Search Results (2,968)

Pollen development is a complex process that is highly sensitive to environmental stresses. Abscisic acid (ABA), a key hormone mediating plant growth and stress responses, has been implicated in the regulation of sexual reproduction, especially pollen development, yet its precise regulatory role remains unclear. This study investigated the effects of exogenous ABA on Arabidopsis thaliana pollen development and function through integrated phenotypic, cytological, and transcriptomic approaches. ABA treatment specifically impaired pollen function by reducing germination rates and inhibiting pollen tube elongation, which resulted in shortened siliques and decreased seed set, without affecting pollen morphology or viability. Transcriptome analysis of mature anthers revealed a transient and time-dependent transcriptional response, with the number of differentially expressed genes (DEGs) peaking at 8 h post-ABA treatment and markedly declining by 22 h. These DEGs were enriched in stress-response pathways (e.g., salt, cold, and dehydration), hormone signaling, and carbohydrate metabolism. Moreover, we identified 25 differentially expressed transcription factors and 16 pollen development and function-related genes, highlighting their key roles in ABA-mediated regulation. In parallel, 146 differentially expressed lncRNAs (DELs) were identified, which formed 144 cis-regulatory pairs with genes involved in ABA response and pollen tube growth, with their predicted targets enriched in pathways such as hormone and MAPK signaling, carbohydrate metabolism and stress response. Trans-regulatory analysis further revealed that these DELs co-expressed with DEGs in modules enriched for stress response, pollen development, and tube growth pathways. Notably, key pollen function genes showed strong co-expression with DELs, indicating that lncRNAs participate in ABA-induced transcriptional reprogramming that shifts metabolic resources from growth to defense, thereby suppressing pollen germination and tube elongation. Together, these findings elucidate a coordinated regulatory network involving mRNAs, lncRNAs and transcription factors roles in modulating ABA responses during pollen/anther development. Full article

Accumulating studies have identified the pivotal role of long non-coding RNAs (lncRNAs) in participating in host–virus interactions during virus infections. However, the regulatory roles of lncRNAs in influenza A virus (IAV) infection are still not fully elucidated. In this study, using high-throughput sequencing, we comprehensively compared the expression profiles of lncRNAs and mRNAs in mouse lungs infected either with the nonpathogenic parental (SDL124) H7N9 virus or its moderately pathogenic mouse-adapted (S8) variant. A total of 7636 significantly differentially expressed (SDE) lncRNAs were obtained in the S8-infected group compared to the mock group. As for the SDL124 group, 1042 SDE lncRNAs were identified. Subsequently, the mRNAs co-expressed with SDE lncRNAs were subjected to functional annotation and pathway enrichment analysis. The results indicated that the target mRNAs regulated by the S8 virus were mainly enriched in various immunological processes and exhibited a strong correlation with inflammatory-related signaling pathways. Moreover, 12 lncRNAs and 10 mRNAs co-expressed with SDE lncRNAs were selected and successfully verified by RT-qPCR. Among these lncRNAs, NONMMUG032982.2 and NONMMUG032328.2 exhibited strong antiviral activity against IAV. Additionally, these two lncRNAs were chosen for further in-depth bioinformatics analysis, including transcription factor prediction, coding capacity assessment, genomic location, construction of secondary structure, and prediction of potential interacting proteins. Taken together, these findings provide a cluster of lncRNAs probably associated with the virulence of IAV in mice and shed light on the anti-IAV effects of two functional lncRNAs, establishing a molecular foundation for further exploring the regulatory mechanisms of lncRNAs in IAV infection. Full article

Long non-coding RNAs (lncRNAs) are transcripts constituted of more than 200 nucleotides that have been associated with the regulation of different biological processes by modulating the expression of key genes. In horses, evidence suggests that lncRNAs play a role in female reproductive fitness, yet their functional implications remain poorly characterized. The objective of this study was to investigate potential DNA:RNA triplex interactions between the promoter regions of fertility-related genes and lncRNAs transcribed from non-coding loci located within ±50 kb of these genes. By doing so, we aimed to elucidate the regulatory mechanisms underlying fertility in Pura Raza Española (PRE) horses. The observed distances (1.2–49.8 kb) were consistent with cis-acting lncRNAs. Furthermore, genomic context and structural accessibility analyses revealed that some predicted DNA-binding sites reside within CpG islands. This strategic localization in active promoter regions points toward a regulatory mechanism where lncRNAs may modulate transcriptional activity via triplex formation. Our results provide a concrete set of biologically plausible lncRNAs within fertility-associated genomic regions, representing targets for further functional validation and potential applications in genomic improvement strategies. Full article

