Search Results (180)

The presence of an extra DNA segment in a genome could indicate a transposon or another repetitive element on the move. In Neurospora crassa, a surveillance mechanism called meiotic silencing by unpaired DNA (MSUD) is maintained to monitor these selfish elements. MSUD utilizes common RNA interference (RNAi) factors, including the SMS-2 Argonaute, to target mRNAs from genes lacking a pairing partner during meiosis. In eukaryotes, an mRNA transcript is typically bound at the 5′ cap by the cap-binding complex (CBC), which assists in its nuclear export. Previously, we discovered that CBC and its interactor NCBP3 mediate MSUD, possibly by guiding the perinuclear SMS-2 to effectively recognize exported mRNAs. Here, we report that ARS2, a CBC cofactor, is involved in MSUD. ARS2 interacts with both CBC and NCBP3, and it may help bring them together. In addition to its role in silencing, ARS2 also contributes to vegetative growth and sexual sporulation. Full article

N6-methyladenosine (m⁶A) represents the most abundant and tightly controlled modification within eukaryotic mRNA, critically influencing RNA metabolism and function. The m⁶A methyltransferase Like-3 (METTL3), responsible for the complex’s catalytic function, has emerged as a central epitranscriptomic regulator governing mRNA stability, alternative splicing, nuclear export, and the efficiency of mRNA translation. Converging research shows that METTL3 is involved in the pathogenesis of numerous disorders via m⁶A-dependent, post-transcriptional regulation of gene programs controlling cell growth, migration, and immune pathways. Regarding pulmonary pathophysiology, METTL3-mediated m⁶A is tied to disease initiation and progression in conditions such as asthma, chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), lung infections, acute respiratory distress syndrome (ARDS). This review summarizes the contemporary evidence for METTL3’s roles and regulatory network in diverse pulmonary pathologies. We further highlight emerging strategies for targeting METTL3 as a potential therapeutic approach, underscoring its promise as a novel epitranscriptomic target. Beyond inflammatory and fibrotic disorders, we also summarize emerging evidence linking METTL3 to lung cancer and briefly outline other respiratory conditions (e.g., ILD, bronchiectasis, and secondary pulmonary hypertension), highlighting common translational themes and remaining gaps. Further studies are required to clarify the disease-specific and context-dependent actions of METTL3 and to advance the clinical translation of m⁶A-based therapies. Full article

5-Methylcytosine (m5C) methylation is a widely present nucleic acid modification in various RNAs and is a reversible epigenetic modification that affects RNA stability, nuclear export, and translation processes. Methylation writers are responsible for adding methyl groups to RNA molecules, regulating gene expression and cellular function through catalyzing methyl transfer reactions. In order to more intuitively demonstrate the important value of NOL1/NOP2/SUN domain (NSUN) family genes in both tumor and non-tumor diseases, we conducted a relevant review. The NSUN family genes (NSUN1/NOP2, NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, NSUN7) are the main writers of m5C methylation. These genes can regulate methylation and affect the expression of other genes and are important in tumor and non-tumor diseases. Pieces of research on 7 NSUN family genes regarding methylation, diagnostic value, inflammatory diseases, cancer, and other diseases were searched for and summarized separately. Differences in NSUN family genes have been observed in many cancers, which can affect tumor growth, metastasis, chemotherapy resistance, and m5C methylation. In addition to affecting cancer, NSUN family genes have also attracted widespread attention due to their involvement in diseases related to growth, development, and metabolism. NSUN2 is the most studied NSUN family gene, which exhibits cancer promoting effects in various cancers such as lung cancer, liver cancer, and colorectal cancer. This review provides an overview of the roles of NSUN family genes in methylation, diagnostic value, inflammatory diseases, cancer, and other diseases. Full article

