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Volume 12, June
 
 

Non-Coding RNA, Volume 12, Issue 4 (August 2026) – 11 articles

Cover Story (view full-size image): Circular RNAs (circRNAs) are abundant, stable non-coding transcripts enriched in the nervous system, showing compartmentalized localization within dendrites, axons and synapses. In this review, we examine how circRNAs reach these sites, focusing on RNP complexes exploiting kinesin/dynein cytoskeletal transport. Using circHomer1, CDR1as and circDlc1(2) as paradigms, we discuss how circRNA trafficking shapes synaptic gene expression via microRNA interaction and RNA-binding protein (RBP) scaffolding, while circPcmtd1 is locally translated into a functional micropeptide. We further show how disease-linked RBPs such as FUS disrupt circRNA transport in ALS, trapping transcripts within pathological aggregates. Altogether, we position circRNAs as dynamically and spatially regulated components of neuronal RNA biology relevant to synaptic function. View this paper
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25 pages, 13900 KB  
Article
Long-Read RNA Sequencing Reveals an Isoform Switching Pattern in Healthy Microglial Cell Lines Exposed to Radiotherapy
by Tatiana Zuppelli, Laura Orlando, Giuseppe N. Conti, Sofia P. Lombardo, Lucia Longhitano, Giulia Chisari, Cesarina Giallongo, Francesco Bellia, Maria Gabriella Sabini, Stefania Mele, Ignazio A. Barbagallo, Nunzio Vicario, Rosalba Parenti, Michelino Di Rosa, Enrico La Spina, Stefano Forte, Daniele Tibullo and Giovanni Li Volti
Non-Coding RNA 2026, 12(4), 31; https://doi.org/10.3390/ncrna12040031 - 6 Aug 2026
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Abstract
Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT [...] Read more.
Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT exposure. Methods: The HMC3 human microglial cell line was treated with standard radiotherapy and, after RNA extraction and library preparation, LR-RNA-seq was performed. Further bioinformatic analyses allowed to investigate on the isoform switching pattern after radiotherapy exposure. Results: Gene-level analysis found 591 differentially expressed genes, with positive enrichment of PI3K/AKT-related pathways and negative enrichment of translation-associated processes. Isoform-level analysis uncovered 827 significant isoform switching events across 420 genes, often involving shifts from protein-coding transcripts to non-coding variants. Functional annotation showed that most isoform switches resulted in the loss of open reading frames and protein domains, especially in ribosomal proteins and translation machinery components. Exploratory proteomic analysis identified 191 differentially abundant proteins, including a significant reduction in RPL7A, providing partial protein-level support for translation-associated transcriptomic remodeling. Conclusions: RT-induced stress causes qualitative transcriptomic remodeling beyond changes in overall gene expression. These findings indicate that radiotherapy induces coordinated gene-, transcript-, and isoform-level changes in HMC3 cells. The alterations observed in translation-associated genes, together with partial proteomic concordance, identify candidate mechanisms for future functional investigation. Full article
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18 pages, 3699 KB  
Article
An Exploratory Study on Transcriptomic Profiling of Circulating miRNA Associated with Hub Genes in the Development of Polycystic Ovary Syndrome
by Yogesh Vetriselvan, Jayakumar Swetha, Manoranjani Murugan, Irisappan Ganesh, Vishnu Bhat Ballambattu, Pushpa Premanath Kotur, Deepa Shanmugam, Marcella Sherin Samuel and Sambandam Ravikumar
Non-Coding RNA 2026, 12(4), 30; https://doi.org/10.3390/ncrna12040030 - 5 Aug 2026
Viewed by 462
Abstract
Background: Polycystic ovary syndrome (PCOS) is a complex endocrine disorder that affects women of reproductive age, often associated with metabolic issues, causing infertility. Although it is common, the cause of PCOS remains unknown, and early diagnosis is challenging. MicroRNAs (miRNAs) serve as post-transcriptional [...] Read more.
