bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–02–01
95 papers selected by
Cédric Chaveroux, CNRS
  1. Regulation of Translation of ATF4 mRNA: A Focus on Translation Initiation Factors and RNA-Binding Proteins.
  2. RNA modifications in cancer and their detection: a review.
  3. FIR/PUF60: Multifunctional Molecule Through RNA Splicing for Revealing the Novel Disease Mechanism and Effective Individualized Therapies.
  4. m6A-Modified Nucleotide Bases Improve Translation of In Vitro-Transcribed Chimeric Antigen Receptor (CAR) mRNA in T Cells.
  5. Preserving the Poly(A) Tail: Strategies Viruses Use to 'CYA' (Cover Your A's).
  6. Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay.
  7. The Cold Shock Protein CspB from Mycobacterium tuberculosis Binds to MTS0997 sRNA and MTS1338 sRNA as a Dimer.
  8. RNA helicase DDX5 regulates the translation and genomic replication of foot-and-mouth disease virus.
  9. Nucleocapsid protein captures DDX5 and RNMT facilitating viral RNA synthesis and viral protein translation for coronavirus replication.
  10. Structure-informed mutagenesis identifies combinatorial contributions to mouse insulin receptor IRES function.
  11. Identification of Key Sequence Motifs Essential for the Recognition of m6A Modification in RNA.
  12. Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity?
  13. Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33.
  14. Constant trouble with prolines-navigating a global translation dilemma.
  15. Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis.
  16. RNA Processing in Cardiac Hypertrophy: Coordinating Physiological Adaptation and Pathological Remodeling.
  17. EPR spectroscopy in the study of ribosomal complexes.
  18. Decoding RNA triple helices: identification from sequence and secondary structure.
  19. Why m⁶A? An RNA surveillance model.
  20. MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.
  21. The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis.
  22. Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.
  23. Molecular Insights into Widespread Pseudouridine RNA Modifications: Implications for Women's Health and Disease.
  24. The epitranscriptome meets non-coding RNA: m6A-mediated regulation in oncogenesis and therapy.
  25. 3' Processing of Animal Replication-Dependent Histone mRNAs.
  26. [The function and application of nucleolar small RNAs in digestive tract tumors].
  27. Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease.
  28. 4E-BP2-dependent translational control in GABAergic interneurons is required for long-term memory.
  29. RNA splicing in bone diseases: mechanisms, pathogenesis and therapeutics.
  30. Chronic stress antagonizes formation of stress granules.
  31. Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.
  32. Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs.
  33. Molecular gatekeepers: eukaryotic translation factors decoding plant-virus dynamics for resistance engineering.
  34. A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response.
  35. Enhancing mRNA vaccine production: Optimization of in vitro transcription for improved yield and purity.
  36. MiRNA Stability and Degradation: Dynamic Regulators of Cellular Regulatory Networks.
  37. Catalogue of LPS-induced transcriptional changes across vertebrates identifies syntenically conserved human long non-coding RNAs that regulate the innate immune response.
  38. Meeting Review on India EMBO lecture course on RNA-protein complexes: from molecular assembly to physiological functions and disease.
  39. Beginning of a new era of synthetic messenger RNA therapeutics: Comprehensive insights on mRNA drug design, development and applications.
  40. Mechanism of SARS-CoV-2 Nucleocapsid Protein Phosphorylation-Induced Functional Switch.
  41. The DEAD-box RNA helicase eIF4A is a crucial factor for stem-cell activity and reproduction of the parasite Schistosoma mansoni.
  42. The RNA-Binding Protein KSRP Is a Negative Regulator of Innate Immunity.
  43. The role of circular RNAs in mediating the protective effects of exercise against muscle degeneration and aging.
  44. Development of cell-free transcription translation.
  45. Interdependent Regulation of Alternative Splicing by Serine/Arginine-Rich and Heterogeneous Nuclear Ribonucleoprotein Splicing Factors.
  46. Carboxyl-Terminal Region of the Maturation Protein of RNA Coliphage Qβ Mediates Host Attachment, Virion Formation, and Cell Lysis.
  47. Assessing the effect of bovine MSTN variants on pre-mRNA splicing.
  48. Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.
  49. NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes.
  50. Deciphering the regulatory landscape of enhancer RNAs in health and disease.
  51. RNAa-Mediated Gene Activation in the Regulation of Stem Cell Fate.
  52. Transcriptional Control of PI3K/AKT/mTOR by piRNA-651 in Breast Carcinoma.
  53. Spermatogenesis Beyond DNA: Integrated RNA Control of the Epitranscriptome and Three-Dimensional Genome Architecture.