Background/Objectives: Non-coding RNAs provide new chances of targeting multiple oncogenic pathways. Many long non-coding RNAs (lncRNAs) are being characterized as relevant in cancer initiation, progression, and recurrence. Mitochondrial D-loop 1 antisense lncRNA (MDL1AS) is a novel lncRNA that might be important in cancer development, so the aim of this project was to understand its function in differently differentiated cancer cells. Methods: The effects of MDL1AS downregulation on the cellular behavior of NTERA2 and SH-SY5Y cell lines were studied. Results: MDL1AS reduction inhibited oxidative phosphorylation in NTERA2 cells and induced neuritic differentiation in SH-SY5Y cells. This downregulation also produced a strong DNA damage response (DDR) and an increased apoptotic signature by RNAseq analysis, and decreased proliferation in both cell lines. It also decreased radiosensitivity in NTERA2 cells but not in SH-SY5Y. Conclusions: These results suggest that MDL1AS reduction can modulate radiosensitivity, metabolism, and differentiation in a cell type-specific manner. Furthermore, MDL1AS may constitute a predictive biomarker and a molecular target for new therapies. Full article

Grafted plants carrying DNA from both species are prone to new phenotypes. Specific long non-coding RNA (lncRNA) sequences are known to play roles in the formation and development of grafted plants. However, the roles of lncRNAs in phenotypic variation in grafts between peach and apricot remain unexplored. In this study, mixed tissues (leaves, buds and fully bloomed flowers) of peach branches from heterografts between apricot/peach (A/P) and peach/apricot (P/A) and homografted peach (SP) were collected for transcriptome sequencing. The differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) between A/P and P/A were identified as candidates mediating the formation of divergent traits. Compared with SP, 1115 and 624 DEGs were detected in A/P and P/A, respectively. There were 173 DEGs shared between A/P and P/A, whereas the transcripts of 942 genes were specifically altered in A/P and 451 DEGs were specific to P/A. There were 29 DElncRNAs in A/P and 26 DElncRNAs in P/A, of which, 21 DElncRNAs were specific to A/P and 18 were specific to P/A. The biological functions of the DEGs and DElncRNAs were predicted via GO and KEGG enrichment analyses. A total of 24 co-expressed ‘lncRNA-mRNA’ pairs were identified, including 14 ‘lncRNA-mRNA’ pairs in A/P and 10 ‘lncRNA-mRNA’ pairs in P/A. The ‘MSTRG.17020.2-XM_007210198-2’ pair potentially participates in aminoacyl biosynthesis, and the ‘MSTRG.8395.1-XM_007217967.2’ pair may regulate galactose metabolism. The lncRNA MSTRG.6365.3 may regulate defense response through altering the levels of XM_020556240.1 and XM_020556234.1. These findings provide valuable insights into the molecular mechanisms underlying grafting-induced differential trait formation and establish a foundation for further research on the functional roles of ‘lncRNA-mRNA’ pairs in fruit tree grafting systems. Full article

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. Full article

DNA methylation is a fundamental epigenetic regulator in hepatocellular carcinoma (HCC). However, a key paradox remains: how do ubiquitously expressed enzymes like DNMTs and TETs achieve locus-specific regulation without intrinsic sequence specificity? This review aims to elucidate the “lncRNA–DNA methylation axis,” examining how long non-coding RNAs (lncRNAs) confer specificity and plasticity to methylation machinery. We synthesized current literature focusing on the structural mechanisms (e.g., R-loops, DNA:RNA triplexes) by which lncRNAs interact with DNMTs and TETs. We further analyzed the bidirectional regulation between lncRNAs and methylation enzymes and their impact on HCC phenotypes. lncRNAs function as modular scaffolds and guides, directing methylation machinery to specific genomic loci. Rather than binary switches, they act as an “epigenetic rheostat,” fine-tuning methylation intensity to balance stability with plasticity. Crucially, a reciprocal feedback loop exists: aberrant DNA methylation suppresses tumor-suppressive lncRNAs, which in turn unleashes DNMT activity, locking cells into a malignant state. This axis drives proliferation, metastasis, metabolic reprogramming, and therapeutic resistance. The lncRNA–DNA methylation axis is a central determinant of epigenetic heterogeneity in HCC. Moving beyond descriptive cataloging to a mechanistic understanding of this network offers new perspectives for developing targeted epigenetic therapies and biomarkers. Full article