Background: Polycystic ovary syndrome (PCOS) is a complex endocrine disorder that affects women of reproductive age, often associated with metabolic issues, causing infertility. Although it is common, the cause of PCOS remains unknown, and early diagnosis is challenging. MicroRNAs (miRNAs) serve as post-transcriptional regulators of gene expression, play a significant role in PCOS development, and have emerged as biomarkers for reproductive and metabolic disorders. However, research on miRNA signatures in the Indian population is limited. This pilot exploratory study aims to compare the candidate differentially expressed miRNAs (DE miRNAs) in serum samples from individuals with and without PCOS using high-throughput miRNA sequencing. Methods: In the study, patients with PCOS and age-matched controls were included; small RNAs were isolated from their serum, libraries were prepared, and the libraries were analyzed by next-generation sequencing. Bioinformatics analysis, including miRBase annotation, differential expression analysis, target prediction, GO/KEGG enrichment, and hub gene network analysis, was performed. Results: A total of 967 miRNAs were identified, with seven showing differential expression (log2FC > 1, p < 0.05). Among these, six miRNAs of hsa-miR-219a-2-3p, hsa-mir-384, hsa-miR-149-5p, hsa-miR-3182, hsa-miR-3960, and hsa-miR-4508 were upregulated, whereas hsa-mir-139 was downregulated. Functional enrichment and hub gene analyses identified key targets, including TP53, FOXO1, HIF1A, and HDAC1, that are crucial to the cell cycle, insulin signaling, and hypoxia. Conclusions: These preliminary findings identify candidate serum miRNA signatures in Indian women that may be associated with PCOS’s reproductive and metabolic issues. These pilot study results suggest potential miRNAs and their target pathway links with PCOS that need validation in larger cohorts for diagnostic or therapeutic applications. Full article
(This article belongs to the Section Small Non-Coding RNA)
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20 pages, 1767 KB  
Protocol
Fraction-Seq: An Integrated Experimental and Computational Workflow for Determining the Localization and Abundance of Small Non-Coding RNAs in Subcellular Compartments
by Siddhartha Shah, Tess Cherlin, Yi Jing, Stepan Nersisyan, Benjamin Leiby and Isidore Rigoutsos
Non-Coding RNA 2026, 12(4), 29; https://doi.org/10.3390/ncrna12040029 - 5 Aug 2026
Viewed by 636
Abstract
Small non-coding RNAs (sncRNAs) have garnered considerable attention in recent years, following accumulating evidence of their critical roles in many cellular processes. Among sncRNAs, microRNAs (miRNAs) and their isoforms (isomiRs), tRNA-derived fragments (tRFs), rRNA-derived fragments (rRFs), and Y RNA-derived fragments (yRFs) account for [...] Read more.
Small non-coding RNAs (sncRNAs) have garnered considerable attention in recent years, following accumulating evidence of their critical roles in many cellular processes. Among sncRNAs, microRNAs (miRNAs) and their isoforms (isomiRs), tRNA-derived fragments (tRFs), rRNA-derived fragments (rRFs), and Y RNA-derived fragments (yRFs) account for more than 95% of all sncRNAs found in cells. Despite their critical regulatory roles, most sncRNAs remain uncharacterized because their functionalization is a lengthy and challenging undertaking. Knowing an sncRNA’s abundance helps prioritize among the various choices, while knowing where it localizes in the cell greatly limits the number and identity of its potential targets and helps understand its function. Most studies to date have assumed that the subcellular localization of the various sncRNA classes is understood and remains unchanged across cell types. However, as we have recently demonstrated, the subcellular distribution of sncRNAs follows complex patterns that depend on the sequence of the sncRNA, the presence or absence of post-transcriptionally added non-templated nucleotides, and the cell type. To determine the subcellular localization and abundance of sncRNAs and aid the design of targeted experimental studies of sncRNA function, we developed “Fraction-seq.” The method combines an experimental and an analytical component to remove cross-fraction contamination and reconstruct the true abundance of sncRNAs in each considered fraction. Fraction-seq can be applied to any adherent cells from any organism without modifications and can reconstruct the abundance of all categories of sncRNAs. Accompanying this detailed protocol is a newly developed port of the original SAS codes to the widely used R programming language. The codes and an example are freely available through our center’s GitHub page. Full article
(This article belongs to the Section Small Non-Coding RNA)
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9 pages, 1566 KB  
Article
Induced RNA Interference Can Suppress Persistent Drosophila A Virus (DAV) Infection in Cultured Drosophila Melanogaster S2 Cells
by Wiebke Kochendörfer and Klaus Förstemann
Non-Coding RNA 2026, 12(4), 28; https://doi.org/10.3390/ncrna12040028 - 30 Jul 2026
Viewed by 412
Abstract
Background: The RNA interference (RNAi) pathway is a highly conserved antiviral mechanism in eukaryotes, including insects such as fruit flies. Many viruses have therefore evolved mechanisms that protect their transcripts and/or genomes; how effectively RNAi can act is thus a question that [...] Read more.