  54. Multi-Omics and Functional Analyses Identify let-7b-3p as a Negative Regulator of EMT in Lung Adenocarcinoma.
  55. Cleavage of host tRNAs by mycoplasma membrane-associated nuclease.
  56. Ribosome plasticity in glioblastoma: a multi-omics framework for future investigation.
  57. Stress Granule-Driven Resistance in Cancer: Mechanisms and Emerging Strategies.
  58. Regulation of RNA methylation linked to drug resistance in gastric cancer.
  59. Aptamer-mediated targeted approach to disrupt oncogenic HSP90α.
  60. Extracellular Vesicles and Extracellular RNAs in Plant-Microbe Interactions.
  61. The latest progression of N6-methyladenosine (m6A) RNA modification in diabetes mellitus and diabetic complications.
  62. Oculopharyngeal muscular dystrophy (OPMD) associated alanine expansion impairs the function of the nuclear polyadenosine RNA binding protein PABPN1 as revealed by proximity labeling and comparative proteomics.
  63. Dissecting the Interaction Domains of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicase DDX3X and Search for Potential Inhibitors.
  64. Mutagenesis-Centered Integrative Approaches for Identifying Binding Sites in Ion Channels and Uncovering Modulatory Mechanisms.
  65. Ribosomal RNA methylation in HSCs: it's so "good for you".
  66. Regulation of ribosome hibernation controls Legionella survival, infection, antibiotic tolerance, and phenotypic heterogeneity.
  67. Transfer RNA-Derived Small RNAs: Novel Predictive Biomarkers for Diagnosis and Prognosis of Breast Cancer.
  68. SUMOylation machinery protein, PIAS4 role in breast cancer cell proliferation and drug sensitivity.
  69. Making Sense from Structure: What the Immune System Sees in Viral RNA.
  70. Coordinating mRNA maturation: The U1 relay model.
  71. DNA Flap-Mediated Control of Transcription for Programmable RNA Synthesis.
  72. Astragalus Polysaccharide Attenuates Breast Cancer Progression by Regulating METTL3-Mediated MAL2 m6A Modification.
  73. Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response.
  74. Let go or retain: role of calmodulin in orchestrating nuclear protein transport in eukaryotes.
  75. Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.
  76. An antibody uniquely binding short 2'-O-methyl RNA oligonucleotide duplexes: formation and recognition of target duplexes on cell surfaces.
  77. Long Non-Coding RNA RAB11B-AS1 Suppresses Cervical Cancer Progression by Upregulating RPL26 Expression.
  78. The ability of alphavirus replicases to synthesize non-viral type I interferon-inducing RNAs correlates with viral RNA synthesis and has a diverse impact on virus replication and pathogenicity.
  79. Transcriptomic and Epitranscriptomic Landscape of Integrated HTLV-1 in MT2 Cells.
  80. Heterogeneous Folding Intermediates Govern the Conformational Pathway of the RNA Recognition Motif Domain of the Ewing Sarcoma Protein.
  81. Emerging roles of mRNA acetylation in plants.
  82. Discovery of the MELK-Nucleostemin Axis in Glioblastoma: Implications for p53 Regulation and Tumor Progression.
  83. Expression and clinical value of key m6A RNA modification regulators in tuberculosis.
  84. Identification and Validation of Tissue-Specific Housekeeping Markers for the Amazon River Prawn Macrobrachium amazonicum (Heller, 1862).
  85. Directional Modulation of the Integrated Stress Response in Neurodegeneration: A Systematic Review of eIF2B Activators, PERK-Pathway Agents, and ISR Prolongers.
  86. Distinct Argonaute2-associated small RNA profiles in microglia and neurons drive cell-specific responses in a mouse model of temporal lobe epilepsy.
  87. miRNAs in Glomerular Diseases: From Pathogenic Insight to Therapeutic Potential: A Narrative Review.
  88. The Roles and Implications of m6A Methylation in Radiotherapy for Gastrointestinal Tumors.
  89. METTL14 regulate LRIG1 expression via m6A to affect nucleus pulposus cell senescence in intervertebral disc degeneration.
  90. Unresolved questions on the GADD45GIP1-RPL35 axis in osteosarcoma: mechanistic links to ER stress and therapeutic targeting.
  91. Circuitous Ways of EWS::FLI1 Using Circular RNA ZNF609 to Evade Translational Repression by miR-145 in Ewing's Sarcoma.
