RNA editing of pathogenic variants causing inherited retinal diseases using endogenous ADAR-current and future perspectives.

The METTL14/YTHDF3 axis regulates EPSTI1-mediated osteogenic differentiation of human bone marrow mesenchymal stem cells.

Epitranscriptomic signatures of malignancy: how RNA modifications shape breast and ovarian tumor progression.

The m7G modification: An emerging player in neurological diseases.

NSUN2-mediated RNA m5C dysregulation links HBV infection to TFEB silencing and lysosomal impairment.

m6A epitranscriptomic remodeling links redox stress to mitochondrial quality control and programmed cell death in sepsis-induced myocardial dysfunction.

Epitranscriptomic variation in banded newts (Ommatotriton vittatus) across life stages and sexes in the semi-arid habitat in northern Israel.

Molecular evolutionary insights into the host-virus relationship between Marburg Virus and its bat reservoir.

The cleavage and formation of phosphodiester bonds in nucleic acids is performed by diverse cellular machineries ranging from small protein enzymes to large complexes composed of proteins and/or RNA strands. While it has long been believed that these processes depend solely on a two-metal-ion mechanism, comparative structural analyses revealed that some complexes also contain highly conserved second-shell monovalent cations. The two-Mg 2+ -aided catalytic mechanism, in which both ions function as Lewis acids, with one metal activating the nucleophile (water or ribose hydroxyl) for the scissile phosphate group attack and the other stabilizing the leaving group, is well-established. In contrast, the function of monovalent ions has been largely overlooked, yielding divergent results across different catalytic settings. Nevertheless, recent evidence points to monovalent ions assisting catalysis beyond their roles in RNA folding and assembly. Here, building on recent computational studies on two-metal-ion dependent ribozymes, we showcase how divalent and monovalent ions finely tune the catalytic site arrangements and dynamics, affecting the kinetic and thermodynamic properties of RNA cleavage reactions. We discuss optimal catalytic mechanisms depending on nucleophile type and illuminate strategies adopted by second-shell monovalent ions to optimize catalytic geometries, which enable efficient proton transfer from nucleophile to the leaving group, a key event for effective catalysis. This review expands understanding of nucleic acid-processing machinery, providing key knowledge for potentially designing innovative gene-modulating tools and therapeutic strategies. • Second-shell monovalent cations are shown to actively aid RNA catalysis. • K + ions fine-tune active sites to facilitate essential proton transfer events. • Hybrid QM/MM MD simulations reveal subatomic reaction pathway details. • Distinct proton transfer pathways exist for water vs. ribose nucleophiles. • Monovalent ion pockets offer potential new targets for RNA therapeutic design.

CsMORF9.3 regulates chlorophyll biosynthesis, affecting the RNA editing efficiency of matK-445, rpoA-200, ndhD-674 and ndhD-1310, and it interacts with CsMORFs, CsPPRs and CsCHLD proteins. Leaf color is an important factor affecting tea quality as well as the growth and development. It has been reported that several genes and transcription factors participated in chlorophyll metabolism in tea plants (Camellia sinensis). However, the role of chloroplast RNA editing factors in chlorophyll biosynthesis in C. sinensis remains poorly understood. In this study, multiple dysregulated RNA editing sites in the chloroplast genome were identified from etiolation and albino tea cultivars. Multiple organellar RNA editing factor 9.3 (CsMORF9.3), a core RNA editing factor localized in the chloroplasts, was identified as a candidate regulator of leaf coloration. Antisense oligonucleotide (AsODN) and virus-induced gene silencing (VIGS) confirmed that suppressing CsMORF9.3 expression reduces chlorophyll content, downregulates genes involved in chlorophyll biosynthesis and chloroplast development, as well as disrupts chloroplast RNA editing. Protein-protein interaction assays confirmed that CsMORF9.3 could form both homodimers and heterodimers with itself or other MORF proteins through yeast two-hybrid (Y2H), luciferase complementation imaging (LCI) assays, and bimolecular fluorescence complementation (BiFC) assays. Moreover, CsMORF9.3 was found to interact with multiple PLS-type pentatricopeptide repeat (PPR) proteins, including CsCRR21, CsCRR28, CsOTP84, and CsLPA66, as well as with CsCHLD, a key subunit of magnesium chelatase in chlorophyll biosynthesis. Our study provides the protein interaction of CsMORF9.3, demonstrating its potential role in regulating RNA editing and chlorophyll biosynthesis in C. sinensis. These results broaden the understanding of the regulatory mechanisms of chlorophyll biosynthesis and provide new insights into the breeding of etiolation and albino tea plant germplasm.

