Search Results (515)

Argonaute (AGO) proteins are central components of RNA silencing. While OsAGO18 is a known defense factor in antiviral immunity, its involvement in basal development and its transcriptomic behavior during fungal stress remains to be fully elucidated. In this study, based on its specific dual-localization in chloroplasts and processing bodies (P-bodies), we investigated the pleiotropic effects of OsAGO18 through transcriptomic network analysis of rice responding to the blast fungus Magnaporthe oryzae B.C. Couch. Our analysis revealed that the OsAGO18-mediated co-expression network is highly correlated with ribosome biogenesis and cell wall organization. Notably, the analyzed datasets reveal that this growth-related network is significantly suppressed upon M. oryzae challenge, highlighting a transcriptomic shift in OsAGO18 during the growth-to-defense transition. Phenotypic evaluations demonstrated that OsAGO18 overexpression accelerates early seedling growth and primary root elongation by promoting endogenous indole-3-acetic acid (IAA) accumulation, whereas ago18 mutants maintain basal growth rates without significant IAA fluctuations, reflecting robust genetic compensation within the highly redundant AGO family. Mechanistically, our integrated analysis suggests that OsAGO18 acts as a putative molecular decoy to sequester miR396d, thereby relieving the repression of the Growth-Regulating Factor OsGRF6 and triggering downstream auxin-dependent cascades. Collectively, our findings highlight OsAGO18 as a pivotal regulator of early seedling development and characterize its transcriptomic responsiveness to biotic stress, providing a plausible molecular link between post-transcriptional RNA regulation and rice growth coordination. Full article

Oocyte maturation is a pivotal event in teleost reproduction that directly determines egg quality, fertilization success, and the developmental competence of early embryos. However, the transcriptional and post-transcriptional regulatory mechanisms operating within oocytes during maturation in marine teleosts remain poorly understood. In the present study, the orange-spotted grouper (Epinephelus coioides), an economically important marine aquaculture species, was used as a model. Oocytes at four distinct maturation stages were obtained by microscopically removing the surrounding follicular layers, followed by integrated mRNA-seq and miRNA-seq analyses to characterize the molecular regulatory landscape underlying oocyte maturation and hydration. The results showed that, as maturation progressed, oocyte diameter and wet weight increased significantly, accompanied by a marked decrease in Na⁺ content, a significant increase in K⁺ content, and the continuous accumulation of most free amino acids, indicating the gradual establishment of an osmotic basis favorable for oocyte hydration. Transcriptomic analysis further revealed extensive transcriptional remodeling during both the early and late phases of maturation. Differentially expressed genes were significantly enriched in pathways related to oocyte meiosis, cytokine signaling, lipid metabolism, DNA replication, cell cycle regulation, ribosome biogenesis, spliceosome function, oxidative phosphorylation, and mitochondrial activity, suggesting that oocyte maturation is a dynamic process characterized by a shift from basal growth maintenance to metabolic reprogramming, maternal transcript remodeling, and terminal maturation responses. miRNA profiling identified a large number of stage-specific differentially expressed miRNAs, including let-7d-5p, miR-22a-3p, and novel-miR-20/27/118, whose predicted target genes were mainly enriched in ribosome-related pathways, oxidative phosphorylation, DNA replication, transcriptional regulation, and signal transduction. Moreover, the miRNA–TF–mRNA regulatory network demonstrated that miRNAs may not only directly repress target genes, but also mediate hierarchical regulatory cascades through transcription factors, thereby coordinately participating in cell cycle progression, cytoskeletal remodeling, vesicular transport, and immune- and cell communication-related responses. Collectively, this study provides the first systematic temporal atlas of mRNA and miRNA regulation during oocyte maturation and hydration at the oocyte level in a marine teleost, thereby deepening our understanding of the molecular basis of meiotic resumption and egg quality formation, and offering valuable theoretical support for the optimization of artificial breeding and the identification of key molecular targets in grouper reproduction. Full article

