Journal Description
Non-Coding RNA
Non-Coding RNA
is an international, peer-reviewed, open access journal on non-coding RNA research dealing with elucidating the structure, function and biology of regulatory non-coding RNAs, and published bimonthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), PubMed, PMC, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q1 (Genetics and Heredity) / CiteScore - Q2 (Genetics)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 30.4 days after submission; acceptance to publication is undertaken in 4.6 days (median values for papers published in this journal in the first half of 2026).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
4.2 (2025);
5-Year Impact Factor:
4.2 (2025)
Latest Articles
MeCP2 Dosage Control in Rett Syndrome: Non-Coding RNA-Based and Epigenetic Strategies for Safer Gene Therapy
Non-Coding RNA 2026, 12(4), 25; https://doi.org/10.3390/ncrna12040025 - 22 Jul 2026
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
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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.
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(This article belongs to the Section Clinical Applications of Non-Coding RNA)
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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
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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
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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.
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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.
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Open AccessEditorial
The Non-Coding RNA Journal Club: Highlights on Recent Papers—15
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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
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Non-Coding RNA 2026, 12(4), 23; https://doi.org/10.3390/ncrna12040023 - 17 Jul 2026
Abstract
We are delighted to share with you our fifteenth Journal Club and highlight some of the most interesting papers published recently [...]
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(This article belongs to the Collection The Non-Coding RNA Journal Club: Highlights on Recent Papers)
Open AccessArticle
A Mathematical Approach on the Limits of ceRNA Hypothesis Through an Ordinary Differential Equations (ODE) Model of mRNA-microRNA Interactions
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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
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
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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.
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(This article belongs to the Section Computational Biology)
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Open AccessArticle
P22 Small Noncoding RNAs Are Actively Secreted in Salmonella Outer Membrane Vesicles During Bacteriophage Infection
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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
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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.
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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.
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Open AccessArticle
An Optimized RT-qPCR Protocol for Comprehensive Analysis of microRNAs and mRNAs in Mus musculus Brain Tissues
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Maria V. Lukashevich, Margarita M. Rudenok, Suzanna A. Partevian, Maria I. Shadrina, Petr A. Slominsky and Anelya Kh. Alieva
Non-Coding RNA 2026, 12(3), 20; https://doi.org/10.3390/ncrna12030020 - 11 Jun 2026
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Background/Objectives: MicroRNAs are key post-transcriptional regulators involved in various diseases. Despite its status as the gold standard, real-time RT-PCR faces challenges arising from high sequence homology among closely related microRNAs and the substantial biomaterial required to enrich small RNA fractions. This study aimed
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Background/Objectives: MicroRNAs are key post-transcriptional regulators involved in various diseases. Despite its status as the gold standard, real-time RT-PCR faces challenges arising from high sequence homology among closely related microRNAs and the substantial biomaterial required to enrich small RNA fractions. This study aimed to develop an optimized protocol for simultaneous analysis of microRNA and mRNA expression from a single total RNA sample using mouse (Mus musculus) brain tissue, avoiding dependence on pre-designed commercial assay panels. Methods: We optimized a real-time RT-PCR workflow enabling simultaneous analysis of mature microRNAs and mRNAs from a single total RNA sample. Modifications include a redesigned universal reverse primer, LNA-modified TaqMan probes, and omission of the 65 °C denaturation step during reverse transcription. The method was validated for five microRNAs in mouse brain tissue. Results: The assay showed high specificity, discriminating closely related miR-125a-5p and miR-125b-5p with a ΔCt difference of 6.7 ± 1.2 cycles. Co-analysis with Oligo(dT)18 and Random hexamer primers did not interfere with microRNA detection. Conclusions: The developed approach enables reliable detection of closely related microRNAs and parallel analysis of different RNA types, which is particularly important for studying regulatory networks when working with limited amounts of biomaterial. This protocol provides a complementary, accessible option for targeted studies in resource-limited settings or for non-cataloged miRNA targets.