  92. Yeast Efficiently Utilizes Ribosomal RNA-Derived Oligonucleotides as Bioavailable Nutrient Sources.
  93. Design of Anti-Tumor RNA Nanoparticles and Their Inhibitory Effect on Hep3B Liver Cancer.
  94. METTL3 inhibition alleviates neuroinflammation and apoptosis by reducing ETV4 m6A modification.
  95. Identification of 3D motifs in Rfam with JAR3D.
  1. Cells. 2026 Jan 20. pii: 188. [Epub ahead of print]15(2):
    Regulation of Translation of ATF4 mRNA: A Focus on Translation Initiation Factors and RNA-Binding Proteins.
    Pauline Adjibade, Rachid Mazroui.
      Cells are continuously exposed to physiological and environmental stressors that disrupt homeostasis, triggering adaptive mechanisms such as the integrated stress response (ISR). A central feature of ISR is the selective translation of activating transcription factor 4 (ATF4), which orchestrates gene programs essential for metabolic adaptation and survival. Stress-induced acute ATF4 expression occurs in diverse mammalian cell types and is typically protective; however, chronic activation contributes to pathologies including cancer and neurodegeneration. Canonical ISR (c-ISR) is initiated by phosphorylation of eIF2α in response to stressors such as endoplasmic reticulum or mitochondrial dysfunction, hypoxia, nutrient deprivation, and infections. This modification suppresses global protein synthesis while promoting ATF4 translation through upstream open reading frames (uORFs) in its 5'UTR. Recently, an alternative pathway, split ISR (s-ISR), enabling ATF4 translation independently of eIF2α phosphorylation, was identified in mice, suggesting ISR adaptability, though its relevance in humans remains unclear. Under normal conditions, cap-dependent translation predominates, mediated by the eIF4F complex and requiring the activity of eIF2B at its initial steps. During translational stress, eIF2α phosphorylation inhibits eIF2B activity, resulting in the formation of stalled initiation complexes, which can aggregate into stress granules (SGs). SGs sequester mRNAs and translation initiation factors, further repressing global translation, while ATF4 mRNA largely escapes sequestration, enabling selective translation. This partitioning highlights a finely tuned regulatory mechanism balancing ATF4 expression during stress. Recent advances reveal that, beyond cis-regulatory uORFs, trans-acting factors such as translation initiation factors and associated RNA-binding proteins critically influence ATF4 translation. Understanding these mechanisms provides insight into ISR plasticity and its implications for development, aging, and disease.
    Keywords:  ATF4 mRNA; RNA demethylases; RNA-binding proteins; eIFs; integrated stress response; stress granules; translation regulation; uORFs
    DOI:  https://doi.org/10.3390/cells15020188
  2. Jpn J Clin Oncol. 2026 Jan 30. pii: hyag018. [Epub ahead of print]
    RNA modifications in cancer and their detection: a review.
    Bo-Yi Yu, Hiroki Ueda.
      Ribonucleic acid (RNA) modifications, once viewed as static structural features, are now recognized as dynamic regulators of the 'epitranscriptome' that shape RNA fate. In cancer, dysregulation of RNA-modification writers, erasers, and readers reprograms RNA metabolism and translation, promoting tumorigenesis, metastasis, therapy resistance, and immune evasion. Across messenger RNAs, ribosomal RNA (rRNAs), transfer (tRNAs), and diverse non-coding RNAs, aberrant modification patterns drive alternative splicing, generate onco-ribosomes, enforce codon-biased translation, and remodel gene-expression networks in a context-dependent manner. This review summarizes how major RNA modifications-including m6A, m5C, pseudouridine, inosine, and ac4C-and their regulators contribute to cancer biology, together with disease-associated changes in rRNA, tRNA, and regulatory non-coding RNAs. We then discuss emerging diagnostic and prognostic biomarkers, druggable nodes within the epitranscriptomic machinery, and combination strategies that integrate RNA-modification targeting with existing therapies and immunotherapy. Finally, we outline key technologies for mapping RNA modifications, comparing mass spectrometry and NGS-based chemical or antibody-enrichment approaches with the expanding capabilities of nanopore direct RNA sequencing. Recent advances in nanopore direct RNA sequencing technologies, leveraging new chemistry (e.g. RNA004) and deep-learning basecallers (e.g. Dorado), increasingly enable single-molecule, multi-modification profiling, accelerating discovery despite inherent technical challenges. Collectively, biological, clinical, and technological progress is transforming the epitranscriptome into a tractable dimension of cancer biology and a promising source of future biomarkers and RNA-targeted precision therapies.
