Search Results (3,057)

Long non-coding RNAs (lncRNAs) encoded by viruses play crucial roles in viral infection, pathogenesis processes, the interaction between viruses and hosts, and immune escape. Herein, by employing RNA pull-down, mass spectrometry technology, and RNA immunoprecipitation, we identified a host protein (G3BP2) that specifically interacts with the lncRNA encoded by the infectious bronchitis virus (IBV). Additionally, we identified a novel host miRNA (novel-340) in IBV-infected H1299 cells and further verified that novel-340 can target the 3′-UTR (untranslated region) of G3BP2 and downregulate its expression in a dose-dependent manner. We discovered that IBV-lncRNA may facilitate IBV replication in H1299 cells through direct interaction with G3BP2 and/or the regulation of the IBV-lncRNA/novel-340/G3BP2 interactive regulatory network. This work deepens the understanding of the biological function of IBV-lncRNA. Full article

Background/Objectives: Acute myeloid leukemia is a genetically diverse hematological malignancy where patient outcomes vary significantly. Long non-coding RNA (lncRNA) GAS5 acts as a tumor suppressor and is frequently downregulated in various cancers, as well as in AML. In the current study, we aimed to explore the effects of GAS5 promoter variants on its expression levels in AML patients, their prognostic significance, and to investigate their functional effects. Methods: The GAS5 promoter region containing rs55829688 and rs145204276 was sequenced in 75 AML patients. Statistical analyses were performed to assess their associations with GAS5 expression and outcomes. An in vitro functional study in K562 cells evaluated the effects of these variants on the transcriptional activity of constructs containing each variant. In silico analysis was used to predict changes to transcription factor binding sites. Results: Patients carrying the rs55829688 TC/CC genotype exhibited lower GAS5 expression and were more frequently categorized into the adverse risk group. In intermediate-risk patients, this genotype trended toward lower overall survival and higher bone marrow blast percentages. In vitro, the construct harboring the rs55829688 C allele showed a two-fold decrease in reporter gene activity compared to the construct bearing both wild type alleles. In silico analysis identified RUNX3 as the most likely transcription factor affected by this variant. The variant rs145204276 was considered for the first time in AML; however, no significant clinical associations or transcriptional effects were found. Conclusions: Taken together, our findings provide evidence that the rs55829688 promoter variant reduces GAS5 expression in AML and could potentially be a prognostic marker. Full article

Soil salinity represents a significant abiotic constraint limiting the productivity and geographical expansion of rapeseed (Brassica napus L.), yet the coordination among the signaling, hormonal, metabolic, and regulatory layers underlying salt tolerance remains incompletely understood. This study elucidates the physiological, biochemical, and transcriptomic responses of B. napus inbred line 383-5 to moderate salt stress (100 mM NaCl at day 10), identifying key lncRNA–mRNA regulatory networks. Salt stress induced pronounced, dose-dependent growth inhibition, oxidative damage, and osmotic adjustment, accompanied by extensive transcriptional reprogramming. Genome-wide analyses identified 6215 differentially expressed protein-coding genes and 941 salt-responsive long non-coding RNAs (lncRNAs), revealing coordinated regulation of ion transport, redox homeostasis, phytohormone signaling, and secondary metabolism. Functional enrichment analyses highlighted the central involvement of abscisic acid and ethylene signaling pathways, MAPK cascades, membrane transporters, and antioxidant systems. Notably, salt stress strongly activated the phenylpropanoid and lignin biosynthesis pathways, suggesting reinforced cell wall remodeling and enhanced oxidative stress mitigation. Integration of lncRNA–mRNA regulatory networks further indicated that non-coding transcripts act as important modulators linking hormone signaling, redox balance, and metabolic adaptation. Collectively, these results reveal a multilayered and tightly synchronized regulatory framework underlying salinity tolerance in B. napus and provide valuable molecular targets for the genetic improvement of salt-resilient rapeseed cultivars. Full article