Vairimorpha ceranae (formerly Nosema ceranae) is an obligate intracellular parasite that poses a major threat to the health of the honey bee. Circular RNAs (circRNAs) have been recognized as key regulators in gene expression and pathogen–host interactions. However, their expression patterns and regulatory roles in V. ceranae infection remain largely unexplored. In this study, we performed circRNA profiling in V. ceranae spores (NcCK) and the midguts of Apis mellifera ligustica workers at 7 d post inoculation (dpi) and 10 dpi (Nc7T and Nc10T) based on transcriptome sequencing, followed by in-depth investigation of the regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 243 circRNAs were identified in V. ceranae, with lengths predominantly ranging from 201 to 400 nucleotides. Comparative analysis screened 70 and 192 DEcircRNAs in the NcCK vs. Nc7T and NcCK vs. Nc10T comparison groups, respectively, with a significant majority being downregulated. The parental genes of these DEcircRNAs were significantly enriched in fundamental cellular processes and critical pathways such as protein processing in the endoplasmic reticulum and ribosome biogenesis. Additionally, we constructed a competing endogenous RNA network, suggesting that DEcircRNAs could potentially interact with DEmiRNAs to modulate mRNAs associated with fungal proliferation-relevant signaling pathways like MAPK, PI3K–Akt, and cAMP. Moreover, numerous DEcircRNAs were predicted to contain internal ribosome entry site elements, indicative of their potential for protein coding. The back-splicing junctions and expression trends of selected DEcircRNAs were successfully validated by RT-PCR and qRT-PCR. Our data not only offer a valuable resource for future functional studies but also provide a basis for elucidating the circRNA-mediated mechanisms underlying microsporidian pathogenesis and host–pathogen interactions. Full article

Background/Objectives: CD138 (syndecan-1) is a cell-surface heparan sulfate proteoglycan involved in cell–matrix interactions and growth factor signaling, and it has been implicated in tumor progression. However, the clinical significance of compartment-specific CD138 expression in breast cancer remains unclear. In this study, we investigated the prognostic and transcriptomic features of compartment-specific CD138 expression in invasive breast cancer. Methods: We performed an integrated analysis of immunohistochemistry and RNA sequencing of 111 invasive ductal carcinoma specimens. Tumors were classified into four groups according to CD138 expression in the tumor and stromal compartments. Clinicopathological data and survival outcomes were obtained from medical records, and transcriptomic profiles were analyzed using RNA sequencing. Results: The tumor-positive/stroma-negative phenotype (Group 1) was associated with poorer recurrence-free survival than the other phenotypes. According to multivariable Cox regression analysis, Group 1 remained an independent prognostic factor after adjustment for age, lymph node status, and Ki-67 index (hazard ratio, 5.493; p = 0.0028). Group 1 was also associated with lymph node metastasis and HER2 expression. All brain metastases occurred in Group 1, although the number of events was low. Transcriptomic profiling identified the upregulation of small nucleolar RNAs in Group 1 tumors, with the enrichment of pathways related to ribosome biogenesis, RNA processing, and translational regulation. Conclusions: Compartment-specific CD138 expression identifies an aggressive breast cancer phenotype with distinct transcriptomic features. This phenotype may have prognostic value and warrants validation using larger, independent cohorts. Full article

The Tahe red deer is derived from the wild Tarim red deer, an endemic subspecies native to the Tarim Basin in Xinjiang, China. It has recently received official approval as a locally bred deer variety, developed through artificial breeding programs. This breed retains several advantageous traits from its wild ancestors, including tolerance to coarse forage, drought resistance, and a high yield of velvet antlers. To investigate the genetic mechanisms underlying velvet antler production, phenotypic data for antler weight and blood samples were collected from 73 adult Tahe red deer. Whole-genome sequencing and genome-wide association analysis were performed to identify genetic variants associated with antler weight. Population genetic analysis revealed that the observed heterozygosity (Ho) and expected heterozygosity (He) were 0.31291 and 0.32832, respectively, while the nucleotide diversity (π) was 2.17 × 10⁻³, indicating relatively high genetic diversity within the Tahe red deer population. Using a mixed linear model (MLM), a total of 189 candidate genes and 1387 significant SNP loci associated with antler weight were identified (p < 1.0 × 10⁻⁵). Gene Ontology (GO) enrichment analysis revealed that these candidate genes are primarily involved in intracellular calcium ion homeostasis, peptide and protein biosynthesis, extracellular matrix organization, the regulation of glycolysis, and cytoskeleton-related processes, including actin filaments and microfibrils. These biological functions are closely related to cell proliferation, differentiation, energy metabolism, and tissue remodeling. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that the candidate genes are significantly enriched in several pathways, including the Notch signaling pathway, the cGMP–PKG signaling pathway, the regulation of the actin cytoskeleton, ribosome biogenesis, and mucin type O-glycan biosynthesis. These results suggest that these genes may participate in velvet antler growth and development by regulating cell proliferation and differentiation, cytoskeletal remodeling, and protein synthesis. Overall, this study identifies SNP loci and candidate genes significantly associated with antler weight in Tahe red deer, providing a theoretical basis for genetic improvement and marker-assisted selection for velvet antler production in this breed. Full article