Background: The RNA interference (RNAi) pathway is a highly conserved antiviral mechanism in eukaryotes, including insects such as fruit flies. Many viruses have therefore evolved mechanisms that protect their transcripts and/or genomes; how effectively RNAi can act is thus a question that must be answered case-by-case. Methods: We demonstrate that the RNAi machinery can successfully combat Drosophila A virus (DAV) in persistently infected Drosophila melanogaster S2 cell lines, but only when supported with exogenous triggers. Since such an infection poses a challenge to the fitness of cells and the reproducibility of results obtained with them, our approach provides a convenient method to recover precious experimentally modified cell lines from infection through the application of exogenous double-stranded RNA (dsRNA) targeting the DAV sequence. The in vitro transcribed dsRNAs were applied to infected S2 cells via direct “soaking,” utilizing the cells’ natural endocytic uptake. Results: We monitored treatment efficacy via RT-PCR-based detection of viral sequences, and our results demonstrate that continued application of DAV-specific dsRNAs led to a reduction in viral abundance and all eight tested cell lines appeared DAV-negative within several weeks of treatment. While a set of cell lines exhibited viral recurrence several weeks after the cessation of treatment, others remained virus-free for at least 16 weeks, suggesting that a permanent “cure” can indeed be achieved. Notably, while RNAi activation effectively cleared DAV in some cell lines, no beneficial effect was observed for a concomitantly applied Drosophila X-virus (DXV) treatment in the co-infected cultures. Conclusions: This suggests that DXV has more efficient evasion mechanisms but cannot protect DAV in trans. Our protocol thus provides a robust, scalable approach for clearing persistent DAV infections, but may not be effective against all viruses known to infect Drosophila cell cultures. Full article
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13 pages, 1967 KB  
Review
Circular RNAs in Neurons: From Transport to Function
by Nicolò Salvi and Mariangela Morlando
Non-Coding RNA 2026, 12(4), 27; https://doi.org/10.3390/ncrna12040027 - 29 Jul 2026
Viewed by 486
Abstract
Circular RNAs (circRNAs) have recently emerged as a class of abundant and remarkably stable non-coding RNAs preferentially enriched in the nervous system. In neurons, the fine-tuned spatial regulation of gene expression is critical for proper synaptic function; accordingly, several studies have demonstrated that [...] Read more.
Circular RNAs (circRNAs) have recently emerged as a class of abundant and remarkably stable non-coding RNAs preferentially enriched in the nervous system. In neurons, the fine-tuned spatial regulation of gene expression is critical for proper synaptic function; accordingly, several studies have demonstrated that circRNAs exhibit highly compartmentalized localization, specifically within dendrites, axons, and synapses. These spatial localization properties imply the presence of active transport mechanisms, which control the intracellular trafficking of circRNAs. This review highlights the current understanding of circRNA transport in neurons, focusing on the molecular machinery driving synaptic enrichment. We explore the potential role of ribonucleoprotein-based transport as a primary mechanism driving circRNA localization and examine how such spatial distribution influences synaptic plasticity and post-transcriptional gene regulation. Finally, we discuss the clinical implications of these processes, exploring the link between dysregulated RNA transport and the development of neuronal abnormalities. Full article
(This article belongs to the Section Long Non-Coding RNA)
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21 pages, 2947 KB  
Article
Efficacy of Bioengineered PD-L1 siRNA for Immunotherapy Against Non-Small Cell Lung Cancer Cells
by Neelu Batra, Mei-Juan Tu, Su Guan, Jonathan W. Riess and Ai-Ming Yu
Non-Coding RNA 2026, 12(4), 26; https://doi.org/10.3390/ncrna12040026 - 27 Jul 2026
Viewed by 431
Abstract
Background/Objectives: Recent advances in immunotherapy have revolutionized cancer treatment, as exemplified by multiple monoclonal antibodies against programmed cell death protein 1 (PD-1) or programmed death-ligand 1 (PD-L1). Nevertheless, immunotherapeutic antibodies exhibit certain limitations, which drives the development of alternative approaches, such as [...] Read more.