Oral squamous cell carcinoma (OSCC) is a highly aggressive malignancy characterized by frequent recurrence and metastasis, which poses a significant global health problem. One of the prominent hallmarks of cancer is glucose metabolic reprogramming, wherein glycolysis is preferred over oxidative phosphorylation for macromolecule biosynthesis and energy production, even in the presence of oxygen. Non-coding RNAs (ncRNAs) are defined as a class of RNAs that are not translated into proteins, which include microRNAs, long non-coding RNAs, and circular RNAs. Recent studies have found that ncRNAs are crucial in regulating glycolysis in OSCC, wherein they reshape the metabolic landscape by modulating the expression of glucose transporters, essential enzymes, and transcription factors, ultimately influencing tumorigenesis. This comprehensive review systematically summarizes the regulatory mechanisms of ncRNAs involved in glucose metabolic reprogramming in OSCC, evaluates their potential as diagnostic biomarkers and therapeutic targets, and identifies clinically relevant ncRNAs through an integrative analysis of patient-derived data. These insights provide a mechanistic understanding of the metabolic alterations that drive progression in OSCC, as well as knowledge that can facilitate the development of clinically translatable targeted interventions for this aggressive malignancy. Full article

Early detection of hepatocellular carcinoma (HCC) remains challenging due to limitations including the lack of reliable biomarkers. While molecular diagnostics hold promise, their use is limited because tissue biopsies are not routinely performed in HCC. Long non-coding RNAs (lncRNA), such as HOXA transcript at the distal tip (HOTTIP), have been implicated in HCC, with single-nucleotide polymorphisms forming haplotypes that may influence disease progression. This study investigated the clinical relevance of HOTTIP SNPs rs17501292 and rs2067087 in 198 Egyptian HCC patients (129 non-metastatic, 69 metastatic). Moreover, molecular docking was used to design small interfering RNAs (siRNAs) targeting HOTTIP. Genotypes TT and TG (rs17501292) and GG and GC (rs2067087) were associated with reduced metastatic risk compared to GG and CC genotypes, respectively. Survival analysis revealed that TT (rs17501292) and GC (rs2067087) genotypes correlated with improved outcomes. ROC curve analysis confirmed the diagnostic and prognostic value of specific genetic models, affirming their value as biomarkers for metastasis and survival. Molecular docking identified two promising therapeutic candidates. Overall, we can conclude that HOTTIP SNPs may serve as promising potential non-invasive biomarkers for HCC metastasis and prognosis, while the identified siRNAs offer a novel targeted therapeutic approach. Full article

LINC01270 is a long intergenic noncoding RNA implicated in the progression of various cancers. In our previous study, we demonstrated that LINC01270 plays a role in regulating the pro-inflammatory response in the THP-1 monocytic cell line, partly through modulation of NF-κB activation. Given the multifaceted nature of inflammation and the ability of noncoding RNAs to influence this process at multiple levels, we further investigated the potential role of LINC01270 in modulating additional inflammatory signaling pathways in lipopolysaccharide (LPS)-stimulated THP-1 cells. We found that attenuation of LINC01270 levels led to increased transcription and phosphorylation of STAT1, accompanied by elevated expression of the genes under STAT1 regulation. Further investigation revealed that LINC01270 regulates STAT1 expression via the miR-326/leucine zipper downregulated in cancer 1 (LDOC1) axis. Notably, inhibition of the interaction between LINC01270 and miR-326 effectively reversed the effects of LINC01270 knockdown on STAT1 expression and its downstream targets. Interestingly, both gain- and loss-of-function experiments with LDOC1 resulted in a consistent upregulation of STAT1 transcription. Taken together, our findings highlight a pleiotropic role of the LINC01270 in regulating the pro-inflammatory response through modulation of STAT1 signaling, in addition to its previously established role in NF-κB regulation. Furthermore, this study uncovers a novel function of the LDOC1 in inflammation through its regulation of STAT1. These findings provide new mechanistic insights into lncRNA–microRNA–protein interactions in inflammatory signaling and may open avenues for developing novel therapeutic strategies targeting chronic inflammatory diseases. Full article