Background: Myocardial ischemic injury, encompassing acute myocardial infarction (MI) and ischemia/reperfusion (I/R) injury, remains a major cause of cardiac morbidity and mortality worldwide, and is driven by interconnected molecular and cellular processes, including cardiomyocyte apoptosis, inflammatory activation, mitochondrial dysfunction, oxidative stress, and impaired angiogenesis. Mesenchymal stem cell (MSC)-derived exosomes have emerged as a promising cell-free nanotherapeutic strategy for cardiac repair due to their ability to transfer bioactive molecules that modulate multiple signaling networks involved in myocardial survival and regeneration. This systematic review aimed to synthesize evidence on the mechanistic basis of MSC-derived exosome mediated cardioprotection in myocardial ischemic injury. Methods: A systematic search of Ovid MEDLINE, Scopus, and Web of Science was conducted to identify studies investigating the effects of MSC-derived exosomes on myocardial ischemic injury. Eligible studies included clinical and preclinical models of MI or I/R injury assessing functional, biochemical, and molecular outcomes. Results: Seven preclinical studies published between 2015 and 2025 met the inclusion criteria. Exosome administration consistently improved cardiac function, reduced infarct size, and preserved myocardial architecture. Biochemical analyses revealed decreased cardiac injury markers, alongside suppressed apoptosis, inflammation, and oxidative stress. Mechanistically, MSC-derived exosomes delivered regulatory miRNAs (e.g., miR-19a, miR-125b, miR-205, miR-294) and lncRNAs (HAND2-AS1) that modulated key signaling pathways including PI3K/Akt, JAK2/STAT3, HAND2-AS1/miR-17-5p/Mfn2, and HIF-1α/VEGF. These molecular effects collectively inhibited apoptotic and inflammatory responses, enhanced mitochondrial integrity, and promoted angiogenesis and myocardial repair. Conclusions: MSC-derived exosomes confer robust cardioprotection against myocardial ischemic injury through integrated anti-apoptotic, anti-inflammatory, antioxidant, and pro-angiogenic mechanisms. Their multifaceted bioactivity, low immunogenicity, and potential for targeted delivery highlight their potential as a next-generation nanomedicine for ischemic heart disease. Future studies should emphasize standardized exosome production, mechanistic profiling, and translational validation in large-animal and clinical models. Full article

The lack of reliable diagnostic tools and relapse monitoring for latent tuberculosis infection (LTBI) constitutes a major obstacle to global tuberculosis (TB) control. This highlights an urgent need for robust animal models and predictive biomarkers. To address this, we report the successful establishment of a rapid murine model of recapitulating the active, latent, and relapse phases of TB within a compressed ten-week timeframe—hence termed the rapid multi-stage TB murine model. In this model, mice were first intravenously infected with Mycobacterium tuberculosis, followed by a four-week isoniazid (INH) regimen starting at two weeks post-infection. By week six, pulmonary bacterial loads in most mice dropped below the detection limit, signifying the establishment of latency. Reactivation was subsequently triggered by a four-week administration of anti-TNF-α (Tumor Necrosis Factor-α) monoclonal antibody. Leveraging this reproducible and time-efficient model, we performed transcriptomic profiling of peripheral blood and identified a distinct sixteen-gene signature (including Ets2, Fam111a, Fosl2, Gadd45b, Nfkbid, Rgs1, Bhlhe40, Il1r2, Clec2d, Kmo, Lynx1, Papd4, Trim34a, Wrb, Nlrp12, Spns1) that dynamically tracks disease progression. Collectively, these findings not only provide a valuable and efficient preclinical tool but also deliver transformable candidate biomarkers with immediate potential to guide the development of novel diagnostic strategies for LTBI surveillance and management. Full article