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Open AccessArticle
Investigation of Long Non-Coding RNAs H19 rs3741219, MEG3 rs7158663, POLR2E rs3787016, and ANRIL rs10757274 with Breast Cancer Susceptibility and Clinicopathological Characteristics in a Mexican Population
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Mónica Alejandra Rosales-Reynoso, Anilú Margarita Saucedo-Sariñana, Clara Ibet Juárez-Vázquez, César de Jesús Tovar-Jácome, Rubria Alicia González-Sánchez, Karen Guadalupe Mestas-Villagran, Gustavo Andrés Torres-Sánchez, José Elías García-Ortíz, Efraín Salas-González and Martha Patricia Gallegos-Arreola
Non-Coding RNA 2026, 12(3), 19; https://doi.org/10.3390/ncrna12030019 - 4 Jun 2026
Abstract
Recent evidence has highlighted the crucial role of non-coding genetic elements in regulating gene expression and has been linked to a broad range of biological functions. Notably, dysregulation of long non-coding RNAs has been strongly associated with tumorigenesis and cancer progression. Background/Objectives:
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Recent evidence has highlighted the crucial role of non-coding genetic elements in regulating gene expression and has been linked to a broad range of biological functions. Notably, dysregulation of long non-coding RNAs has been strongly associated with tumorigenesis and cancer progression. Background/Objectives: This study aimed to investigate the potential association between the H19 rs3741219 T>C, MEG3 rs7158663 G>A, POLR2E rs3787016 T>C, and ANRIL rs10757274 A>G variants and Breast Cancer (BC) susceptibility, as well as their relationship with clinicopathological characteristics in Mexican patients. Methods: DNA was obtained from peripheral blood samples of 505 women (254 patients and 251 control females). Genotyping was performed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methodology. Associations were calculated using odds ratios (ORs), with p-values adjusted by the Bonferroni test (p < 0.012). In silico analyses were conducted to predict the functional impact of the variants associated. Results: Patients carrying the C/C genotypes in H19 rs3741219 and POLR2E rs3787016 variants showed increased susceptibility to developing BC and with clinical and pathological characteristics (age at diagnosis, TNM stage, histologic type and molecular subtype) (p < 0.001). Conclusions: The results suggest that H19 rs3741219 and POLR2E rs3787016 variants significantly influence BC risk.
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(This article belongs to the Section Long Non-Coding RNA)
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Comprehensive lincRNA Transcriptome in Acute Myeloid Leukemia: Integrating Known and Newly Identified lincRNAs Across Pediatric and Adult Cohorts
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Saioa Arza-Apalategi, Daan Gilissen, Anne C. van der Grinten, Seline N. van den Oever, Erik B. van den Akker, Marieke Griffioen, Joop H. Jansen, Joost H. A. Martens, Anna E. Marneth and Bert A. van der Reijden
Non-Coding RNA 2026, 12(3), 18; https://doi.org/10.3390/ncrna12030018 - 27 May 2026
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Background/Objectives: Acute myeloid leukemia (AML) comprises genetic subclasses with distinct gene expression profiles. While AML gene expression studies have mainly focused on protein-coding genes, our understanding of expression patterns of long intergenic noncoding RNAs (lincRNAs) remains incomplete. This is due to limited
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Background/Objectives: Acute myeloid leukemia (AML) comprises genetic subclasses with distinct gene expression profiles. While AML gene expression studies have mainly focused on protein-coding genes, our understanding of expression patterns of long intergenic noncoding RNAs (lincRNAs) remains incomplete. This is due to limited sample sizes, as well as incomplete annotation of lncRNAs with context-dependent expression. Methods: To address this gap, we developed the bioinformatic pipeline LIRA (long intergenic noncoding RNA annotator) to identify novel lincRNAs using stringent criteria, including spliced and intergenic transcripts, and algorithms to exclude coding potential. Results: By applying LIRA to RNA-sequencing data from 878 pediatric and adult AML cases and 20 healthy controls, we identified 1560 novel lincRNAs, expanding the GENCODE v38 lincRNA catalog by 27%. Integration of in-house-generated CAGE- and ChIP-sequencing data from KMT2A::MLLT3 samples revealed that 80% of the novel lincRNAs are 5′ capped, and at least 67% harbor activating epigenetic marks at their transcription start sites. Unsupervised analysis of the 1000 most variable known and newly identified lincRNAs uncovered subclass-specific expression patterns, mirroring those observed for protein-coding genes. Weighted Gene Co-expression Network Analysis identified 17 lincRNA expression modules associated with AML subclasses. Notably, expression of these modules decreased upon degradation of the leukemogenic onco-fusion proteins KMT2A::MLLT3 and PML::RARA, indicating that lincRNA expression is responsive to oncogenic signaling. Conclusions: This comprehensive analysis shows that lincRNAs exhibit similar subclass-specific expression patterns as protein-coding genes and establishes a valuable resource for future studies on genetically defined AML subclasses, with potential implications for biomarker discovery and therapeutic targeting.