Mitochondrial RNA (mtRNA) modifications have emerged as critical regulators of pancreatic β-cell bioenergetics, influencing glucose-stimulated insulin secretion (GSIS) and the early pathogenesis of diabetes mellitus (DM). This review synthesizes current evidence on the diversity, mechanisms, and functional implications of mtRNA modifications—such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), and 5-formylcytosine (f5C)—within β-cell mitochondria. These chemical marks, installed and recognized by specific writer, eraser, and reader proteins, regulate mitochondrial translation, oxidative phosphorylation (OXPHOS) complex assembly, and redox balance. Defects in mtRNA modification machinery, exemplified by β-cell-specific knockout of TFB1M, MRM2, or PUS1, impair ribosome biogenesis, disrupt ATP production, and precipitate insulin secretory failure, as demonstrated in human islets, rodent models, and monogenic diabetes syndromes. Advances in epitranscriptomic mapping technologies—including nanopore direct RNA sequencing, RNA immunoprecipitation (RIP)-seq, and mass spectrometry—have enabled high-resolution profiling of mtRNA modification landscapes under physiological and diabetic conditions, revealing their dynamic regulation in response to metabolic stress. Furthermore, mtRNA modifications interact with environmental stressors, such as oxidative damage and toxic metals, modulating β-cell vulnerability via pathways like the mitochondrial unfolded protein response (UPRmt). Therapeutically, modulation of RNA-modifying enzymes or restoration of specific chemical marks holds promise for preserving β-cell function, with potential applications in early diagnosis, risk stratification, and precision medicine approaches for DM. Despite substantial progress, critical gaps remain in understanding the interplay between mtRNA modifications, mitochondrial-nuclear crosstalk, and β-cell plasticity. Addressing these gaps will be pivotal for translating mtRNA biology into novel biomarkers and targeted interventions for early-stage diabetes. Full article

This article explores the complex interplay between the process of protein translation and DNA methylation, discussing their combined involvement in brain development. We will emphasize on DNA methylation and related proteins such as DNMTs, TETs, and MeCP2, the latter being the prototype of DNA methyl-binding proteins. Collectively, DNA methylation machinery may be involved in controlling the cell fate commitment of brain cells, as well as their neuronal and glial lineage specification. We aim to summarize current knowledge on the dynamics of protein translation, ribosome biogenesis, and relevant cellular pathways, including the mTOR signaling, in the context of brain development. Special attention is given to MeCP2 because of its unique role as an epigenetic factor that influences the chromatin states with a link to protein translation and its relevance to human disease. We also discuss the impact of DNA methylation-mediated chromatin regulation and protein translation in neurodevelopmental disorders. Our discussions include multi-omics techniques and integrative mechanisms that connect DNA methylation with protein translation. Full article

Although the ATP-binding cassette (ABC) transporter superfamily of proteins typically facilitates the movement of compounds across cellular membranes, the ABC E subfamily (ABCE) influences protein synthesis via non-transporter roles in ribosome biogenesis. Despite this essential role, our understanding of the impact that ABCE proteins have on insect physiology is limited. Here, we identified and characterized the ABCE gene from Lygus hesperus, a major agricultural pest of crops in North America. LhABCE transcripts were constitutively expressed throughout development and were present in all adult tissues tested. RNA interference (RNAi)-mediated knockdown of LhABCE transcripts in fifth instar nymphs resulted in high nymphal mortality and an incomplete molt. LhABCE knockdown in adults disrupted gametogenesis and reduced longevity. In females, oogenesis was impaired and oocytes did not progress beyond the pre-vitellogenic phase. In males, LhABCE knockdown reduced both spermatozoa abundance and male fertility. LhABCE knockdown, however, had little to no impact on hemolymph protein levels or the levels of circulating vitellogenin. Taken together, the results indicate that LhABCE is critical for the normal progression of processes like molting and gametogenesis that require coordinated bursts of protein synthesis and suggest that ABCE may play an important role in the mechanisms underlying those bursts. Full article