Cibotium barometz (L.) J. Sm., a medicinally significant fern in traditional Chinese medicine, is little explored at the genomic level regarding its bioactive compounds. Using an integrated approach combining Illumina and PacBio sequencing technologies, we profiled its root, rachis, and pinna transcriptomes, identifying 12,718, 21,341, and 11,441 unigenes, respectively. Our analysis systematically characterized the transcriptional features of transcription factors (TFs), simple sequence repeats (SSRs), long non-coding RNAs (lncRNAs), and differentially expressed genes (DEGs). Enrichment analyses highlighted the roles of highly expressed unigenes in secondary metabolism. Seventeen key enzymes involved in polysaccharide biosynthesis showed tissue-specific expression patterns. Notably, total polysaccharide content correlated positively with UDP-arabinose 4-epimerase (UXE) expression but negatively with phosphoglucomutase (PGM) and 3,5-epimerase/4-reductase (UER1). Flavonoid accumulation inversely correlated with chalcone synthase (CHS) expression. Two lignin pathways (H-lignin and G-lignin) were characterized, with phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and cinnamyl alcohol dehydrogenase (CAD) as key genes. The absence of ferulate-5-hydroxylase (F5H) explains the undetected S-lignin pathway. Regulatory network analysis revealed positive correlations between PAL expression and NAC72/NAC78/WRKY35 and C4H expression and WRKY65/WRKY69/WRKY71, while a negative correlation was revealed between flavonoid 3′,5′-hydroxylase (F3′5′H) and MYB3R4. This study provides comprehensive transcriptomic insights into C. barometz bioactive compound biosynthesis, serving as a foundation for mechanistic research. Full article

Ovarian follicular development determines the egg-laying performance in chickens. Besides hormonal signaling, epigenetic and post-transcriptional regulators, long non-coding RNAs (lncRNAs) also play a vital role in follicular development. We previously identified that RAR-related orphan receptor B-intronic transcript 1 (RORB-IT1), a novel lncRNA located in the intron of RORB, was differentially expressed in chicken pre-hierarchical and hierarchical follicular granulosa cells (Post-GCs). However, it remains unknown whether RORB-IT1 participates in regulating the development of chicken ovarian follicles. In this study, we further characterized the expression pattern of RORB-IT1 and explored its role in regulating the progesterone synthesis, proliferation and apoptosis of chicken Post-GCs. The results showed that RORB-IT1, with a full length of 383 bp, exhibits a uniform distribution in both the cytoplasm and nucleus of chicken Post-GCs. RORB-IT1 was specifically expressed in Post-GCs and upregulated by follicle-stimulating hormone (FSH), progesterone (P4) and estradiol (E2) in a dose-dependent manner. Functionally, RORB-IT1 promoted P4 synthesis and proliferation, while inhibiting the apoptosis of Post-GCs. Furthermore, we demonstrated that RORB-IT1 encoded a functional micropeptide exhibiting dual localization in both cytoplasmic and nuclear compartments. This micropeptide enhanced progesterone synthesis and proliferation, but paradoxically induced the apoptosis of Post-GCs when overexpressed independently. Collectively, this study uncovered the expression pattern and function of RORB-IT1 in chicken Post-GCs and provided a theoretical basis for improving the egg-laying performance in chickens. Full article

Hepatoblastoma is the predominant primary liver malignancy in children, and outcomes remain poor for patients with metastatic disease. Long non-coding RNAs (lncRNAs) regulate tumor behavior, but their role in metastatic hepatoblastoma is not well defined. This study investigates the expression and functional significance of the lncRNA, maternally expressed gene 3 (MEG3), in a metastatic hepatoblastoma model. RNA sequencing comparing the metastatic hepatoblastoma cell line, HLM_2, with its parental HuH6 cell line identified MEG3 as being significantly upregulated in metastatic cells. MEG3 expression was examined using hepatoblastoma patient datasets and validated using qPCR in cell lines, orthotopic tumors, and COA67 patient-derived xenografts. The effects of siRNA MEG3 knockdown in HLM_2 cells on clonogenicity, migration, and invasion were evaluated. The effects of MEG3 overexpression on migration and invasion were assessed in HuH6 cells. MEG3 was significantly upregulated in metastatic cells and orthotopic tumors compared with controls. MEG3 silencing reduced clonogenicity, tumorsphere formation, migration, and invasion. MEG3 overexpression increased migration and invasion. These findings indicate that MEG3 contributes to an aggressive tumor phenotype, highlighting the need for further examination into its mechanistic role in hepatoblastoma and its potential as a biomarker or therapeutic target. Full article