Aspergillus flavus infection and accumulation of carcinogenic aflatoxins are detrimental to maize (Zea mays) production and consumption. We investigated lncRNA–RBP interactions during maize–A. flavus crosstalk using transcriptomic profiling, structural analysis, molecular docking simulations, and machine learning approaches. Analysis of 18 RNA-seq datasets identified 2104 lncRNAs in maize, of which 461 were differentially expressed under A. flavus infection. Distinct lncRNAs were preferentially induced under infection (e.g., Zm00001eb303170) or normal germination (e.g., Zm00001eb144150, Zm00001eb406410). RNA secondary structure predictions indicated high structural heterogeneity and thermodynamic stability, consistent with dynamic regulatory potential. Docking simulations with six key RNA binding proteins (RBPs)—including branch point bridging protein (BPB), KH domain protein, and pentatricopeptide repeat (PPR) proteins—demonstrated strong lncRNA–protein binding, with the lncRNA1–BPB complex exhibiting the highest binding affinity. ML algorithms identified the crucial role of tryptophan in determining interactions, while lncRNA17-KH and lncRNA1-BP complexes were found to have the best interaction under normal germination and A. flavus infection, respectively. The lncRNA–miRNA–mRNA regulatory network highlighted lncRNAs functioning as decoys or precursors of stress-responsive miRNAs (e.g., zma-miR156, zma-miR164, zma-miR399). These interactions targeted transcriptional regulators, splicing factors, and metabolic enzymes implicated in stress tolerance, seed germination, and systemic acquired resistance. The maize lncRNAs are active regulatory molecules embedded in complex RBP and miRNA interaction networks that fine-tune gene expression during A. flavus infection. The study provides novel insights into lncRNA-mediated resistance mechanisms and offers potential molecular targets for breeding or gene editing to mitigate aflatoxin contamination. Full article

Congenital heart defects (CHDs) represent the most common category of congenital malformations and constitute a significant cause of infant morbidity and mortality. Despite advances in prenatal imaging, such as fetal echocardiography, early detection remains challenging, particularly in pregnancies without identified risk factors. Recent studies suggest that maternal circulating non-coding RNAs, including microRNAs and long non-coding RNAs (lncRNAs), may serve as promising non-invasive biomarkers for the prenatal diagnosis of CHDs. Following a review of the most relevant clinical and preclinical studies, it was found that maternal circulating RNA, particularly microRNAs and lncRNAs, shows potential as non-invasive biomarkers for detecting fetal congenital heart defects. Among microRNAs, miR-146a-5p demonstrated the highest diagnostic accuracy for ventricular septal defects (VSDs), while panels of lncRNAs, such as LINC00598, LINC01551, and GATA3-AS1, exhibited high performance for atrial septal defects (ASDs). In addition, miR-19b, miR-29c, and miR-375 were associated with both VSDs and ASDs, suggesting a shared role in septal development. However, the studies displayed variability in biomarker selection and analytical methodologies. The findings indicate that maternal circulating microRNAs and lncRNAs hold significant potential as non-invasive biomarkers for the early detection of CHDs. Nonetheless, methodological heterogeneity and small sample sizes highlight the need for standardized protocols and larger multicenter studies prior to clinical implementation. These observations support the future integration of RNA biomarkers with fetal echocardiography to enhance early CHD screening and to inform prenatal counseling. Full article

The etiology of pediatric cancers is unique, stemming from developmental dysregulation rather than acquired mutations from carcinogenic exposure. These diseases demonstrate vastly different underlying genetic and epigenetic alterations and unique tissue microenvironments which are only now beginning to be explored. While many pediatric cancers have seen improved overall and event-free survival rates thanks to innovations in diagnosis and treatment, many have seen little to no improvement in patient outcomes. This highlights a critical need for additional research into the underlying genetic and epigenetic alterations in these pathologies. Non-coding RNAs (ncRNAs) are functional RNA molecules known to regulate gene expression at epigenetic, transcriptional, and translational levels and can serve as biomarkers of disease. Here, we examine current knowledge of the roles of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the onset, progression, and therapeutic response of pediatric solid tumors. We discuss the current and future potential and pitfalls of these molecules as therapeutics and biomarkers and highlight critical knowledge gaps where future research might provide insight to improve current therapeutic strategies and improve clinical outcomes. Full article

