Search Results (175)

Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by thrombotic and inflammatory manifestations whose molecular regulatory mechanisms remain incompletely understood. Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A)-related regulation are increasingly recognized as components of immune gene regulation, but their involvement in APS remains poorly characterized. This study investigated BRD3OS (LINC00094) expression in APS and explored its molecular and predicted structural context in relation to m6A-associated regulation. An exploratory case–control study was conducted using an initial lncRNA PCR-array discovery cohort followed by targeted RT-qPCR validation in an independent cohort. Candidate prioritization incorporated multiple expression and technical features and was evaluated through sensitivity analyses. BRD3OS expression, selected m6A regulators (METTL3, METTL14, WTAP, and FTO), inflammatory mediators, and global m6A abundance in total peripheral blood mononuclear cell (PBMC) RNA were evaluated. Bioinformatic network analysis was used to contextualize BRD3OS within APS- and m6A-related molecular systems. RNAfold and RNAplfold were used to characterize the predicted structural context and accessibility of DRACH consensus motifs, with additional analyses evaluating fragment-boundary and composite-score robustness. BRD3OS was significantly downregulated in PBMCs from patients with APS in the independent validation cohort. METTL3, METTL14, and WTAP expression was also reduced, whereas global m6A levels in total PBMC RNA were increased. These observations indicate concurrent alterations in BRD3OS expression and the broader m6A-related molecular environment but do not establish transcript-specific methylation of BRD3OS. Bioinformatic network analysis placed BRD3OS within predicted RNA-centered regulatory relationships relevant to APS. DRACH motifs exhibited heterogeneous predicted structural accessibility, with unpaired structural environments showing greater RNAplfold-derived accessibility than paired regions. Quantitative accessibility estimates were highly concordant across overlapping transcript fragments, although sensitivity analyses indicated that the identity of individual highest-ranked candidates depended on the weighting scheme. BRD3OS downregulation represents a reproducible molecular finding in APS. Concurrent alterations in global m6A abundance and selected m6A regulators suggest broader epitranscriptomic dysregulation; however, these measurements cannot establish m6A modification of BRD3OS or a causal relationship between these observations. Structural and network analyses therefore provide a hypothesis-generating framework for prioritizing candidate regions and interactions for future transcript-specific methylation mapping and functional validation. Full article

The quail is a valuable model organism for avian developmental biology and genetic improvement; however, the full-length transcriptomic landscape and regulatory networks underlying critical embryonic developmental stages remain poorly characterized. In this study, we employed Oxford Nanopore Technologies full-length transcriptome sequencing to systematically analyze leg muscle tissues from quail embryos at embryonic day 8 (E8, pre-differentiation stage) and embryonic day 14 (E14, later differentiation stage), with four biological replicates per stage (eight libraries in total). Nanopore sequencing identified a total of 54,938 transcripts and 21,574 genes, including 49,678 known transcripts, 20,980 known genes, 5260 novel transcripts, and 594 novel genes. Analysis of transcriptome structure revealed that alternative first exon and exon skipping represented the predominant stage-specific alternative splicing events, and we identified 2692 lncRNAs. Differential expression analysis identified substantial transcriptome dynamics from E8 to E14, with 5934 differentially expressed transcripts and 3745 differentially expressed genes identified. Functional enrichment analyses, including KEGG, GSEA and PPI network analysis, revealed that the E8 transcriptome was predominantly enriched for pathways associated with cell proliferation, whereas the E14 transcriptome shifted toward the coordinated refinement of myofiber structural assembly and energy metabolism. Here, we present a high-resolution full-length transcriptional atlas of quail skeletal muscle development and identify candidate regulatory genes, offering a valuable theoretical framework and data resource for refining quail genome annotation. Full article