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Open AccessArticle
Exploratory Machine Learning Analysis of circRNA-Derived Molecular Features in Autism Spectrum Disorder
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Raunak Sharda, Valentina L. Kouznetsova and Igor F. Tsigelny
Non-Coding RNA 2026, 12(3), 17; https://doi.org/10.3390/ncrna12030017 - 15 May 2026
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Background/Objectives: Autism Spectrum Disorder (ASD) is a set of neurological and neurodevelopmental disorders characterized by difficulties in social communication and interaction, repetitive behaviors, and sensory processing differences. Recent studies have shown that circRNAs play a crucial role in the pathophysiology of ASD. In
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Background/Objectives: Autism Spectrum Disorder (ASD) is a set of neurological and neurodevelopmental disorders characterized by difficulties in social communication and interaction, repetitive behaviors, and sensory processing differences. Recent studies have shown that circRNAs play a crucial role in the pathophysiology of ASD. In this study, we present an exploratory machine learning framework integrating circRNA sequence features, miRNA interactions, gene targets, and pathway enrichment analysis to investigate ASD-associated molecular signatures. Methods: Differential circRNAs were identified from human peripheral blood datasets, and informative features were selected using attribute-based filtering and Information Gain ranking. Machine learning models were developed using the WEKA platform. Results: The HyperPipes classifier achieved the highest performance (92.5% accuracy under cross-validation). Analysis using an independent ASD gene expression dataset showed consistent discriminative patterns of the derived gene-level signatures across multiple machine learning classifiers. The competitive endogenous RNA network and enriched gene pathways were also analyzed. Conclusions: Overall, this study provides a computational, preliminary framework for analyzing circRNA-associated molecular patterns in ASD. Findings should be interpreted in the context of limited sample size and dataset availability.
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Open AccessArticle
Urinary Exosomal microRNAs as a Novel Approach to Study People with Multiple Sclerosis and Severe Gait Disability: A Preliminary Observation
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Silvia Grassilli, Andrea Baroni, Marina Pierantoni, Federica Brugnoli, Nicola Lamberti, Sofia Straudi, Fabio Manfredini and Valeria Bertagnolo
Non-Coding RNA 2026, 12(3), 16; https://doi.org/10.3390/ncrna12030016 - 8 May 2026
Abstract
Background: MiRNAs within extracellular vesicles can encompass body barriers, reflecting stage, progression, and response to treatments of various diseases, including multiple sclerosis (MS)—a chronic immune-mediated disease of the central nervous system that causes progressive disability, with highly variable clinical courses. In this context,
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Background: MiRNAs within extracellular vesicles can encompass body barriers, reflecting stage, progression, and response to treatments of various diseases, including multiple sclerosis (MS)—a chronic immune-mediated disease of the central nervous system that causes progressive disability, with highly variable clinical courses. In this context, urinary exosomal miRNAs could be an appealing source of biomarkers, thanks to their non-invasive and easily repeatable collection. Methods: In this exploratory investigation, we tried to assess if profiling urinary exosomal miRNAs could reveal subtle differences within an apparently homogeneous MS population. The study involved 24 patients with primary or secondary progressive MS, whose urinary exosomes (UEs) were subjected to evaluation of a panel of 87 miRNAs variously correlated with neuroinflammation, cardiovascular functions, and/or involved in MS. Results: We revealed that the examined miRNAs were heterogeneously expressed across the patients, reflecting, as expected, their gender and/or hormonal status. Two miRNAs discriminated against primary or secondary progressive MS, and a panel of 14 commonly upmodulated miRNAs identified patients with longer disease duration and a greater degree of disability. Conclusions: Even if preliminary, these data represent the first relationship between UEs and MS features in humans and suggest that urine could constitute a non-invasive source of exosomal miRNAs, which could prove useful in complementing conventional monitoring to provide a more personalized management of MS patients.