    Keywords:  RNA modifications; nanopore direct RNA sequencing; non-coding RNA
    DOI:  https://doi.org/10.1093/jjco/hyag018
  3. Int J Mol Sci. 2026 Jan 08. pii: 643. [Epub ahead of print]27(2):
    FIR/PUF60: Multifunctional Molecule Through RNA Splicing for Revealing the Novel Disease Mechanism and Effective Individualized Therapies.
    Kazuyuki Matsushita, Kouichi Kitamura, Nobuko Tanaka, Sohei Kobayashi, Yusuke Suenaga, Tyuji Hoshino.
      Disease-specific diversity in RNA transcripts stems from RNA splicing, ribosomal abnormalities, and other factors. However, the mechanisms underlying the regulation of rRNA expression in the nucleolus and mRNA expression in the cytoplasm during cancer and neuronal differentiation remain largely unknown. In this article, we review current knowledge and discuss the regulatory mechanisms of rRNA and mRNA expression in human diseases using the splicing model of PUF60 (poly(U) binding splicing factor 60)-also known as FUSE-binding protein-interacting repressor (FIR) (FUBP1-interacting repressor), RoBPI, SIAHBP1, and VRJS (Gene ID: 22827). Noncoding RNAs, much like coding RNAs, have been found to be translated into proteins with significant physiological functions. Splicing is also involved in dominant ORF RNAs implicated in the expression of both noncoding and coding RNAs. Here, we analyze recent findings regarding gene splicing, ribosome formation, and the determination of selected ORFs (dominant ORFs) in a system modeled on FIR splicing in two databases (RefSeq and ENSEMBL). rRNA transcription affects ribosomes, whereas mRNA expression and splicing affect the intracellular proteome. Our objective is to develop efficient methods for identifying biomarkers for disease diagnosis and therapeutic targets. In the field of cancer treatment, therapeutic drugs targeting intracellular signaling have proven effective.
    Keywords:  FIR/PUF60; RNA splicing; c-Myc; cancer; mRNA; rRNA; rare disease
    DOI:  https://doi.org/10.3390/ijms27020643
  4. Int J Mol Sci. 2026 Jan 13. pii: 796. [Epub ahead of print]27(2):
    m6A-Modified Nucleotide Bases Improve Translation of In Vitro-Transcribed Chimeric Antigen Receptor (CAR) mRNA in T Cells.
    Nga Lao, Simeng Li, Marina Ainciburu, Niall Barron.
      Lentiviral transduction remains the gold standard in adoptive modified cellular therapy, such as CAR-T; however, genome integration is not always desirable, such as when treating non-fatal autoimmune disease or for additional editing steps using CRISPR to produce allogeneic CAR-modified cells. Delivering in vitro-transcribed (IVT) mRNA represents an alternative solution but the labile nature of mRNA has led to efforts to improve half-life and translation efficiencies using a range of approaches including chemical and structural modifications. In this study, we explore the role of N6-methyladenosine (m6A) in a CD19-CAR sequence when delivered to T cells as an IVT mRNA. In silico analysis predicted the presence of four m6A consensus (DRACH) motifs in the CAR coding sequence and treating T cells with an inhibitor of the m6A methyltransferase (METTL3) resulted in a significant reduction in CAR protein expression. RNA analysis confirmed m6A bases at three of the predicted sites, indicating that the modification occurs independently of nuclear transcription. Synonymous mutation of the DRACH sites reduced the levels of CAR protein from 15 to >50% depending on the T cell donor. We also tested a panel of CAR transcripts with different UTRs, some containing m6A consensus motifs, and identified those which further improved protein expression. Furthermore, we found that the methylation of consensus m6A sites seems to be somewhat sequence-context-dependent. These findings demonstrate the importance of the m6A modification in stabilising and enhancing expression from IVT-derived mRNA and that this occurs within the cell, meaning targeted in vitro chemical modification during mRNA manufacturing may not be necessary.
    Keywords:  RNA therapy; T cell engineering; UTR engineering; cell therapy; in vitro transcription; m6A; transient CAR-T
    DOI:  https://doi.org/10.3390/ijms27020796
  5. Viruses. 2026 Jan 09. pii: 90. [Epub ahead of print]18(1):
    Preserving the Poly(A) Tail: Strategies Viruses Use to 'CYA' (Cover Your A's).
    Jeffrey Wilusz.