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

Vairimorpha ceranae is a fungal pathogen that infects the honeybee midgut and poses a serious threat to colony health. However, the role of long noncoding RNAs (lncRNAs) of V. ceranae in its infection of the host remains poorly understood. Using lncRNA-seq data from the midguts of Apis mellifera workers at 7 and 10 days post-inoculation with V. ceranae (NcT1L and NcT2L groups), along with controls inoculated with spores (NcCKL group), we performed transcriptome-wide identification and structural characterization of lncRNAs. We identified lncRNAs in V. ceranae and analyzed the regulatory network of the differentially expressed lncRNAs (DElncRNAs). A total of 27 V. ceranae lncRNAs were identified in the midguts. The 19, 21, and 4 DElncRNAs were identified in the NcCKL vs. NcT1L, NcCKL vs. NcT2L, and NcT1L vs. NcT2L comparison groups. These DElncRNAs were predicted to regulate 26, 27, and 2 upstream/downstream genes. Furthermore, 15, 23, and 4 DElncRNAs were found to target 195, 211, and 94 miRNAs, which in turn targeted 204, 216, and 73 mRNAs into the respective comparisons. The ceRNA network prediction revealed that DElncRNAs, miRNAs and mRNAs form a complex regulatory network. This study presents the expression profile of lncRNAs during V. ceranae infection and highlights their potential regulatory functions in pathogenesis. Our findings provide new molecular insights into host–pathogen interactions at the RNA level and establish a foundation for developing targeted strategies to control nosemosis. Full article

Piscirickettsia salmonis is one of the most significant pathogens affecting salmon farming. Besides liver, head kidney and spleen, skeletal muscle has shown transcriptional immune responses to these bacteria, but the contribution of non-coding RNAs remains poorly understood. This study investigates the role of long non-coding RNAs (lncRNAs) in the immune response of rainbow trout skeletal muscle and primary myotube cultures infected with P. salmonis. Using RNA-seq data from both in vivo and in vitro muscle under control and infected conditions, the analysis identified 4263 candidate lncRNAs through a stringent bioinformatics pipeline. These lncRNAs were mostly classified as exonic and intergenic, showing distinct genomic distributions and structural differences depending on the source. Expression analyses revealed that cell type had a stronger effect on lncRNA profiles than infection status. From 764 differentially expressed lncRNAs, 191 were uniquely associated with infected and 180 with control conditions, mainly unannotated. Functional predictions based on co-expression and proximity to coding genes suggest that lncRNAs are primarily involved in downregulation of structural-cellular maintenance under control conditions, whereas during infection, they are related to immunity, signaling, and apoptosis. Overall, the findings indicate that lncRNAs exhibit origin-specific regulatory roles and are modulated by P. salmonis infection, highlighting their potential importance in fish immune responses. Full article

Structural and functional disruptions of the epigenome are hallmarks of breast and ovarian carcinogenesis. This review dissects the reciprocal regulatory networks co-operated by DNA methyltransferases (DNMTs), ten-eleven translocation enzymes (TETs), and key non-coding RNAs (microRNAs and lncRNAs). We map the precise molecular mechanisms through which these epigenetic modulators alter chromatin accessibility, drive transcriptional reprogramming, and promote phenotypic plasticity in hormone-dependent malignancies. By systematically contrasting the distinct yet overlapping epigenetic profiles of breast and ovarian tumors, we elucidate how these aberrations dictate clinical outcomes. This comprehensive synthesis offers critical insights into the dual utility of these epigenetic elements as dual-purpose diagnostic biomarkers and druggable therapeutic targets, laying the groundwork for next-generation targeted epigenetical therapies. Full article

Yaks have long inhabited the Qinghai-Tibetan Plateau. This region features low-oxygen, frigid temperatures and pronounced seasonal variation in nutrient availability. They have evolved adaptive phenotypes centered on energy metabolism reprogramming, tissue structure remodeling, and stress homeostasis maintenance. In recent years, non-coding RNAs (ncRNAs) have been confirmed as an important component of the yak’s post-transcriptional regulatory network. They play a key bridging role between environmental stress perception and phenotypic output through mechanisms such as influencing RNA splicing, stability, translation activity, and constructing competitive endogenous RNA (ceRNA) networks. This article systematically reviews the biogenesis pathways and core regulatory patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). It focuses on summarizing the expression profile characteristics and dynamic spatiotemporal changes of these three types of ncRNAs in physiological contexts such as muscle and fat deposition, mammary gland lactation, testicular development, and hypoxia response in the heart, lungs, and vascular system of yaks. Current research evidence indicates that the regulatory network of yaks ncRNAs shows significant convergence on multiple key signaling pathways, mainly concentrating on lipid metabolism (PPAR/AMPK), nutrition and growth signals (PI3K-Akt/MAPK/mTOR), extracellular matrix remodeling (ECM-receptor interaction, Wnt/TGF-β), and cell stress fate determination (apoptosis, oxidative stress/ferroptosis) modules. Among them, some core circRNA and lncRNA-miRNA-mRNA regulatory axes have been functionally validated in vitro. Despite the phased progress, current research on ncRNA in yaks still faces bottlenecks: the multi-omics molecular atlases (encompassing genomics, transcriptomics, proteomics, and metabolomics) of key high-altitude adaptive organs remain incomplete, analysis processes lack sufficient standardization, and most studies stay at the association network level with limited causal mechanism validation. To address these limitations, future research should focus on building a standardized evidence chain, integrating multi-omics and single-cell/spatial transcriptome technologies, and conducting mechanism verification for traits in independent populations, thereby providing a solid theoretical basis for understanding the extreme environmental adaptation mechanisms of yaks and molecular breeding improvement. Full article

