Cis, Cristian Ripoli, Dante Rotili, Francesco Pierconti, Francesco Pinto, Claudio Grassi, Carlo Gaetano, Antonella Farsetti and Simona Nanni

Non-Coding RNA 2025, 11(3), 33; https://doi.org/10.3390/ncrna11030033 - 29 Apr 2025

Abstract

Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain [...] Read more.

Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain and Extra-Terminal (BET) proteins BRD2, BRD3, and BRD4 in the H19-dependent transcriptional regulation of cell adhesion molecules. Currently, the major effects of BET inhibitors require androgen receptor (AR) expression. Methods: H19 was stably silenced in PC-3 (AR-null) and 22Rv1 (AR-positive) castration-resistant PCa cells. The cells were treated with the pan-BET inhibitors JQ1 and OTX015 or the BET degrader dBET6. In vivo, the effects of JQ1 were evaluated in xenograft mouse models. Chromatin immunoprecipitation (ChIP) and RNA-ChIP were used to assess BET protein recruitment and interaction with cell adhesion gene loci and H19. Organotypic slice cultures (OSCs) from fresh PCa surgical specimens were used as ex vivo models to validate transcriptional changes and BRD4 recruitment. Results: BET inhibition significantly reduced the expression of β4 integrin and E-cadherin and cell proliferation in both basal conditions, and following H19 knockdown in PC-3 and 22Rv1 cells. These effects were mirrored in JQ1-treated tumor xenografts, which showed marker downregulation and tumor regression. ChIP assays revealed that BRD4, more than BRD2/3, was enriched on β4 integrin and E-cadherin promoters, especially in regions marked by H3K27ac. H19 silencing markedly enhanced BRD4 promoter occupancy. RNA-ChIP confirmed a specific interaction between BRD4 and H19. These findings were validated in OSCs, reinforcing their clinical relevance. Conclusions: Our study demonstrates that BRD4 epigenetically regulates the H19-mediated transcriptional control of adhesion molecules involved in collective migration and metastatic dissemination. Importantly, these effects are independent of AR status, suggesting that targeting the H19/BRD4 axis may represent a promising therapeutic avenue for advanced PCa. Full article

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