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(This article belongs to the Special Issue ncRNAs in Human Diseases and Therapeutics)
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Hnf1aos1 as a Metabolic Coordinator of Hepatic Lipid Homeostasis and Feedback Control
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Beshoy Armanios, Jing Jin, Ankit P. Laddha, Le Tra Giang Nguyen, Sherouk M. Tawfik, Neha Mishra, Jose E. Manautou and Xiao-Bo Zhong
Non-Coding RNA 2026, 12(3), 15; https://doi.org/10.3390/ncrna12030015 - 30 Apr 2026
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Background: Long noncoding RNAs (lncRNAs) have emerged as critical regulators of hepatic metabolism and disease progression. The hepatocyte nuclear factor 1 alpha antisense 1 (HNF1A-AS1) lncRNA modulates liver-specific transcription factors; however, its physiological role in diet-dependent lipid homeostasis remains poorly defined. Methods: In
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Background: Long noncoding RNAs (lncRNAs) have emerged as critical regulators of hepatic metabolism and disease progression. The hepatocyte nuclear factor 1 alpha antisense 1 (HNF1A-AS1) lncRNA modulates liver-specific transcription factors; however, its physiological role in diet-dependent lipid homeostasis remains poorly defined. Methods: In this study, we investigated the mouse ortholog, Hnf1a opposite strand 1 (Hnf1aos1), using AAV-mediated knockdown in C57BL/6J mice fed either a chow diet (10% kcal from fat) or a high-fat diet (HFD; 60% kcal from fat) for 12 weeks. Metabolic phenotyping included hepatic lipid quantification, histological analysis, serum biochemistry, and quantitative gene expression profiling. Results: Loss of Hnf1aos1 produced distinct, diet-dependent alterations in hepatic lipid handling. Under chow conditions, knockdown mice exhibited selective hepatic cholesterol accumulation (6.10 ± 2.9 mg/g tissue vs. 3.51 ± 1.1 mg/g in controls), accompanied by dysregulation of cholesterol clearance pathways. In contrast, under HFD conditions, knockdown precipitated severe macrovesicular degeneration, with hepatic triglyceride levels approximately doubled relative to HFD-fed controls (51.72 ± 19.8 mg/g vs. 26.34 ± 11.9 mg/g) and a numerically elevated triglyceride-to-cholesterol ratio (TG:TC ≈ 6.1:1; p = 0.0621, trend). Chow/Kd mice gained significantly less weight than chow-fed controls, whereas HFD/Kd mice exhibited weight gain comparable to HFD controls despite severe hepatic steatosis. This paradoxical phenotype suggests impaired metabolic feedback at the post-transcriptional level, in which compensatory upregulation of Hnf1a mRNA is insufficient to suppress lipid-associated genes such as Cd36, despite profound lipid overload; however, HNF1A protein levels were not directly measured in this study. Conclusion: Collectively, these findings identify Hnf1aos1 as a regulator of hepatic lipid homeostasis whose loss produces a phenotype consistent with inappropriate lipid accumulation during nutrient excess, without defining the underlying molecular mechanism. Our results support a role for Hnf1aos1 in shaping hepatic metabolic plasticity and provide insight into lncRNA-associated MASLD phenotypes.
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Open AccessReview
Circular RNAs in Intestinal Mucosal Homeostasis and Pathologies
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Hee Kyoung Chung, Lan Xiao and Jian-Ying Wang
Non-Coding RNA 2026, 12(3), 14; https://doi.org/10.3390/ncrna12030014 - 30 Apr 2026
Abstract
The mammalian intestinal epithelium is a rapid self-renewal tissue in the body, serving as a critical interface between the host and the external environment. Maintaining the intestinal epithelium homeostasis requires precise coordination of cellular processes, including proliferation, migration, differentiation, autophagy, and cell-to-cell interaction.
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The mammalian intestinal epithelium is a rapid self-renewal tissue in the body, serving as a critical interface between the host and the external environment. Maintaining the intestinal epithelium homeostasis requires precise coordination of cellular processes, including proliferation, migration, differentiation, autophagy, and cell-to-cell interaction. An increasing body of evidence has unveiled circular RNAs (circRNAs) as abundant and stable regulatory molecules that play pivotal roles in the intestinal epithelial biology and are intimately involved in many aspects of gut mucosal pathologies. Unlike linear RNAs, circRNAs form covalently closed loop structures through back-splicing events, conferring remarkable stability and resistance to exonucleolytic degradation. circRNAs regulate the growth of the intestinal mucosa, injury-induced epithelial regeneration, and gut barrier function via diverse mechanisms, including interactions with microRNAs and RNA-binding proteins. Deregulated circRNAs are implicated in the pathogenesis of various gut mucosal disorders such as inflammatory bowel disease and malignancies. In this review, we highlight pathobiological functions and mechanisms of intestinal epithelium-enriched circRNAs, particularly circHIPK3, Cdrlas, and circPABPN1, in the epithelium homeostasis and pathologies and also discuss potential clinical application of circRNAs as diagnostic biomarkers and therapeutic targets in patients with critical diseases.