Background/Objectives: Cervical cancer is mainly driven by persistent infection with high-risk human papillomaviruses (HPV), particularly HPV16 and HPV18. Despite advances in cytology, HPV-DNA testing and vaccination, challenges remain in the triage of HPV-positive individuals, prognostic stratification and prediction of treatment response. Non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs and circular RNAs, together with host genetic factors influencing ncRNA expression and emerging lncRNA-encoded peptides, are increasingly recognized as regulators of HPV-associated carcinogenesis. This review summarizes their biological and potential clinical relevance. Methods: A structured literature search was conducted in PubMed and Scopus. Eligible studies included experimental, clinical, observational, genomic and translational investigations on ncRNA dysregulation, circulating or exosomal ncRNAs, treatment-response signatures, host genetic variation and lncRNA-encoded peptides in HPV-associated cervical precancer and cancer. Results: HPV oncoproteins can reshape host ncRNA networks through transcriptional and epigenetic mechanisms. Several miRNAs, lncRNAs and circRNAs are involved in cell-cycle control, apoptosis, senescence, epithelial–mesenchymal transition, immune regulation, DNA repair and treatment resistance. Circulating, exosomal and urinary ncRNA signatures have shown diagnostic or prognostic potential in exploratory cohorts. Specific lncRNAs, including ENSG00000267838/lnc-LENG9-5 and lncRNA-EME1, have been associated with chemoradiotherapy response and radioresistance. The lncRNA-encoded peptide TUBORF represents a novel preclinical therapeutic candidate, while genetic variation may further modulate lncRNA function in HPV-related cervical cancer. Conclusions: ncRNAs are promising candidates for risk stratification, non-invasive diagnosis, treatment-response prediction and therapeutic development in HPV-associated cervical disease. However, evidence remains exploratory, requiring prospective multicentre validation and standardized workflows before clinical implementation. Full article

Background: Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression, playing pivotal roles in diverse biological processes, including reproduction. This study identified and characterized lncRNAs located near fertility-associated genes in Retinta beef cattle, exploring their potential regulatory roles via DNA–RNA triplex formation using in silico approaches. Methods: We applied an integrative bioinformatics pipeline to identify potential triplex interactions, predicting structurally accessible regions within the lncRNAs and demonstrating the statistical enrichment of binding sites across known regulatory genomic elements. Results: Twelve protein-coding genes previously linked to female fertility or male scrotal circumference were analyzed, revealing 16 unique lncRNAs within ±50 kb windows, predominantly on BTA5. We predicted high-confidence triplex-forming oligonucleotides (TFOs) for most gene-lncRNA pairs. Our results suggest robustness and sequence specificity, as interactions were disrupted by sequence permutation or when a control background sequence was used. RNA secondary-structure analysis revealed that TFOs generally lie in exposed regions, supporting their accessibility for triplex formation. Furthermore, promoter and regulatory regions of fertility-associated genes were enriched in predicted triplex target sites (TTSs), with some overlapping CpG islands and enhancer regions, leading to the hypothesis that these lncRNAs might play a role in epigenetic regulation. Conclusions: Overall, these findings establish computationally derived hypotheses regarding the potential molecular mechanisms by which lncRNAs may modulate reproductive efficiency in cattle and highlight specific lncRNAs as promising targets for functional studies and marker-assisted breeding. Full article