Mitochondrial dysfunction plays a major role in diabetic retinopathy development and in its resistance to halt after the reversal of hyperglycemia (metabolic memory). Diabetes also upregulates many long noncoding RNAs, RNAs with >200 nucleotides with no reading frame, and several of them resist reversal after hyperglycemia cessation. Our aim was to investigate the role of LncRNA HOTAIR, a master regulator of chromatin dynamics, in mitochondrial biogenesis in diabetic retinopathy and in metabolic memory. Using retinal endothelial cells and Müller cells, incubated in high glucose (20 mM D-glucose), the effect of HOTAIR-siRNA on mitochondrial biogenesis was investigated by quantifying mitochondrial mass, copy numbers, and mtDNA replication, structure, and function. HOTAIR’s role in metabolic memory was investigated by analyzing mitochondrial biogenesis in HOTAIR-siRNA transfected cells incubated in high glucose for four days, followed by normal glucose (5 mM D-glucose) for four days. HOTAIR was upregulated in both retinal vascular and nonvascular cells, and HOTAIR-siRNA ameliorated decreases in mtDNA biogenesis and protected their mitochondria from structural/functional damage. Reversal of high glucose insult failed to ameliorate HOTAIR upregulation and impaired mtDNA biogenesis in both endothelial and Müller cells, but regulation of HOTAIR during high glucose incubation, which followed normal glucose, prevented a decrease in mitochondrial mass and mtDNA copies. Thus, HOTAIR has a major role in mitochondrial biogenesis and in the continued impaired biogenesis in both vascular and nonvascular cells. Regulating HOTAIR may provide a therapeutic option to inhibit the development/progression of diabetic retinopathy. Full article

Triple-negative breast cancer (TNBC) is characterized by marked clinical and molecular heterogeneity, which underlies the limited success of currently available targeted therapies and results in most patients relying on cytotoxic chemotherapy. This therapeutic gap underscores the pressing need for novel therapeutic approaches, in which non-coding RNAs (ncRNAs) have emerged as promising candidates. In this systematic review, 35 pre-clinical studies published between 2020 and 2025 were analyzed to evaluate the therapeutic potential of targeting ncRNAs in TNBC, including miRNAs, lncRNAs, and circRNAs. The original articles employed in vivo tumor models to assess the therapeutic response of ncRNA expression modulation, using miRNA mimics, antagomiRs, ASOs, shRNAs, and siRNAs integrated into advanced targeted delivery systems, such as nanoparticles and exosomes. According to the selected studies, 28 specific ncRNAs were identified as actionable molecular targets. Modulation of these molecules consistently resulted in tumor growth suppression, metastasis inhibition, and restoration of sensitivity to standard chemotherapeutic agents. Collectively, the pre-clinical evidence presented in these studies positions ncRNA-based therapies as innovative, promising, and potentially effective strategies for advancing TNBC treatment. Full article

Yaks are important livestock in high-altitude regions, and their polled trait can effectively improve breeding and management efficiency. In this study, whole-genome resequencing combined with a GWAS was employed to identify a significantly associated region of approximately 273.6 kb on chromosome 1 (36,313,286–36,586,879 bp) in Xueduo yaks. This region contains 1001 significant single-nucleotide polymorphism (SNP) loci and is located within a long intergenic non-coding RNA (lincRNA) region. Candidate genes EPCIP, OLIG1 and PAXBP1 adjacent to this region were identified. Among these, the PAXBP1 gene plays a crucial role in neural crest development, suggesting that it may be a core gene regulating horn development in yaks. Further analysis of Ashdan yaks (a polled breed developed from Datong yaks) indicated that the two breeds share the same candidate genes and a subset of associated genetic variants for the polled trait, suggesting a degree of genetic conservation underlying this trait across yak breeds. This study provides a theoretical basis for polled yak breeding. Full article