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(This article belongs to the Special Issue Non-Coding RNA: 10th Anniversary)
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Open AccessReview
Neuropathic Pain: Mapping the miRNA Landscape
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Mario García-Domínguez
Non-Coding RNA 2026, 12(2), 13; https://doi.org/10.3390/ncrna12020013 - 6 Apr 2026
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Neuropathic pain represents a complex, prolonged pain state arising from lesions within the somatosensory nervous system. Despite significant advances in elucidating its pathophysiology, current therapeutic approaches remain largely symptomatic and frequently inadequate. MicroRNAs, a class of small non-coding RNAs that regulate gene expression
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Neuropathic pain represents a complex, prolonged pain state arising from lesions within the somatosensory nervous system. Despite significant advances in elucidating its pathophysiology, current therapeutic approaches remain largely symptomatic and frequently inadequate. MicroRNAs, a class of small non-coding RNAs that regulate gene expression post-transcriptionally, have recently emerged as critical modulators of neuronal excitability, neuroinflammation, and synaptic plasticity, which are crucial processes in the development and maintenance of neuropathic pain. This review summarizes the current evidence linking specific miRNAs to the onset and maintenance of neuropathic pain, with an emphasis on their roles in peripheral and central sensitization. The potential of miRNA-based biomarkers for diagnosis and prognostic evaluation is also highlighted. A thorough understanding of the complex miRNA regulatory networks underlying neuropathic pain could facilitate the development of novel, mechanism-based therapies and ultimately improve clinical outcomes.
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Open AccessArticle
Paraspeckles Are Associated with the Activation and Nuclear Localization of Unphosphorylated miR-34a
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Graham H. Read, Kristen McGreevy, Hanny Issawi, Tiffany Yang, Cynthia Tsang, Ihsan A. Turk, Emily Rietdorf, Whitaker Cohn, David W. Salzman, Julian P. Whitelegge and Joanne B. Weidhaas
Non-Coding RNA 2026, 12(2), 12; https://doi.org/10.3390/ncrna12020012 - 31 Mar 2026
Abstract
Background/Objectives: Canonical microRNAs possess a 5′ phosphate required for Argonaute binding and activity. However, prior work identified an unphosphorylated, inactive nuclear pool of the important radiation-responsive microRNA, miR-34, that is rapidly phosphorylated and activated in response to ionizing radiation (IR). Here, we extend
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Background/Objectives: Canonical microRNAs possess a 5′ phosphate required for Argonaute binding and activity. However, prior work identified an unphosphorylated, inactive nuclear pool of the important radiation-responsive microRNA, miR-34, that is rapidly phosphorylated and activated in response to ionizing radiation (IR). Here, we extend this work and investigate the role of paraspeckles, a phase-separated nuclear sub-compartment, and their association with the localization of unphosphorylated miR-34a. Methods: Mass spectrometry was performed to identify interacting partners of unphosphorylated mir-34. CRISPR-mediated deletion of the paraspeckle NEAT1_2 triple helix motif was performed to create an A549 cell line lacking paraspeckles (dTH). Activity and expression of mir-34a post-irradiation were evaluated by qRT-PCR and luciferase assays comparing dTH and wild-type (WT) A549 cell lines. In situ hybridization (ISH) was performed to evaluate mir-34a localization before and after IR, comparing dTH and WT cell lines. Results: Mass spectrometry identified paraspeckle proteins as significantly enriched interacting partners of unphosphorylated mir-34 mimics. By qRT-PCR and luciferase assays, we found that paraspeckle loss prevented radiation-induced early activation of unphosphorylated mir-34a. We found no difference in radiation-induced transcription of pri-miR-34a, but early processing to pre-miR-34a appeared delayed. ISH confirmed that loss of paraspeckles altered the nuclear localization of miR-34a before and after IR. Conclusions: These data suggest that paraspeckles are associated with nuclear localization and early radiation-responsive activation of unphosphorylated miR-34a. This suggests a coordinated nuclear sequestration of this important miR in its unphosphorylated state to enable an enhanced radiation response.