Gliomas are aggressive brain tumors with poor prognosis. The contribution of Toxoplasma gondii (T. gondii)-related transcriptional programs to glioma remains unclear. We identified T. gondii infection-related genes from neuroepithelial cell transcriptomes, mapped them to TCGA and CGGA glioma datasets, and validated their expression via RT-qPCR. A prognostic signature (TGRisk) was constructed via Cox and LASSO regression and validated across independent cohorts. Functional, immune, and drug sensitivity analyses were conducted. Forty infection-related genes were identified, enriched in stress responses, microRNA regulation, ribosome biogenesis, and metabolism. The 13-gene TGRisk model significantly separated survival between high- and low-risk groups. A nomogram combining TGRisk with clinical features improved prediction accuracy. High-risk tumors showed immune activation and higher infiltration of CD8⁺ T cells, Tregs, macrophages, and neutrophils, while low-risk tumors showed enhanced neuronal signaling and NK cell activity. Drug sensitivity prediction suggested low-risk patients were more responsive to temozolomide and bortezomib, whereas high-risk patients were more sensitive to dasatinib and ruxolitinib. We developed a novel T. gongdii infection-related gene signature that stratifies glioma patients by prognosis, immune features, and therapeutic vulnerabilities. These findings suggest host–T. gondii interactions and a potential biomarker for patient stratification and personalized therapy. Full article

Natural products represent an important reservoir for GPCR ligand discovery. In this study, we established an integrated workflow combining virtual screening, biophysical validation, functional signaling assays, and transcriptomic profiling to identify reticuline, a dopamine-derived intermediate from the genus of Stephania, as a potential agonist of dopamine D5 receptor (D5R). Molecular docking revealed that most dopamine-derived compounds along the BIA synthetic pathway exhibit predicted binding affinities for the D5R that are lower than that of dopamine. As expected, the reticuline–D5R complex has a favorable predicted binding affinity of −7.9 kcal/mol. As for binding validation, direct interaction between reticuline and D5R was experimentally confirmed using cell membrane chromatography (CMC) and bio-layer interferometry (BLI), yielding a dissociation constant of 1.07 μM. cAMP assay demonstrated that reticuline activates D5R-mediated Gs-cAMP increasement in a concentration-responsive manner, which exhibits agonist-like activity with an EC₅₀ value of 0.07 μM. The transcriptomic profiling further revealed that reticuline treatment induces transcriptional reprogramming in D5R-overexpressing cells, with enrichment of pathways related to ribosome biogenesis, mitochondrial oxidative phosphorylation, and neurodegenerative diseases. In summary, this study demonstrates that reticuline acts as a potential D5R agonist and highlights a systematic natural product-GPCR discovery strategy integrating computational prediction, experimental validation, and transcriptome-level mechanistic exploration. Full article

Chandipura virus (CHPV) is a neurotropic rhabdovirus associated with recurrent outbreaks of acute encephalitis in children and a high case fatality rate, particularly in India. Despite its public health relevance, the host molecular processes governing CHPV infection and disease progression remain poorly defined. To address this gap, we conducted a time-resolved transcriptomic analysis to characterize host responses to CHPV infection and to explore host-directed therapeutic opportunities. Human HEK293T cells were infected with CHPV, followed by RNA sequencing (RNA-seq) at 6, 12, 18, and 24 h post infection (hpi). Transcriptome profiling revealed a temporally ordered host response. At 6 hpi, CHPV infection was dominated by strong activation of innate immune and inflammatory pathways, including interferon-stimulated genes and cytokine signaling. Antiviral responses persisted at 12 hpi, accompanied by suppression of metabolic and translational processes, indicating a shift in host cellular priorities. By 18 hpi, metabolic reprogramming—particularly involving lipid and sphingolipid metabolism—was observed alongside altered immune signaling, consistent with viral exploitation of host cellular machinery. At 24 hpi, repression of genes involved in chromatin organization, RNA processing, spliceosome assembly, and ribosome biogenesis reflected a global transcriptional shutdown associated with cytopathic effects. Integration of temporal transcriptomic signatures enabled identification of host pathways amenable to pharmacological targeting. Selected host-directed compounds were evaluated in vitro and exhibited antiviral activity against CHPV in a neuronal cell line. Collectively, this study provides the first time-resolved transcriptomic landscape of CHPV infection in human cells and identifies host-targeted strategies relevant for antiviral development. Full article

The anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole) ruthenate (III)—also known as KP1019—inhibits cancer cell proliferation in vitro, causes tumor regression in animal models, and showed no dose-limiting toxicity in a phase I clinical trial. Previous studies found that KP1019 damages DNA in both cancer cells and the budding yeast Saccharomyces cerevisiae. To identify other potential targets of KP1019 along with pathways that modulate the drug’s cellular effects, we screened the yeast gene deletion strain library by quantitative high-throughput cell array phenotyping (Q-HTCP). Fitness differences, as judged by growth curve analysis, identified genes for which loss of function (gene deletion) interacts with (enhances or suppresses) KP1019 effects. Drug-enhancing deletions were enriched for DNA repair functions, consistent with DNA damage being a primary target of KP1019 in yeast. pH homeostasis also modified the effects of KP1019. Drug-suppressing deletions prominently involved ribosomal proteins. A mechanistic link between ribosomal protein function and KP1019 toxicity was supported by dose-dependent accumulation of Rpl7a-GFP in the nucleolus, which is a hallmark of ribosomal biogenesis stress. Furthermore, KP1019 acted synergistically with the TOR pathway inhibitor everolimus to inhibit cell proliferation. The resulting model, wherein KP1019 perturbs ribosome assembly, can inform the design of future combination therapies. Full article

The ATRX gene encodes an SWI/SNF-type chromatin remodeling protein that is critical for proper development of the mammalian central nervous system and musculoskeletal system. While significant progress has been made in understanding the molecular functions of the full-length (FL) ATRX protein, there is still very little known about its conserved alternative spliceoform, ATRXt. ATRXt is a truncated isoform of ATRX which lacks the entire SWI/SNF domain due to the retention of intron 10, which results in the in-frame addition of 61 unique amino acids (exon 10a) at its C-terminus. Here, we demonstrate that ATRXt accounts for 5–20% of total ATRX protein levels, while showing tissue- and differentiation-specific changes in expression levels compared to its full-length counterpart. ATRXt shows enriched localization at H3K9me3-positive heterochromatin but not at PML-nuclear bodies, while physically interacting with the known FL-ATRX protein partners, DAXX and HP1α. Exon 10a can target a GFP-fusion protein to the nucleolus, but removal of exon 10a from ATRXt does not prevent nucleolar localization. Finally, re-introducing ATRXt into the ATRX-negative U2OS cell line reduced rRNA transcription and severely hampered cell growth, similar to previous studies using FL-ATRX. Our study highlights that ATRXt has many of the same properties as FL-ATRX, suggesting that some roles of ATRX do not require remodeling activity, while highlighting the need to distinguish ATRXt’s functions from those of the full-length protein. Full article

Upstream binding transcription factor (UBTF) is a nuclear transcription factor implicated in ribosome biogenesis, yet its pancancer relevance and immunological associations remain incompletely understood. We integrated datasets from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA), Cancer Cell Line Encyclopedia (CCLE), and cBioPortal databases to characterize UBTF expression, genomic alterations, and prognostic value across 33 cancer types. Immune microenvironment analyses were performed using ESTIMATE and multiple deconvolution algorithms. CRISPR-Cas9–mediated UBTF depletion was conducted in breast invasive carcinoma (BRCA) cell lines to evaluate functional roles. UBTF was broadly upregulated in multiple tumors with recurrent copy number gains. Survival analyses revealed cancer type–dependent prognostic associations. UBTF expression correlated with immune/stromal contexture, checkpoint features, and predicted immunotherapy response. In BRCA, UBTF depletion reduced proliferation and migration while increasing apoptosis. A UBTF-related prognostic signature effectively stratified patient outcomes and was associated with immune infiltration and predicted immunotherapy response. UBTF represents a pancancer biomarker linked to tumor immunity, with validated functional significance in BRCA and potential utility for risk stratification. Full article

Ribosome biogenesis is a fundamental process underlying plant growth, development, and environmental adaptation, and processing of precursor rRNA (pre-rRNA) represents one of its most critical regulatory steps. This review provides a systematic overview of the multi-layered regulatory mechanisms controlling pre-rRNA processing in plants, with Arabidopsis thaliana as the primary model system. We focus on the genomic organization of ribosomal DNA (rDNA) and its epigenetic regulation, illustrating how highly repetitive and sequence-diverse rDNA arrays maintain genomic stability while enabling tissue-specific expression of distinct rDNA variants. We further summarize the dynamic pathways of pre-rRNA processing and their plastic regulation under environmental conditions such as elevated temperature. In addition, we review the quality control systems that monitor pre-rRNA maturation, including non-templated tailing and exonuclease-dependent degradation pathways, which play essential roles in removing aberrant processing intermediates. We further examine how perturbations in pre-rRNA processing give rise to plant ribosomopathies and discuss complementary models of ribosome homeostasis and ribosome heterogeneity as frameworks for interpreting shared developmental phenotypes. Finally, by synthesizing genetic and molecular evidence, we highlight the pivotal role of pre-rRNA processing in orchestrating plant development and propose directions for future research. Full article