The islet of Langerhans (or pancreatic islet) is a unique endocrine organ that secretes multiple hormones that in turn orchestrate energy metabolism in humans. As in other metabolic organs, growth factor(s) regulate functional islet mass to maintain whole-body glucose homeostasis. Over the past decades, a large body of evidence has pointed to insulin and insulin-like growth factors (IGFs) as playing central roles in modulating diverse aspects of islet cell biology and a dysregulated insulin/IGF pathway has come to be recognized as a pathophysiological hallmark of type 2 diabetes (T2D). Several recent reports, especially focused on β-cells, highlight emerging aspects of insulin/IGF signaling, including a role for RNA modifications, transcriptional regulation by nuclear insulin and IGF-1 receptors, and the discovery of an insulin inhibitory receptor, inceptor. In this review, we summarize the functional roles of insulin/IGF signaling in regulating islet cell biology, the short- and long-term effects of insulin therapy in humans, and discuss potential strategies to maximize the beneficial effects of insulin action in islets to counter diabetes.

Accurate identification of RNA 5-methylcytidine (m5C) at the single-nucleotide resolution remains a central challenge in nanopore direct RNA sequencing (DRS). Current global scanning and modification-aware basecalling methods enable transcriptome-wide profiling but often yield high false-positive rates and lack site-specific accuracy. To address this, we repurposed ModiDeC, originally a de novo multimodification classifier, into a targeted, high-precision validation tool for RNA modification sites with prior biochemical knowledge. This was implemented through a three-step calibration workflow that alternates between biochemical and computational modules using the well-characterized m5C2278 site in 25S rRNA as a starting point. Baseline training uses short synthetic RNAs carrying either a methylated or unmodified C2278 as ground truth, followed by IVT-derived calibration and validation in methyltransferase knockout yeast. The baseline model accurately detected the bona fide m5C2278 site but initially produced off-target predictions. Iterative retraining with unmodified IVT signals progressively reduced and ultimately eliminated false positives while maintaining a strong signal at the bona fide site. The final model retained enzyme-dependent detection in wild-type versus knockout yeast and, when explicitly targeted, was also able to detect the second rRNA site, C2870, which remained invisible in the initial analysis. Application to native human prerRNA processing intermediates further resolved two distinct m5C deposition regimes on 28S rRNA, while generalization to dengue virus genomic RNA confirmed that the same calibration logic transfers across diverse RNA contexts. Together, this study establishes a reproducible and transferable framework that integrates biochemical validation with iterative neural network refinement, providing a route toward reliable site-specific m5C confirmation by nanopore direct RNA sequencing.

Stress granules (SGs) are RNA and protein assemblies that form rapidly in the cytoplasm in response to cellular or environmental stress. SGs, traditionally recognized as transient repressors of translation, are now understood as versatile regulatory centers that shape RNA metabolism, signaling, proteostasis, and cell fate. In this review, we collate recent findings showing SGs' role in steady-state and regenerative stress in erythropoiesis. Blood loss, anemia caused by ribosomal mutations, has been reported to alter the SG axis and protein translation. During regeneration stress, SGs selectively capture lineage-defining RNAs to regulate their translation during recovery phases. This process ensures that blood progenitors and differentiating cells retain essential transcripts, supporting proper fate decisions and regeneration. Pathological SG accumulation disrupts RNA metabolism and translational reprogramming, key to blood cell regeneration. SGs regulate the transcriptome to endure stress via translational control mechanisms during erythropoiesis. SG deregulation can undermine these adaptive processes. Therapies modulating SG formation, dissolving pathological SGs, or influencing RNA sorting via genetics or targeted small molecules promise new directions to restore blood health, treat anemia, and regeneration in a range of blood disorders.