N6-methyladenosine (m⁶A) is the most abundant internal RNA modification in eukaryotes and plays a critical role in gene expression regulation by influencing RNA stability, splicing, nuclear export, and translation. Emerging evidence suggests that dysregulation of m⁶A contributes to neuroinflammation, neurotoxicity, and synaptic dysfunction—key features of neurodegenerative diseases. This review aims to examine the role of m6A modification in neurodegenerative diseases from a cell-type-specific perspective. We systematically reviewed recent studies investigating m⁶A modifications in neurons and glial cells. Data from transcriptomic, epitranscriptomic, and functional studies were analyzed to understand how m⁶A dynamics influence disease-related processes. Findings indicate that m⁶A modifications regulate neuroinflammation and immune responses in microglia, modulate astrocytic support functions, affect myelination through oligodendrocytes, and alter m⁶A patterns in neurons, impacting synaptic plasticity, stress responses, and neuronal survival. These cell-type-specific roles of m⁶A contribute to the progression of neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and Amyotrophic lateral sclerosis (ALS). Understanding m⁶A-modulated mechanisms in specific neural cell types may facilitate the development of targeted interventions for neurodegenerative diseases. Full article

Aluminum (Al) is solubilized as phytotoxic Al³⁺ in acidic soils, rapidly inhibiting root elongation. To detoxify Al, plant roots secrete organic acids that chelate the ion. The transcription factor SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1) regulates the export, distribution and metabolism of organic acids, which is crucial for Al resistance. Plant DICARBOXYLATE-CARRIERs (DICs) located in the inner mitochondrial membrane are presumed to exchange the dicarboxylates. However, whether Al or STOP1 modulates DIC expression to coordinate the organic acid shuttle remains unclear. Here, in the model legume Medicago truncatula, we identified three DIC genes and twelve in tetraploid Medicago sativa. Phylogenetic analysis places all Medicago DICs in a clade with Arabidopsis AtDIC1 and AtDIC2, whereas AtDIC3 lacks an ortholog in M. truncatula. Mining RNA-seq datasets followed by qRT-PCR validation showed that MtDIC2 is upregulated by Al in roots in a MtSTOP1-dependent manner. Consistently, STOP1-binding motifs exist in the MtDIC2 promoter, and MtSTOP1 binds to the MtDIC2 promoter in yeast. Furthermore, MsDIC2.4 shows an increase under Al treatment. Our study provides a genome-wide characterization of Medicago DICs and identifies MtDIC2 as a candidate target of MtSTOP1, whose Al-responsive induction may enhance organic acid flux across the mitochondrial membrane. Full article

The TREX-2 complex is conserved from yeast to humans and is responsible for mRNA export from the nucleus to the cytoplasm. In yeast and humans, the TPR and Nup153 nucleoporins of the nuclear pore complex are involved in TREX-2-dependent mRNA export, but data on their involvement in this process is rather controversial. In the present work, we have studied the role of TPR and Nup153 in the TREX-2-dependent export of hsp70 mRNA in Drosophila. We have shown that Nup153 and TPR are required for the TREX-2-dependent export of hsp70 mRNA, and their knockdown leads to mRNA accumulation in the cell nucleus. We have also demonstrated that Nup153 knockdown leads to TPR relocation to the nucleoplasm. Both nucleoporins are required for TREX-2 subunits’ association with the nuclear pore. Nup153 depletion leads to the TREX-2 subunits’ relocation from the nuclear pore to the nucleoplasm. The depletion of TPR leads to PCID2 relocation to the nucleoplasm and Xmas-2 retention at the nuclear pore and does not affect ENY2 redistribution. The TREX-2 subunits form several contacts with Nup153 and TPR. Hence, both nucleoporins are involved in the interaction with TREX-2 and TREX-2-dependent export in Drosophila. Full article