Colorectal cancer (CRC) is a significant cause of cancer mortality in the world, and its etiology is complicated by genetic and epigenetic changes. As one of the most important tumor progression regulators, Zinc Finger E-box Binding Homeobox 1 (ZEB1) is a transcription factor that has a key role in epithelial–mesenchymal transition (EMT), which is essential in the metastasis, drug resistance, and plasticity of cancer cells in CRC. ZEB1 silences the expression of epithelial markers, including E-cadherin, and it induces the development of mesenchymal properties, such as invasion and metastasis, i.e., tumor aggressiveness. ZEB1 drives epigenetic reprogramming in CRC by coordinating histone deacetylation, histone methylation, and DNA methylation of epithelial tumor suppressor gene promoters and by engaging in reciprocal regulatory interactions with non-coding RNAs, including the miR-200 family. Furthermore, multiple oncogenic signaling cascades, including Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α, converge on ZEB1 to amplify its transcriptional and epigenetic activity, positioning ZEB1 as a nodal integrator of extracellular cues and epigenetic reprogramming in CRC metastasis. This review integrates three interconnected regulatory layers, i.e., (1) ZEB1’s direct epigenetic control of target gene expression via histone modification and DNA methylation, (2) post-transcriptional regulation of ZEB1 itself by ncRNAs (miRNAs, circRNAs, and lncRNAs) that create feedback circuits modulating layer 1, and (3) upstream modulation of ZEB1 transcriptional activity by oncogenic signaling pathways (Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α) to provide a comprehensive picture of ZEB1 in CRC metastasis and its therapeutic implications. Full article

Diabetic kidney disease (DKD) remains a leading cause of end-stage renal disease worldwide, with current therapies often failing to halt its progression due to an incomplete understanding of intrinsic renal molecular mechanisms. This review highlights the pivotal role of non-coding RNAs (ncRNAs)—including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)—as central regulators in the pathogenesis and progression of DKD. We systematically examine how the diabetic milieu dysregulates specific ncRNA profiles in renal cells, driving core pathological processes such as metabolic dysfunction, inflammation, fibrosis, and podocyte injury. Furthermore, we explore the emerging roles of exosomal ncRNAs in intercellular communication and their potential as non-invasive liquid biopsy biomarkers for early diagnosis and disease monitoring. Finally, we discuss the translational prospects of targeting ncRNAs through innovative therapeutic strategies, such as antisense oligonucleotides and miRNA mimics, while addressing the challenges of tissue-specific delivery and clinical implementation. Understanding ncRNA networks offers a refined, systems-level perspective on DKD and opens new avenues for precision diagnostics and targeted interventions aimed at modifying the disease course. Full article

Extracellular vesicles (EVs) have emerged as promising tools for cancer diagnosis and therapy owing to their excellent biocompatibility, low immunogenicity, and ability to transport diverse bioactive molecules. This review summarizes recent advances in EVs research, focusing on isolation and detection technologies, their diagnostic and therapeutic applications in oncology, and the key challenges limiting clinical translation. Conventional EVs isolation methods, including ultracentrifugation, density-gradient centrifugation, and polymer-based precipitation, are discussed alongside emerging strategies such as immunoaffinity enrichment, microfluidic separation, lipid-mediated isolation, and thermophoretic enrichment, with comparative evaluation of their yield, purity, cost, and scalability. In cancer diagnosis, EV-associated biomolecules, such as miRNAs, mRNAs, proteins, and lncRNAs, show strong potential as liquid biopsy biomarkers for noninvasive early detection and dynamic disease monitoring. In therapeutic contexts, EVs serve as versatile carriers for gene molecules, chemotherapeutic agents, and small-molecule drugs, and can enhance immunotherapy and RNA-based treatments. Importantly, EVs released from metabolically active tissues, particularly skeletal muscle, contribute to systemic immune regulation and metabolic homeostasis, and their biogenesis and molecular cargo can be influenced by physical activity and exercise-related nutritional status. These insights highlight the need to integrate microengineering technologies, biomolecular profiling, standardized manufacturing systems, and lifestyle-related factors such as exercise and nutrition to accelerate the clinical translation of EV-based strategies in precision oncology and regenerative medicine. Full article