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(This article belongs to the Section RNA Modifications)
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Open AccessReview
Circular and Long Non-Coding RNAs in Cancer Metabolism: Dual Perspective of Biomarkers and Therapeutic Targets
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Francesca Pia Carbone, Stefania Hanau and Nicoletta Bianchi
Non-Coding RNA 2026, 12(2), 11; https://doi.org/10.3390/ncrna12020011 - 19 Mar 2026
Cited by 1
Abstract
Background/Objectives: Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to sustain proliferation, survive under metabolic stress, and develop therapeutic resistance. While oncogenic signaling pathways regulating cancer metabolism have been extensively studied, increasing evidence indicates that non-coding RNAs (ncRNAs) play essential
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Background/Objectives: Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to sustain proliferation, survive under metabolic stress, and develop therapeutic resistance. While oncogenic signaling pathways regulating cancer metabolism have been extensively studied, increasing evidence indicates that non-coding RNAs (ncRNAs) play essential roles in coordinating metabolic adaptation. This review aims to synthesize current knowledge on long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) as important but relatively less characterized regulators of cancer metabolic adaptation and discuss their potential as biomarkers and therapeutic targets. Methods: We analyzed their roles across multiple types of cancer, prioritizing studies that integrate ncRNA profiling with metabolomics and mechanistic investigations, with particular attention to their diagnostic, prognostic, and predictive value. Results: LncRNAs and circRNAs regulate major metabolic pathways, including glycolysis, mitochondrial function, glutaminolysis, lipid metabolism, and redox balance. They act through transcriptional and epigenetic mechanisms, protein scaffolding, peptide encoding, and miRNA sponging, frequently converging on key regulators such as HIF-1α, c-Myc, p53, AMPK, and mTOR. However, many reported associations remain largely correlative, with limited integration of quantitative metabolic flux analyses and insufficient validation in physiologically relevant models. Conclusions: Although lncRNAs and circRNAs constitute an important context-dependent regulatory layer linking oncogenic signaling to metabolic reprogramming, future studies should combine ncRNA perturbation with stable isotope tracing, fluxomics, spatial metabolomics, long-read sequencing, and single-cell approaches to define causal and spatially resolved metabolic functions. Such integrative strategies may improve biomarker development and support ncRNA-informed, metabolism-oriented therapeutic interventions.
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(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)
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Open AccessArticle
Vape-Associated lncRNA Transcript 1 (VALT1) Amplifies the Tumorigenic Effects of e-Cigarette Vapor in Lung Epithelial Cells
by
Daniel Angelo R. Mirador, Jose Lorenzo M. Ferrer, Kim Denyse Hao Lin and Reynaldo L. Garcia
Non-Coding RNA 2026, 12(2), 10; https://doi.org/10.3390/ncrna12020010 - 16 Mar 2026
Abstract
Background/Objectives: Lung cancer remains a major global health burden, largely driven by cigarette use. Although electronic cigarettes (e-cigarettes) are viewed as safer alternatives due to their reduced chemical load, growing evidence shows their vapor can disrupt cellular transcriptomes, including long noncoding RNAs
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Background/Objectives: Lung cancer remains a major global health burden, largely driven by cigarette use. Although electronic cigarettes (e-cigarettes) are viewed as safer alternatives due to their reduced chemical load, growing evidence shows their vapor can disrupt cellular transcriptomes, including long noncoding RNAs (lncRNAs). In this study, we examined the regulation and function of vape-associated lncRNA transcript 1 (VALT1), a novel transcript upregulated in the oral transcriptomes of e-cigarette users and similarly elevated in non-small-cell lung cancer (NSCLC) tumors. Methods: Publicly available RNA-seq datasets were analyzed, and VALT1 was identified as an e-cigarette-responsive lncRNA. Its dose-dependent induction by e-cigarette smoke extract (eCSE) and cytoplasmic localization were confirmed via RT-qPCR. Its effects on cancer-associated phenotypes including proliferation, ROS detoxification, resistance to apoptosis, migration, cytoskeletal disorganization, and nuclear remodeling were assessed through overexpression and siRNA-mediated knockdown in A549 and BEAS-2B cells. Results: Acute eCSE exposure induced a biphasic, dose-dependent increase in VALT1 expression, accompanied by enhanced proliferation, ROS detoxification, apoptosis resistance, migration, cytoskeletal disorganization, and nuclear remodeling in A549 cells. VALT1 overexpression reproduced these phenotypes in both cell lines without eCSE treatment, whereas knockdown attenuated them. VALT1 promoted survival under cytotoxic stress in A549 but not BEAS-2B cells. Conclusions: These findings support an active role for VALT1 as an e-cigarette vapor-upregulated transcript that contributes to its phenotypic readout and enhances cellular survival under extracellular chemical stress—thereby aggravating tumorigenic phenotypes even in the absence of mutations that contribute to malignant transformation.