Background/Objectives: Recent advances in immunotherapy have revolutionized cancer treatment, as exemplified by multiple monoclonal antibodies against programmed cell death protein 1 (PD-1) or programmed death-ligand 1 (PD-L1). Nevertheless, immunotherapeutic antibodies exhibit certain limitations, which drives the development of alternative approaches, such as small interfering RNA (siRNA)-based therapeutics. The aim of this study was to design and produce new biological PD-L1 siRNA (BioRNA/PD-L1-siRNA) molecules and further define their immunotherapeutic efficacy against non-small cell lung cancer (NSCLC) in vitro. Methods: A novel RNA molecular bioengineering platform was employed to produce new BioRNA/PD-L1-siRNA agents. The functions of BioRNA/PD-L1-siRNAs were determined by quantitative PCR, Western blot, immunofluorescence confocal imaging, flow cytometry, and PD-1/PD-L1 blockade assays in human NSCLC cells, alone and co-cultured with human peripheral blood mononuclear cells (PBMCs). Results: After heterologous overexpression and purification of five BioRNA molecules, one siRNA named BioRNA/PD-L1-siRNA-1 was identified as the most effective to selectively suppress human PD-L1 mRNA and protein levels in H460 and H1975 cells. Disruption of PD-1/PD-L1 interactions by BioRNA/PD-L1-siRNA-1 was further demonstrated via a PD-1/PD-L1 blockade bioassay. In addition, the immunomodulatory effectiveness of BioRNA/PD-L1-siRNA-1 was established in co-culture models, as indicated by the induction of T-cell and natural killer cell populations and an increase in specific cytokines and cytotoxic granules, and subsequent enhancement of apoptosis and greater inhibition of NSCLC cell viability. Conclusions: Overall, these findings demonstrate the potential of bioengineered PD-L1 siRNA entities for NSCLC immunotherapy. Full article
(This article belongs to the Section Small Non-Coding RNA)
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20 pages, 4468 KB  
Review
MeCP2 Dosage Control in Rett Syndrome: Non-Coding RNA-Based and Epigenetic Strategies for Safer Gene Therapy
by Ilyas M. Kabdesh, Albert A. Rizvanov and Yana O. Mukhamedshina
Non-Coding RNA 2026, 12(4), 25; https://doi.org/10.3390/ncrna12040025 - 22 Jul 2026
Viewed by 791
Abstract
Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder that is caused in most cases by pathogenic variants in MECP2, the gene encoding methyl-CpG-binding protein 2 (MeCP2). Despite substantial progress in the development of gene therapy, restoring MECP2 expression remains challenging because [...] Read more.
Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder that is caused in most cases by pathogenic variants in MECP2, the gene encoding methyl-CpG-binding protein 2 (MeCP2). Despite substantial progress in the development of gene therapy, restoring MECP2 expression remains challenging because MeCP2 is highly dosage-sensitive. Both deficiency and excessive expression of this protein are associated with severe neurological abnormalities. This makes simple viral vector-mediated replacement of MECP2 potentially unsafe and underscores the need for multilayered systems that control transgene expression. This review discusses current and emerging strategies for regulating MeCP2 expression in RTT, with an emphasis on non-coding RNA-based and epigenetic mechanisms. Particular attention is given to the limitations of conventional AAV-mediated gene therapy, the use of cell-specific and endogenous promoters, miRNA-regulated elements, autoregulatory systems, and post-transcriptional control of MECP2 expression. Strategies for reactivating the inactive X chromosome are also discussed, including XIST-dependent regulation and epigenome editing. In addition, the review considers CRISPR-mediated regulation, selective epigenetic activation, and combined therapeutic platforms that integrate viral delivery, RNA-dependent post-transcriptional control, and endogenous gene regulation. Overall, clinically applicable gene therapy for RTT will likely need to move beyond simple MECP2 replacement and instead rely on precise cell- and dose-dependent regulation of its expression. Non-coding RNA and epigenetic mechanisms represent important layers of such control and may contribute to the development of safer gene therapy strategies for RTT. Full article
(This article belongs to the Section Clinical Applications of Non-Coding RNA)
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24 pages, 4389 KB  
Article
Integrated Transcriptomic, In Silico, and In Vitro Characterization of lncRNA ENST00000615487.1 Reveals Epithelial-Specific Expression, Differential Subcellular Distribution Between Normal and Colorectal Cancer Cells, and Potential Regulatory Functions
by Nataša Đokić, Anastasija Bubanja, Jelena Karanović and Jovana Despotović
Non-Coding RNA 2026, 12(4), 24; https://doi.org/10.3390/ncrna12040024 - 17 Jul 2026
Viewed by 690
Abstract
Background/Objectives: Long non-coding RNAs (lncRNAs) are important regulators of tumor biology through their interactions with DNA, proteins, and non-coding RNAs. Although ENST00000615487.1 (also known as CTD-2396E7.11/AC010503.4) has been associated with multiple malignancies, its biological role in colorectal cancer (CRC) remains poorly characterized. [...] Read more.