ADP-ribosylation is an essential post-translational modification that contributes to key cellular processes, such as DNA damage repair, cell-cycle progression, chromatin remodeling, mitochondrial function, and immune responses in mammalian cells. This modification derives from NAD+ and is regulated by dedicated writer, eraser, and reader proteins that govern its installation, removal, and recognition. Traditionally viewed as a protein-centered modification, ADP-ribosylation has recently been extended to nucleic acids, with ADP-ribosylated DNA and RNA now identified in both mammalian and bacterial systems. These discoveries reveal previously underappreciated layers of nucleic acid-based regulation and suggest that NAD+-dependent chemistry integrates genome maintenance, RNA metabolism, and cellular stress responses. In this review, we first outline the major mammalian ADP-ribosylation machineries, including the families of writer, eraser, and reader proteins, and discuss how their activities are coordinated. We then examine emerging roles of ADP-ribosylation in mitochondria, with a focus on mitochondrial DNA repair and metabolic control. Finally, we highlight recent advances in understanding NAD+-dependent modifications of DNA and RNA in mammalian and bacterial cells, including terminal and nucleobase-linked ADP-ribosylation and NAD capping, and discuss outstanding questions regarding their physiological functions and interplay with protein post-translational modification and other nucleic acid modifications.

Tagetes erecta, commonly known as marigold, is a vibrant-flowered plant native to Mexico and Central America, widely appreciated for its striking golden-yellow or orange blossoms and diverse applications in traditional medicine. Despite its significance, the mitochondrial genome of T. erecta has not been thoroughly characterized, leaving a gap in understanding genomic variation within the Asteraceae family. In this study, we sequenced and assembled the mitochondrial genome (mitogenome) of T. erecta, revealing five independent circular chromosomes with a total length of 259,855bp and an average GC content of 44.81%. Repeat analysis identified 104 SSRs, 22 tandem repeats, and 83 dispersed repeats in T. erecta mitogenome. We identified nine mitochondrial plastid DNA sequences (MTPTs) ranging from 33 to 771bp, which included complete plastid gene sequences and partial plastid protein-coding genes (PCGs). Phylogenetic analysis of 40 Asteraceae species indicated that T. erecta was clustered within Heliantheae alliance. Additionally, 573 RNA editing sites were identified across 30 PCGs based on RNA-seq data. These findings provide new mitochondrial genomic resources that enhance our understanding of the evolution and genomic variation in Asteraceae, offering insights that may benefit breeding processes and resource conservation efforts.

DKC1, a key coordinator of RNA modification and telomerase activity, has been implicated in colorectal cancer (CRC), yet its role in disease pathogenesis remains incompletely understood. We show that DKC1 drives CRC by promoting cell cycle progression, suppressing apoptosis, conferring stemness and drug resistance. Elevated DKC1 in CRC associates with poor prognosis and WNT-enriched Consensus Molecular Subtype 2 gene signature. Mechanistically, canonical WNT-signaling forms a feedback loop with DKC1, driving its expression and oncogenic activity. Comprehensive transcriptomic and lipidomic analyses reveal perturbed sphingolipid metabolism and abundance of specific very-long-chain fatty acid ceramides. Further, a regulatory axis involving DKC1 and SOX2 drives the expression of SGPP2, a critical sphingolipid metabolism mediator. Importantly, DKC1-mediated sphingolipid dysregulation promotes first-line chemoresistance, and FOLFOX-resistant patient-derived organoids effectively respond to DKC1 and WNT signaling inhibitors. Conclusively, we identify the DKC1/WNT axis as a therapeutic target in therapy-resistant CRC and underscore complex sphingolipids as promising plasma-based biomarkers.

Selenium-containing nucleosides, such as 2-selenouridine, represent natural transfer RNA (tRNA) modifications that influence translation fidelity and cellular stress responses. In this study, we investigated the oxidative behavior of Se2U and its derivatives, including 5-methylaminomethyl-2-selenouridine, both as free nucleosides and within a tRNA anticodon stem-loop model. Electrochemical and spectroelectrochemical analyses revealed that Se2U exhibits greater redox reactivity than its sulfur analogue, 2-thiouridine, undergoing rapid and reversible oxidation to diselenide species under anaerobic conditions. Chemical oxidation with hydrogen peroxide produced diselenides and deselenated products, while biologically relevant thiols, such as glutathione and dithiothreitol, efficiently restored the parent nucleosides. Oxidation of Se2U within RNA led to uridine and 4-pyrimidinone riboside formation, potentially altering codon recognition, and enabled nucleophilic substitution at the C2 position both by glutathione, as a biologically relevant nucleophile, and by hexafluoroisopropanol, a nucleophilic buffer component used in our experiments, underscoring the general character of this transformation. These findings suggest that oxidation proceeds via transient acidic selenium species, which act as efficient leaving groups and may facilitate additional post-transcriptional modifications under oxidative stress. Overall, this study provides mechanistic insight into Se2U oxidation and suggests that oxidative activation - mediated tRNA modifications, could influence translation and cellular stress adaptation.