Neurodegeneration is increasingly recognized not as a linear trajectory of protein accumulation, but as a multidimensional collapse of biological organization—spanning intracellular signaling, transcriptional identity, proteostatic integrity, organelle communication, and network-level computation. This review intends to synthesize emerging frameworks that reposition neurodegenerative diseases (ND) as progressive breakdowns of interpretive cellular logic, rather than mere terminal consequences of protein aggregation or synaptic attrition. The discussion aims to provide a detailed mapping of how critical signaling pathways—including PI3K–AKT–mTOR, MAPK, Wnt/β-catenin, and integrated stress response cascades—undergo spatial and temporal disintegration. Special attention is directed toward the roles of RNA-binding proteins (e.g., TDP-43, FUS, ELAVL2), m6A epitranscriptomic modifiers (METTL3, YTHDF1, IGF2BP1), and non-canonical post-translational modifications (SUMOylation, crotonylation) in disrupting translation fidelity, proteostasis, and subcellular targeting. At the organelle level, the review seeks to highlight how the failure of ribosome-associated quality control (RQC), autophagosome–lysosome fusion machinery (STX17, SNAP29), and mitochondrial import/export systems (TIM/TOM complexes) generates cumulative stress and impairs neuronal triage. These dysfunctions are compounded by mitochondrial protease overload (LONP1, CLPP), UPR maladaptation, and phase-transitioned stress granules that sequester nucleocytoplasmic transport proteins and ribosomal subunits, especially in ALS and FTD contexts. Synaptic disassembly is treated not only as a downstream event, but as an early tipping point, driven by impaired PSD scaffolding, aberrant endosomal recycling (Rab5, Rab11), complement-mediated pruning (C1q/C3–CR3 axis), and excitatory–inhibitory imbalance linked to parvalbumin interneuron decay. Using insights from single-cell and spatial transcriptomics, the review illustrates how regional vulnerability to proteostatic and metabolic stress converges with signaling noise to produce entropic attractor collapse within core networks such as the DMN, SN, and FPCN. By framing neurodegeneration as an active loss of cellular and network “meaning-making”—a collapse of coordinated signal interpretation, triage prioritization, and adaptive response—the review aims to support a more integrative conceptual model. In this context, therapeutic direction may shift from damage containment toward restoring high-dimensional neuronal agency, via strategies that include the following elements: reprogrammable proteome-targeting agents (e.g., PROTACs), engineered autophagy adaptors, CRISPR-based BDNF enhancers, mitochondrial gatekeeping stabilizers, and glial-exosome neuroengineering. This synthesis intends to offer a translational scaffold for viewing neurodegeneration as not only a disorder of accumulation but as a systems-level failure of cellular reasoning—a perspective that may inform future efforts in resilience-based intervention and precision neurorestoration. Full article

Ribosome biogenesis is a highly coordinated, multi-step process that assembles the ribosomal machinery responsible for translating mRNAs into proteins. It begins with the rate-limiting step of RNA polymerase I (Pol I) transcription of the 47S ribosomal RNA (rRNA) genes within a specialised nucleolar region in the nucleus, followed by rRNA processing, modification, and assembly with ribosomal proteins and the 5S rRNA produced by Pol III. The ribosomal subunits are then exported to the cytoplasm to form functional ribosomes. This process is tightly regulated by the PI3K/RAS/MYC oncogenic network, which is frequently deregulated in many cancers. As a result, ribosome synthesis, mRNA translation, and protein synthesis rates are increased. Growing evidence supports the notion that dysregulation of ribosome biogenesis and mRNA translation plays a pivotal role in the pathogenesis of cancer, positioning the ribosome as a promising therapeutic target. In this review, we summarise current understanding of dysregulated ribosome biogenesis and function in cancer, evaluate the clinical development of ribosome targeting therapies, and explore emerging targets for therapeutic intervention in this rapidly evolving field. Full article

Lymphoma is the most common neoplasm of lymphoid tissues in dogs. Exportin 1 (XPO1) is an important major nuclear receptor for exporting proteins and RNA species. The XPO1 upregulation can eliminate some tumor suppressor proteins (TSPs) function upon their nuclear–cytoplasmic export. The XPO1 inhibitor, KPT-335, blocks the translocation of TSPs and restores their function to induce cell cycle arrest, apoptosis, and cell proliferation. This in vitro study aimed to evaluate the XPO1 mRNA and protein expression in canine lymphoma cell lines and confirm the relevance with KPT-335. XPO1 mRNA and protein levels were quantified, and the effect of KPT-335 was assessed by a cell proliferation assay. The results indicated that XPO1 mRNA and protein were highly expressed in 17-71, CLBL-1, CLC, CLGL-90, and UL-1, and were moderately expressed in GL-1, Ema, and Nody-1. All canine lymphoma cell lines showed dose-dependent growth inhibition and decreased cell viability in response to KPT-335, with IC₅₀ concentrations ranged from 89.8–418 nM. The expression levels of XPO1 mRNA and protein were related; however, no correlation was found between those expression levels and the efficacy of KPT-335. These findings suggest that XPO1 may represent a promising target for therapeutic intervention in canine lymphoma. Full article