Background/Objectives: Long non-coding RNAs (lncRNAs) are important regulators of tumor biology through their interactions with DNA, proteins, and non-coding RNAs. Although ENST00000615487.1 (also known as CTD-2396E7.11/AC010503.4) has been associated with multiple malignancies, its biological role in colorectal cancer (CRC) remains poorly characterized. This study aimed to investigate the expression pattern, cellular and subcellular localization, and potential functional role of ENST00000615487.1 in CRC using integrated in vitro and in silico approaches. Methods: Molecular characteristics of the transcript were obtained with the CPC2 and RNA Analyzer 3 tools. Differential expression of ENST00000615487.1 across 10 tumor types was analyzed using the UCSC Xena Browser. Transcript expression was experimentally evaluated in normal, tumor, and fibroblastic colon cell lines by PCR, while subcellular localization was assessed through the lncATLAS, lncLocator, and iLoc-LncRNA tools, and experimentally confirmed by qRT-PCR. Single-cell RNA sequencing data from the GSE161277 dataset were analyzed to determine cell type-specific expression patterns. Potential interactions with DNA, miRNAs, and proteins were investigated using Fasim-LongTarget, miRDB, and AnnoLnc2, followed by functional enrichment analyses using STRING and Enrichr. Results: ENST00000615487.1 was identified as a structurally stable non-coding transcript with a highly organized secondary structure. Differential expression analysis demonstrated significant downregulation in CRC compared with that in normal colon tissue. Single-cell transcriptomic analysis revealed predominantly epithelial-specific expression. In silico and experimental analyses demonstrated predominant nuclear localization in normal colon cells, whereas cytoplasmic enrichment was observed in CRC cells. Functional analyses identified potential interactions with HIP1R, RPH3AL, specific miRNAs, and proteins involved in transcriptional regulation and RNA processing pathways, as well as functional connections with proteins involved in vesicular transport. Conclusions: ENST00000615487.1 is a structurally stable lncRNA exhibiting context-dependent expression and localization patterns in CRC, suggesting a potential shift from nuclear transcriptional regulation toward cytoplasmic post-transcriptional functions during colorectal carcinogenesis. Full article
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12 pages, 237 KB  
Editorial
The Non-Coding RNA Journal Club: Highlights on Recent Papers—15
by Francisco J. Enguita, Suresh K. Alahari, Luca Agnelli, Raphaël Zemmour, Florent Hubé, Patrick K. T. Shiu, Sophia M. Zhang, Mohammadjavad Mohammadi, Shuxing Zhang, Sreyasree Dhar, Simon J. Conn, Agnieszka Bronisz, Jakub Godlewski, Abhishek Kaushik, Alexander Serganov, Barbara Pardini, André P. Gerber, Mark W. Feinberg, Eleonora Leucci, Phoebe Philpott, Andrea Caporali, Toshiaki Takahashi, Ajay Goel and Ling Yangadd Show full author list remove Hide full author list
Non-Coding RNA 2026, 12(4), 23; https://doi.org/10.3390/ncrna12040023 - 17 Jul 2026
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Abstract
We are delighted to share with you our fifteenth Journal Club and highlight some of the most interesting papers published recently [...] Full article
(This article belongs to the Collection The Non-Coding RNA Journal Club: Highlights on Recent Papers)
17 pages, 1537 KB  
Article
A Mathematical Approach on the Limits of ceRNA Hypothesis Through an Ordinary Differential Equations (ODE) Model of mRNA-microRNA Interactions
by Paul Flondor, Mircea Olteanu, Radu Stefan, Corina Elena Minciuna and Catalin Vasilescu
Non-Coding RNA 2026, 12(4), 22; https://doi.org/10.3390/ncrna12040022 - 29 Jun 2026
Viewed by 652
Abstract
Background: MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression post-transcriptionally by binding to target messenger RNAs (mRNAs) and suppressing their expression. Competing endogenous RNAs (ceRNAs), including mRNAs and circular RNAs (circRNAs), modulate miRNA availability through competitive binding, forming regulatory networks [...] Read more.