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(This article belongs to the Section Long Non-Coding RNA)
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Open AccessArticle
Comprehensive Schistosoma mansoni Hierarchical Transcriptome Assembly Points to Novel lncRNAs Associated with Sexual Dimorphism
by
Caio Felipe Freire, Thalles Souza-Lopes, Murilo Sena Amaral, Ana Carolina Tahira and Sergio Verjovski-Almeida
Non-Coding RNA 2026, 12(2), 9; https://doi.org/10.3390/ncrna12020009 - 12 Mar 2026
Cited by 2
Abstract
Background/Objectives: Schistosomiasis is a neglected tropical disease affecting >200 million people worldwide. Praziquantel is the sole recommended drug against Schistosoma mansoni; however, it lacks activity against juvenile forms and cannot prevent reinfection. Thus, there is an urgent need to identify novel therapeutic
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Background/Objectives: Schistosomiasis is a neglected tropical disease affecting >200 million people worldwide. Praziquantel is the sole recommended drug against Schistosoma mansoni; however, it lacks activity against juvenile forms and cannot prevent reinfection. Thus, there is an urgent need to identify novel therapeutic targets. Long noncoding RNAs (lncRNAs) are known to regulate various biological processes in S. mansoni, including parasite pairing and fertility; therefore, screening for novel lncRNAs could reveal new potential targets. Methods: We compiled all publicly available RNA-seq data from the Sequence Read Archive (SRA) and performed a hierarchical transcriptome assembly using the multi-sample assembler Ryūtō, combined with version 10 of the S. mansoni genome. We applied HOMER for peak-calling and identification of histone marks and used weighted gene co-expression network analysis (WGCNA) to infer putative functions of lncRNAs in sexual dimorphism. Results: Using a robust pipeline, we identified 10,170 novel lncRNA genes comprising 16,990 novel lncRNA transcripts, including 8783 intergenic, 7918 antisense, and 289 intronic lncRNA transcripts. Most (78.7%) have histone regulatory marks (H3K4me3, H3K27me3, H3K27ac, or H4K20me1) near their transcription start sites, indicating potential expression regulation. Comparing male and female samples, we identified 1991 differentially expressed genes (FDR < 5%, |log2FC| ≥ 1.5), including 296 known lncRNAs and 339 novel lncRNAs. WGCNA identified hub lncRNAs within co-expression modules, and Gene Ontology enrichment analyses (FDR ≤ 5%) suggest that these lncRNAs are involved in cell differentiation and morphogenesis pathways. Conclusions: We provide a comprehensive catalog of S. mansoni lncRNAs. These findings offer opportunities to discover potential new therapeutic targets, advancing the future development of anti-schistosome therapies.
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(This article belongs to the Section Long Non-Coding RNA)
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Open AccessReview
Short and Long Non-Coding RNAs in Renal Cell Carcinoma
by
Monia Cecati, Valentina Pozzi, Valentina Schiavoni, Giuseppina Barrasso, Veronica Pompei, Daniela Marzioni, Nicoletta Bonci, Stefania Fumarola, Andrea Ballini, Davide Sartini and Roberto Campagna
Non-Coding RNA 2026, 12(2), 8; https://doi.org/10.3390/ncrna12020008 - 27 Feb 2026
Abstract
Renal cell carcinoma (RCC) represents the most frequent kidney malignancy and remains a major clinical challenge due to its often silent onset, high metastatic potential, and limited responsiveness to conventional chemotherapy. Increasing evidence indicates that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding
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Renal cell carcinoma (RCC) represents the most frequent kidney malignancy and remains a major clinical challenge due to its often silent onset, high metastatic potential, and limited responsiveness to conventional chemotherapy. Increasing evidence indicates that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are key regulators of RCC tumorigenesis, progression, and therapy resistance. Rather than providing a purely descriptive overview, this review focuses on emerging mechanistic paradigms through which ncRNAs actively shape tumor behavior and therapeutic response in RCC. This review summarizes current knowledge on the biological and clinical relevance of ncRNAs in RCC, highlighting their dual roles as oncogenic drivers or tumor suppressors through the modulation of pathways involved in proliferation, apoptosis, angiogenesis, invasion, immune evasion, metabolic reprogramming, and ferroptosis. Particular emphasis is placed on mechanistically defined ncRNA regulatory axes controlling ferroptosis, autophagy, metabolic reprogramming, and immune escape, as well as on ncRNA-mediated intercellular communication via extracellular vesicles, which promotes the dissemination of resistance to targeted therapies. The review also addresses ncRNA-based diagnostic and prognostic applications, including miRNA signatures capable of discriminating RCC subtypes and circulating ncRNAs as minimally invasive biomarkers. Moreover, the manuscript discusses ncRNA-mediated mechanisms of resistance to targeted therapies such as sunitinib, sorafenib, and axitinib, emphasizing regulatory networks involving miRNA targets, lncRNA–miRNA sponging, RNA-binding proteins, extracellular vesicle transfer, and epigenetic modulation. Emerging therapeutic opportunities are also addressed, including strategies aimed at inhibiting oncogenic ncRNAs or restoring tumor-suppressive ncRNAs to enhance drug sensitivity and improve patient stratification.