Pyroptosis enables host cells to eliminate intracellular pathogens effectively. However, how Chlamydia trachomatis (C. trachomatis) evades host pyroptosis remains unclear. This study reveals that C. trachomatis exploits the host Long non-coding RNA (lncRNA) SBF2-AS1 as a key factor to regulate the host pyroptosis. The SBF2-AS1 was significantly upregulated during C. trachomatis infection. Knockdown of SBF2-AS1 activated NLRP3/caspase-1/GSDMD pyroptosis pathway. Mechanistically, it verified that SBF2-AS1 functions as a competing endogenous RNA for miR-196b-5p targeting RIPK2 through dual-luciferase reporter gene assay. We further identified the interaction between RIPK2 and Caspase-1 by Co-immunoprecipitation (Co-IP). Silencing SBF2-AS1 or RIPK2, as well as overexpressing miR-196b-5p, triggered pyroptosis and suppressed the replication of C. trachomatis. In conclusion, C. trachomatis upregulates SBF2-AS1 to increase RIPK2 by binding miR-196b-5p, which shields against pyroptosis mediated by Caspase-1 to promote its proliferation. These results uncover a novel mechanism of pathogen–host interaction and provide insights for developing new therapeutic strategies against C. trachomatis infection. Full article

Many long non-coding RNAs (lncRNAs) are able to control interferon-dependent innate immune responses and the susceptibility to influenza infection. These lncRNAs are primarily regulated through the RIG-I/IFN-β/IFNAR1 pathway and can be considered as interferon-stimulated genes with either antiviral or proviral functions. In this review we observe the current knowledge of type I and III interferon signaling regulation and discuss the present data on specific lncRNAs, which are involved in the interferon response. The available data on mechanisms of lncRNA induction and action are summarized. Also, the brief overview of genes coding for lncRNAs involved in interferon expression regulation is presented with a focus on the evolutionary conservation of these regulatory molecules. The lncRNAs belong to various classes: antisense, bidirectional, intronic, or intergenic RNAs. Research of lncRNAs is an extremely promising scientific area. Deeper understanding of lncRNA functions may result in the development of new approaches to influenza infection treatment, as well as advanced understanding of the disease pathogenesis. Further bioinformatic analysis of lncRNAs is required to reveal putative common mechanisms of lncRNA action. Full article

Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with poor patient outcomes. The long non-coding RNA NEAT1 (lncRNA NEAT1) has emerged as a critical driver of HNSCC pathogenesis. This review synthesizes current knowledge on lncRNA NEAT1’s aberrant expression, molecular mechanisms, and functional roles in HNSCC. LncRNA NEAT1 is significantly upregulated in tumors and promotes progression by acting as a competing endogenous RNA (ceRNA) for multiple miRNAs, such as miR-125b-5p, miR-204, and miR-34a-5p, thereby regulating downstream targets including SLC1A5, ZEB1, and components of the Wnt/β-catenin pathway. These interactions drive key oncogenic processes, including proliferation, metastasis, epithelial–mesenchymal transition, therapy resistance, and cell death inhibition. Clinically, high lncRNA NEAT1 expression correlates with advanced T stage, lymph node metastasis, and reduced survival, underscoring its potential as a diagnostic and prognostic biomarker. Therapeutically, emerging approaches such as nanoparticle-mediated delivery of siRNA/shRNA offer a promising strategy to target lncRNA NEAT1, potentially synergizing with existing immunotherapies. Although clinical translation remains challenging, lncRNA NEAT1 represents a highly promising biological target for future precision oncology in HNSCC. Full article