BackgroundAdenosine-to-inosine (A-to-I) RNA editing has been found to function in various neurological disorders; however, the role of A-to-I RNA editing in retinitis pigmentosa (RP) remains unclear.MethodsRNA editing profiles of mouse retinas at different developmental stages, and three RP mouse models that were sampled at the peak of photoreceptor cell death for each model were analyzed to identify significant RNA editing events and genes involved in development and RP pathogenesis. Data from two addtional RP models were used for validation. Key editing sites were validated by Sanger sequencing and dual-luciferase reporter assays.ResultsGlobal A-to-I editing levels increased during normal retinal development, correlating with Adar/Adarb1 expression. In RP models, significant alterations in editing landscapes were observed, including dysregulated editing of 55 IRD-related genes. Functional enrichment and protein-protein interaction (PPI) analyses highlighted 10 hub genes, including Rgs9bp, which showed extensive editing and elevated expression. Editing at specific sites in Rgs9bp enhanced reporter gene expression, implying a functional impact. Notably, Rgs9bp, traditionally linked to cone-specific bradyopsia, exhibited hyper-editing in rod-dominant RP models, suggesting a broader role in retinal degeneration.ConclusionsOur study reveals that A-to-I RNA editing is dynamically regulated during retinal development and profoundly altered in RP, implicating RNA editing as a novel layer of gene regulation in inherited retinal diseases.

N6-methyladenosine (m6A) is one of the important RNA modifications that affect RNA abundance and function and has also been implicated in viral infection. In this study, we identified a number of m6A modification sites within human T-cell leukemia virus type 1 (HTLV-1) RNAs, particularly in the RNA of the Tax oncogene. We demonstrated that YTH domain family member 2 (YTHDF2), a key m6A reader protein that binds m6A-modified RNAs and influences RNA metabolism, is required for HTLV-1 replication in both de novo and persistently infected cells. Mechanistically, YTHDF2 interacts with and stabilizes Tax RNA in an m6A-dependent manner, thereby promoting Tax-driven HTLV-1 replication. Importantly, YTHDF2 activates oncogenic cellular pathways and promotes proliferation in HTLV-1-infected cells, aligning with the functions of Tax. Overall, our findings characterize YTHDF2 as a host factor critical to HTLV-1 RNA metabolism and viral propagation, offering novel insights into the understanding of the HTLV-1 life cycle and the development of targeted interventions.IMPORTANCEm6A is an RNA modification that plays crucial roles in physiological and pathological conditions; however, its roles in HTLV-1 infection are poorly understood. In this study, we identified that m6A modification is widely present in HTLV-1 RNAs, including Tax. We demonstrate that YTHDF2, a prominent m6A reader protein, enhances the stability of Tax RNA, thereby promoting both de novo and persistent HTLV-1 replication. Our findings position YTHDF2 as an essential factor for HTLV-1 persistence and suggest it as a potential therapeutic target for viral clearance.

Small nucleolar RNAs (snoRNAs) are a conserved class of non‑coding RNAs that guide 2'‑O‑methylation and pseudouridylation of ribosomal RNA. First identified over five decades ago, snoRNAs have emerged as critical regulators of cellular function, with high‑throughput sequencing revealing their dysregulation in numerous human diseases, particularly cancer. In the present review, the biogenesis, classification, and modification mechanisms of snoRNAs and snoRNA‑derived fragments (sdRNAs) are comprehensively summarized. Recent advances in understanding their non‑canonical functions are highlighted, which extend beyond ribosomal RNA modification to include regulation of mRNA splicing, stability, and protein interactions. These diverse mechanisms enable snoRNAs to influence key cancer‑related processes such as proliferation, metastasis, metabolic reprogramming, and therapy resistance. A comprehensive overview of snoRNA dysregulation across major cancer types is provided, including colorectal, hepatocellular, gastric, lung, breast, and ovarian cancers, with a detailed discussion of underlying molecular pathways. Furthermore, their emerging potential as diagnostic and prognostic biomarkers detectable in liquid biopsies is examined, as well as their promise as therapeutic targets amenable to antisense oligonucleotide and small molecule intervention. The present review integrates current knowledge of snoRNA/sdRNA biology and highlights critical gaps and future directions, providing a foundation for translating these regulatory RNAs into clinical oncology applications.