N6-methyladenosine (m6A) represents the most common and thoroughly investigated RNA modification and exerts essential functions in regulating gene expression through influencing the RNA stability, the translation efficiency, alternative splicing, and nuclear export processes. The rapid development of high-throughput sequencing approaches, including miCLIP and MeRIP-seq, has profoundly transformed epitranscriptomics research. These techniques facilitate the detailed transcriptome-wide profiling of m6A modifications, shedding light on their crucial roles in diverse biological pathways. This review comprehensively examines the identification, mechanisms of regulation, and functional consequences of m6A modifications. It emphasizes their critical roles in physiological contexts, encompassing immune function, neuronal development, and the differentiation of stem cells. Additionally, the review discusses the contributions of m6A dysregulation to pathological conditions, including cancer, neurodegenerative diseases, and disorders of metabolism. We also discuss the development and application of machine-learning algorithms for m6A site prediction, emphasizing the integration of sequence-based, structural, and evolutionary conservation features to enhance the predictive accuracy. Furthermore, the potential of applying the findings from m6A research in precision medicine and drug development is examined. By synthesizing the current knowledge and emerging trends, this review aims to provide a comprehensive understanding of m6A biology and its translational potential, offering new perspectives for future research and therapeutic innovation. Full article

Drought stress is a predominant abiotic constraint adversely affecting global rice (Oryza sativa) production and threatening food security. While the transcriptional and post-transcriptional regulation of drought-responsive pathways has been widely investigated, the emerging field of epitranscriptomics, particularly RNA chemical modifications such as N6-methyladenosine (m⁶A), adds a new dimension to gene regulation under stress. The most prevalent internal modification in eukaryotic messenger RNA influences RNA metabolism by interacting dynamically with enzymes that add, remove, or recognize the modification. Recent studies in rice reveal that m⁶A deposition is not static but dynamically regulated in response to water-deficit conditions, influencing transcript stability, splicing, nuclear export, and translation efficiency of key drought-responsive genes. This review critically synthesizes current findings on the distribution and functional implications of m⁶A and other epitranscriptomic marks (e.g., 5-methylcytosine [m⁵C], pseudouridine [Ψ]) in modulating rice responses to drought. We discuss the regulatory circuitry involving m⁶A effectors such as OsMTA, OsFIP37, and YTH domain proteins and their integration with known drought-signaling pathways including ABA and reactive oxygen species (ROS) cascades. We also highlight emerging high-resolution technologies such as m⁶A-seq, direct RNA sequencing, and nanopore-based detection that facilitate epitranscriptomic profiling in rice. Finally, we propose future directions for translating epitranscriptomic knowledge into crop improvement, including CRISPR/Cas-based modulation of RNA modification machinery to enhance drought tolerance. Full article

Background: Lung cancer, predominantly NSCLC (80%), has a poor prognosis due to late diagnosis and limited treatment efficacy. DMRTA2 (DMRT5), a transcription factor linked to neural/germ cell development, is overexpressed in NSCLC per TCGA data, indicating its potential role in tumorigenesis and as a therapeutic target. Methods: Conduct a comprehensive search of the relevant theoretical foundations. Based on this, differential expression analysis will be performed using the DESeq2 package in R on RNA-seq data from lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. The research will then employ various methods, including CRISPR genome editing, MTS assay, flow cytometry, Western blot, co-immunoprecipitation, immunofluorescence, and qRT-PCR. Results: Through experimental validation, we found that DMRTA2 mRNA is highly expressed in non-small-cell lung cancer (NSCLC) tissues and is negatively correlated with poor prognosis. DMRTA2 binds to HSP90β, inhibiting the interaction between HSP90β and p53, thereby suppressing p53 ubiquitination and nuclear export. This activates the p53 pathway, inhibiting the proliferation and invasion of lung cancer cells. Conclusions: In NSCLC, DMRTA2 acts as a context-dependent regulator, stabilizing wild-type p53 through competitive HSP90β binding to suppress tumors, while in p53-compromised cells, potentially engaging HSP90β or alternative pathways to promote malignancy. Its dual localization and transport interactions reveal multifunctional, stress-responsive roles beyond transcription. Full article