The green sea turtle (Chelonia mydas), a widely distributed species, plays a crucial role in maintaining the marine ecosystem. However, studies on C. mydas require accurate and comprehensive genome annotation information. Long-read direct transcriptome data of C. mydas were obtained using direct RNA sequencing on the Oxford Nanopore Technologies (ONT) platform from blood tissue of a single captive individual. A total of 4061 novel transcripts were obtained by comparing long-read direct transcripts with genome annotation of C. mydas. We also predicted 2402 CDSs on the novel transcripts. Among them, 1208 (50.29%) had functional annotation information in the databases. In addition, we predicted and analyzed AS events, fusion transcripts, methylation sites, poly(A)s, and lncRNAs in the C. mydas long-read direct transcriptome. Overall, our study provides the a long-read direct blood transcriptome for C. mydas to complement and improve its genome annotation. This valuable resource will contribute to future research on C. mydas. Additionally, the analyses of transcriptome structure mentioned above may provide new insights and ideas for the study of C. mydas. Full article

To investigate the response mechanism of cold-resistant Enshi black pig breeds under cold stress, nine Enshi black pigs were randomly divided into three groups with three pigs in each: a control group (18 ± 2 °C for 58 d), a cold-stress-acclimated group (3 to 8 °C to −17 to −21 °C for 58 d), and an acute cold stress group (−17 to −21 °C for 3 d). RNA-seq technology was used to analyze mRNA and lncRNA expression patterns in subcutaneous adipose tissue under cold stress. The results showed that, under acute cold stress, many metabolic pathways were activated, including those involved in rapid energy supply (e.g., the citric acid cycle/TCA cycle, fatty acid degradation and metabolism, and glycolysis/gluconeogenesis), signal transduction pathways (e.g., PI3K Akt, MAPK, PPAR, HIF-1, mTOR, and FoxO), and immune and cellular homeostasis pathways (chemokine signaling pathway, T cell receptor signaling, Toll-like receptor signaling, and apoptosis and autophagy regulation). Under cold stress acclimation, metabolic regulatory pathways (e.g., AMPK, mTOR, FoxO, HIF-1, glycolysis/gluconeogenesis, and fatty acid degradation), immune and inflammatory regulatory pathways (Toll-like receptors, NOD like receptors, and T/B cell receptor signaling pathways), and signal transduction and cell homeostasis pathways (MAPK, PI3K Akt, NF-κB, Notch signaling pathways, apoptosis, and autophagy regulation) were continuously activated to ensure the stability of adipose tissue structure and function. Acute cold stress activated more pathways than cold stress acclimation, but both led to significant changes in energy metabolism. The results identified the molecular regulatory mechanisms of adipose tissue under cold stress, providing a basis for the subsequent breeding of new cold-resistant pig breeds. Full article

Ankylosing spondylitis (AS) is a chronic immune-mediated inflammatory disease affecting the axial skeleton, characterized by progressive structural damage and functional impairment. Although biologic therapies targeting tumor necrosis factor and interleukin-17 have improved clinical outcomes, a substantial proportion of patients fail to achieve sustained disease control. Emerging evidence suggests that metabolic alterations may contribute to AS pathogenesis; however, systematic characterization of metabolism-related biomarkers and their regulatory networks remains limited, and the interplay between metabolic dysfunction and immune dysregulation in AS is poorly understood. Two whole-blood GEO datasets (GSE25101, GSE73754; n = 104) were integrated as the primary analytical cohort. A third dataset (GSE11886, n = 18; monocyte-derived macrophages) was included for exploratory cross-tissue analysis. Differential expression analysis identified 847 DEGs, which were refined to 16 metabolism-related genes through weighted gene co-expression network analysis (WGCNA) and GeneCards database filtering. Eleven machine learning algorithms with 5-fold cross-validation were applied to construct diagnostic models and identify hub genes. Validation analyses included immune cell infiltration estimation using CIBERSORT, metabolic pathway activity assessment via ssGSEA, single-cell transcriptomics from GSE268839, functional enrichment through GSEA/GSVA, and chromosomal localization analysis. A competing endogenous RNA (ceRNA) regulatory network was constructed to map post-transcriptional regulation. Natural compounds from 66 AS-treating traditional Chinese medicines were screened against hub genes using deep learning-based binding prediction. Multiple machine learning algorithms achieved comparable cross-validated performance (CV AUC range 0.741–0.836; top five models: 0.805–0.836) using the six hub genes (MFN2, SLC27A3, RHOB, SMG7, AKR1B1, LCOR) identified through SHAP-based feature importance analysis of the PLS model. Leave-one-dataset-out validation between the two whole-blood cohorts showed that all algorithms exceeded an AUC of 0.77 in Round 1 (validate: GSE73754, n = 72; best AUC 0.861), while Round 2 (validate: GSE25101, n = 32) yielded more modest performance (best AUC, 0.715) reflecting the smaller validation sample. Exploratory application to GSE11886 (macrophage-derived samples) showed near-chance performance, consistent with the tissue-source discrepancy. AS patients exhibited significant downregulation of oxidative phosphorylation, TCA cycle, and glycolysis pathways (p < 0.01), accompanied by elevated glutathione metabolism (p < 0.001). Immune cell deconvolution revealed reduced CD8+ T cell proportions correlating with MFN2 downregulation, and increased neutrophil frequencies correlating with SLC27A3 upregulation. Exploratory single-cell analysis indicated that RHOB expression was relatively enriched in border-associated macrophages and fibroblasts, while AKR1B1 was more prominently expressed in vascular endothelial cells and plasmacytoid dendritic cells. The ceRNA network identified 21 miRNAs and 65 lncRNAs forming 86 regulatory interactions, with four key regulatory axes (SATB1-AS1/miR-539-5p/LCOR, FAM95B1/miR-223-3p/RHOB, LINC01106/miR-106a-5p/MFN2, AATBC/miR-185-5p/SMG7) predicted to regulate hub gene expression. Compound screening identified betaine, pyruvic acid, citric acid, etc., as top-ranking candidates, with MFN2 showing the highest binding capacity among hub genes. This study provides an integrative framework linking metabolic reprogramming with immune dysfunction in AS. The six-gene diagnostic signature showed preliminary discriminatory ability in the available datasets, while the ceRNA regulatory network and natural compound screening results prioritize candidate regulatory pathways and compounds for future validation. These findings advance our understanding of AS pathogenesis and may guide future biomarker development and targeted intervention strategies. Full article