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(This article belongs to the Section Clinical Applications of Non-Coding RNA)
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Open AccessReview
The Stiff Side of Cancer: How Matrix Mechanics Rewrites Non-Coding RNA Expression Programs
by
Alma D. Campos-Parra, Jonathan Puente-Rivera, César López-Camarillo, Stephanie I. Nuñez-Olvera, Nereyda Hernández Nava, Gabriela Alvarado Macias and Macrina Beatriz Silva-Cázares
Non-Coding RNA 2026, 12(1), 7; https://doi.org/10.3390/ncrna12010007 - 18 Feb 2026
Cited by 1
Abstract
Extracellular matrix (ECM) stiffening is a defining biophysical feature of solid tumors that reshape gene regulation through mechanotransduction. Increased collagen crosslinking and stromal remodeling enhance integrin engagement, focal-adhesion signaling and force transmission to the nucleus, where key hubs such as lysyl oxidase (LOX),
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Extracellular matrix (ECM) stiffening is a defining biophysical feature of solid tumors that reshape gene regulation through mechanotransduction. Increased collagen crosslinking and stromal remodeling enhance integrin engagement, focal-adhesion signaling and force transmission to the nucleus, where key hubs such as lysyl oxidase (LOX), focal adhesion kinase (FAK) and the Hippo co-activators YAP1 and TAZ (WWTR1) promote proliferation, invasion, stemness and therapy resistance. Here, we synthesize evidence that quantitative changes in matrix stiffness remodel the miRNome and lncRNome in both tumor and stromal compartments, including extracellular vesicle cargo that reprograms metastatic niches. To address heterogeneity in experimental support, we classify mechanosensitive ncRNAs into studies directly validated by stiffness manipulation (e.g., tunable hydrogels/AFM) versus indirect associations based on mechanosensitive signaling, and we summarize physiological versus pathophysiological stiffness ranges across tissues discussed. We further review competing endogenous RNA (ceRNA) networks converging on mechanotransduction nodes and ECM remodeling enzymes, and discuss translational opportunities and challenges, including targeting mechanosensitive ncRNAs, combining ncRNA modulation with anti-stiffening strategies, delivery barriers in dense tumors, and the potential of circulating/exosomal ncRNAs as biomarkers. Overall, integrating ECM mechanics with ncRNA regulatory circuits provides a framework to identify feed-forward loops sustaining aggressive phenotypes in rigid microenvironments and highlights priorities for validation in physiologically relevant models.
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(This article belongs to the Section Long Non-Coding RNA)
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Open AccessArticle
Computational Analysis of Telomerase RNA Evolution in Caenorhabditis Species
by
Christopher Klapproth, Franziska Reinhardt, Peter F. Stadler and Sven Findeiß
Non-Coding RNA 2026, 12(1), 6; https://doi.org/10.3390/ncrna12010006 - 11 Feb 2026
Abstract
Background/Objectives: The telomerase RNA (TR) is an indispensable part of the telomerase protein complex responsible for telomere elongation in most eukaryotic species. Although the telomere terminal repeat sequence (TTAGGC)n in Caenorhabditis elegans has been known for years, a telomerase RNA gene was
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Background/Objectives: The telomerase RNA (TR) is an indispensable part of the telomerase protein complex responsible for telomere elongation in most eukaryotic species. Although the telomere terminal repeat sequence (TTAGGC)n in Caenorhabditis elegans has been known for years, a telomerase RNA gene was not identified in the entire phylum of Nematoda until recently. Methods: In this exploratory study, we employ a combination of different approaches to identify likely telomerase RNA candidates among putative non-coding transcripts. Results: A detailed analysis of our prime candidate shows compelling evidence that it encodes the missing RNA element of the telomerase complex, which is notably located in an intron of the coding gene nmy-2. Using nmy-2 homologs in other nematodes as anchors, we annotate the conserved TR gene in 21 Caenorhabditis species. We furthermore show that the intronic localization of the TR gene is conserved in two distinct branching groups of the Caenorhabditis phylogeny and demonstrate that this property likely emerged from a single point of origin. Conclusions: While the intronic TR represents a very interesting evolutionary adaption that seems to have been successful in the Elegans and Japonica groups, the question regarding the macroscopic nematode TR evolution remains.
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(This article belongs to the Section Evolution of Non-Coding RNA)
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