Tumor cell heterogeneity, e.g., in stroma-rich pancreatic ductal adenocarcinoma (PDAC), includes a differential metabolism of lactate. While being secreted as waste product by most cancer cells characterized by the glycolytic Warburg metabolism, it is utilized by a subset of highly malignant cancer cells running the reverse Warburg metabolism. Key drivers of lactate transport are the carrier proteins SLC16A1 (import/export) and SLC16A3 (export). Expression and function of both carriers are controlled by the chaperone Basigin (BSG), which itself is functionally controlled by the transmembrane protease serine 11B (TMPRSS11B). In this study we explored the impact of TMPRSS11B on the phenotype of PDAC cells under reverse Warburg conditions. Amongst a panel of PDAC cell lines, Panc1 and BxPc3 cells were identified to express TMPRSS11B at a high level, whilst other cell lines such as T3M4 did not. ShRNA-mediated TMPRSS11B knock-down in Panc1 and BxPc3 cells enhanced lactate import through SLC16A1, as shown by GFP/iLACCO1 lactate uptake assay, whereas TMPRSS1B overexpression in T3M4 dampened SLC16A1-driven lactate uptake. Moreover, knock-down and overexpression of TMPRSS11B differentially impacted proliferation and chemoresistance under reverse Warburg conditions in Panc1 or BxPc3 and T3M4 cells, respectively, as well as their stemness properties indicated by altered colony formation rates and expression of the stem cell markers Nanog, Sox2, KLF4 and Oct4. These effects of TMPRSS11B depended on both SLC16A1 and BSG as shown by gene silencing. Immunohistochemical analysis revealed a reciprocal expression of TMPRSS11B and BSG together with SLC16A1 in some areas of tumor tissues from PDAC patients. Those regions exhibiting low or no TMPRSS11B expression but concomitant high expression of SLC16A1 and BSG revealed greater amounts of KLF4. In contrast, other tumor areas exhibiting high expression of TMPRSS11B together with BSG and SLC16A1 were largely negative for KLF4 expression. Thus, the differential expression of TMPRSS11B adds to metabolic heterogeneity in PDAC and its absence supports the reverse Warburg metabolism in PDAC cells by the enhancement of BSG-supported lactate uptake through SLC16A1 and subsequent phenotype alterations towards greater stemness. Full article

The influenza A virus (IAV) is a major cause of recurrent seasonal epidemics and global pandemics, posing a significant threat to public health. Although lycorine has demonstrated broad-spectrum antiviral activity, its specific mechanisms of action against IAV remain incompletely understood. In this study, we characterized the potent inhibitory effects of lycorine on seasonal and drug-resistant IAV subtypes (H1N1/H3N2) as well as the influenza B virus, showing its ability to suppress viral mRNA, viral titers, and M2 protein expression across multiple cell lines. Time-of-addition and time-course assays revealed that lycorine exerts multiphasic interference, and the critical late stage of the IAV life cycle aroused our interest to study this further. Mechanistically, we discovered that lycorine specifically interferes with the de novo synthesis of nucleoporin Nup93, thereby disrupting the nuclear export of viral nucleoprotein (NP). These findings not only establish lycorine as a promising broad-spectrum anti-influenza candidate but also provide new insights for developing host-targeted antiviral strategies. Full article

The global rise in obesity and its associated metabolic disorders underscores the need for a deeper investigation into their underlying molecular mechanisms. While genetic factors are well-established contributors, recent research has increasingly focused on epigenetic regulators, particularly N6-methyladenosine (m⁶A)—the most prevalent internal RNA modification in eukaryotes. This post-transcriptional modification plays a crucial role in RNA metabolism by regulating mRNA stability, splicing, nuclear export, and translation efficiency. Notably, emerging evidence implicates m⁶A in both adipogenesis and metabolic dysregulation. In this review, we systematically examine three key dimensions: (1) the molecular mechanisms of m⁶A modification, including writers, erasers, and readers, in obesity; (2) dysregulated m⁶A patterns in obesity-related pathologies, such as type 2 diabetes (T2D), insulin resistance, metabolic dysfunction-associated steatotic liver disease (MASLD), and the glycolysis in cancer cells; and (3) the therapeutic potential of targeting m⁶A and the regulators. By critically assessing recent advancements, we highlight m⁶A’s dual role as both a metabolic sensor and a disease modulator, offering novel insights into potential strategies for combating obesity-related metabolic syndromes. Full article