Background: MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression post-transcriptionally by binding to target messenger RNAs (mRNAs) and suppressing their expression. Competing endogenous RNAs (ceRNAs), including mRNAs and circular RNAs (circRNAs), modulate miRNA availability through competitive binding, forming regulatory networks that fine-tune gene expression. CircRNAs can act as miRNA sponges, reducing miRNA-mediated repression of other targets, a mechanism implicated in various pathophysiological processes, including oncogenesis. Methods: We propose a mathematical model describing the dynamics of miRNA–mRNA–protein interactions, extending existing frameworks for miRNA–mRNA regulation. A qualitative analysis of the associated nonlinear differential equations system is performed. Results: We prove the boundedness of all positive solutions, establish the existence of a unique positive attracting equilibrium, and provide a mathematical perspective on the crosstalk mechanism in protein production. Conclusions: The effectiveness of ceRNA interactions depends on the relative abundance of miRNAs and their targets. This highlights the ongoing debate regarding the biological impact of low-abundance RNA transcripts on miRNA-mediated regulation. Full article
(This article belongs to the Section Computational Biology)
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17 pages, 4326 KB  
Article
P22 Small Noncoding RNAs Are Actively Secreted in Salmonella Outer Membrane Vesicles During Bacteriophage Infection
by Sayema Naaz, Haley A. Kominek, Lydia A. Hayes-Guastella, Autumn M. McDaniel, Enas S. Alsatari, Adeyeye I. Haastrup, Olivia G. Clark, Devin M. Katerski, Francois O. Prinsloo, Olivia R. Roberts, Meredith A. Shaddix, Bridgette N. Sullivan, Isabella M. Swan, Emily M. Hartsell, Jeffrey D. DeMeis, Suhas S. Patil, Richard H. Pham, Makala R. Cox and Glen M. Borchert
Non-Coding RNA 2026, 12(4), 21; https://doi.org/10.3390/ncrna12040021 - 26 Jun 2026
Viewed by 1114
Abstract
Background/Objectives: Outer membrane vesicles (OMVs) are membrane-encapsulated spherical structures ~120 nm in diameter derived from Gram-negative bacterial cell envelopes. OMVs are primarily generated by outer membrane blebbing but contain proteins, DNA, and RNAs at concentrations distinct from that of the intracellular complement. [...] Read more.
Background/Objectives: Outer membrane vesicles (OMVs) are membrane-encapsulated spherical structures ~120 nm in diameter derived from Gram-negative bacterial cell envelopes. OMVs are primarily generated by outer membrane blebbing but contain proteins, DNA, and RNAs at concentrations distinct from that of the intracellular complement. OMVs have been associated with a number of different cellular functions including intercellular communication and resistance to phage. Methods: As bacterial small RNAs (sRNAs) also participate in bacteriophage defense and are specifically delivered to and enriched in OMVs, we recently elected to examine the effects of P22 infection on Salmonella cytosolic and OMV sRNA abundance by employing RNA sequencing. Results: We find that P22 infection triggers a global reduction in sRNAs (with Salmonella sRNA expression levels averaging only 15.6% those observed in noninfected cells) coupled with a reciprocal 72.7% global increase in Salmonella tRNA expression levels. Additionally, of note, while OMV small noncoding RNA (sncRNA) abundance is normally ~1/10 that found in the cytosol, we find that P22 infection triggers active OMV encapsulation and secretion of: (1) a subset of sRNAs, (2) all Salmonella tRNAs including one highly complementary to the P22 genome, and, much to our surprise, (3) ten distinct sRNAs expressed from P22. Conclusions: In summary, the work presented here identifies several Salmonella sncRNA cytosolic and/or OMV abundances significantly altered during P22 infection, and to our knowledge, this constitutes the first reported characterization of bacteriophage-encoded sRNAs being actively secreted within host OMVs. Full article
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