The human genome produces a large repertoire of non-coding RNAs (ncRNAs) with important regulatory roles in development, physiology, and most of diseases. Among these, long non-coding RNAs (lncRNAs) have emerged as key modulators of gene expression, chromatin organization, and cellular homeostasis, despite displaying remarkably low primary-sequence conservation across species. This apparent evolutionary paradox questions the limitations of predicting biological function based on conservation, particularly across different biological domains. Here, we examine current evidence on lncRNA evolution, with a focus on their roles in metabolic regulation compared with neurobiological processes. We hypothesize that lncRNAs involved in ancient and conserved pathways such as metabolism may be under stronger evolutionary constraint than those associated with higher-order, species-specific traits, although available data support a more nuanced interpretation. Functional importance often correlates poorly with linear sequence conservation and instead appears to depend on higher-level features, including RNA secondary or tertiary structure, genomic context, regulatory architecture, and interactions with conserved molecular partners. We propose a systematic comparative framework to empirically assess conservation among metabolism- and neuro-associated lncRNAs using phylogenetic, syntenic, structural, and expression-based metrics. Finally, we discuss the therapeutic implications of lncRNA biology, highlighting how a deeper understanding of their evolutionary and mechanistic properties may inform the development of more precise and effective RNA-targeting strategies. Together, these insights underscore the non-coding transcriptome as a critical frontier for both fundamental biology and precision medicine. Full article

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order. Full article

The 5′-proximal region of the citrus tristeza virus (CTV) RNA genome is a hub where several elements involved in different facets of the virus cycle reside, including the sequences driving the production of the viral long non-coding RNA (lncRNA) LMT1. The sequence of this region is one of the most divergent genome areas, allowing for strain differentiation. Beyond its use in assessing viral population diversity, the region provides a valuable model for studying the conservation of RNA structure and function despite sequence variation. Here, we integrated comparative in silico analysis of the LMT1 region from variants of eight CTV strains with selective 2′-hydroxyl acylation, analyzed by primer extension and mutational profiling (SHAPE-MaP) probing of in vitro–generated LMT1 RNAs from two divergent strains, T36 and T68. The predicted consensus structures revealed 19 putative, conserved stem-loops. The SHAPE-MaP reactivity data supported and substantiated the thermodynamics-based predictions for the 15 previously uncharacterized stem-loops and two functional elements identified earlier. The strong structural conservation across strains highlights that the LMT1 RNA structure contributes to its function during CTV infection. These results provide the first experimentally supported structure of this viral lncRNA and lay the foundation for defining how individual RNA motifs influence CTV biology. Full article