      The poly(A) tail on viral mRNAs plays an important role in gene expression, given the role of the 3' mRNA tail in mRNA stability and translation. Viruses have developed several strategies to maintain the integrity of their poly(A) tails. These include attracting stabilizing proteins through elements in the 3' untranslated regions of their mRNA, remodeling their poly(A) tails using terminal nucleotidyl transferases, and blocking deadenylase access to the terminal 3' end of their poly(A) tails using protein-protein interactions or through triple helical RNA structures. Collectively, the presence of these multiple strategies illustrates the vital overall need for viruses to maintain and preserve their poly(A) tails, highlighting a potential avenue for broad-spectrum antiviral development. In addition, poly(A) tail preservation strategies used by viruses may also be applied to RNA vaccines and therapeutics.
    Keywords:  deadenylation; polyadenylation; terminal nucleotidyl transferases; viral mRNA stability
    DOI:  https://doi.org/10.3390/v18010090
  6. Nucleic Acids Res. 2026 Jan 22. pii: gkag047. [Epub ahead of print]54(3):
    Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay.
    Max Müller, Lena Sophie Tittel, Elisabeth Petfalski, Kaushik Viswanathan Iyer, Alina-Andrea Kraft, Stefan Pastore, Tamer Butto, Marie-Luise Winz.
      New1 is a homologue of the essential yeast translation elongation factor eEF3. Lack of New1 has been shown to induce ribosome queuing upstream of the stop codon on messenger RNAs (mRNAs) with specific C-terminal lysine and arginine codons. Here, we used ultraviolet crosslinking and analysis of complementary DNA (cDNA), long-read nanopore sequencing, and proteomics to address the consequences such queues have for the yeast cell. We show that these queues represent collisions, recognized by collision sensor Hel2, triggering mRNA degradation via canonical no-go decay (NGD). We identified 139 target mRNAs, on which decay is initiated by Cue2-mediated cleavage upstream of the stop codon. Compared to other collision-prone mRNAs, ending on the same C-terminal codons, these targets are characterized by stronger secondary structures upstream of the stop codon, longer queues, and stronger queuing signatures. Nanopore sequencing enabled characterization of NGD cleavage fragments across targets. Ultimately, NGD in the absence of New1 leads to downregulation of encoded proteins, including highly abundant and essential metabolic enzymes like Pgk1 and Gpm1, as well as translation elongation factors such as eEF1-alpha and eEF1-beta. We show that New1 protects such mRNAs from degradation by NGD and that NGD is a major determinant of the cold sensitive growth phenotype observed in NEW1 deletants.
    DOI:  https://doi.org/10.1093/nar/gkag047
  7. Int J Mol Sci. 2026 Jan 09. pii: 663. [Epub ahead of print]27(2):
    The Cold Shock Protein CspB from Mycobacterium tuberculosis Binds to MTS0997 sRNA and MTS1338 sRNA as a Dimer.
    Natalia Lekontseva, Alisa Mikhaylina, Polina Pankratova, Alexey Nikulin.
      RNA chaperones play a crucial role in the biogenesis and function of various RNAs in bacteria. They facilitate the interaction of small regulatory trans-encoded sRNAs with mRNAs, thereby significantly altering the pattern of gene expression in cells. This allows bacteria to respond quickly to changing environmental conditions, such as stress or adaptation to host organisms. Despite the identification of a large number of sRNAs in mycobacteria, none of the most common RNA chaperones have been found in their genomes. We determined the crystal structure of the cold shock protein CspB from Mycobacterium tuberculosis. It forms a dimer due to its elongated C-terminal region, which is a hairpin composed of two α-helices. It was also demonstrated that CspB from M. tuberculosis exhibits high affinity for MTS0997 sRNA and MTS1338 sRNA from the same organism, which is consistent with classical RNA chaperons such as Hfq and ProQ. Based on the putative RNA chaperone activity of bacterial proteins with cold-shock domains, we propose that CspB from M. tuberculosis may be involved in the regulation of mycobacterial pathogenesis through interaction with sRNAs.
    Keywords:  CspB; Mycobacterium tuberculosis; RNA chaperone; RNA–protein interactions; cold shock proteins; sRNA; α-helix hairpin
    DOI:  https://doi.org/10.3390/ijms27020663
  8. J Virol. 2026 Jan 30. e0173125
    RNA helicase DDX5 regulates the translation and genomic replication of foot-and-mouth disease virus.
    Jin'en Wu, Sahibzada Waheed Abdullah, Pinghua Li, Xuefei Wang, Mei Ren, Yuanyuan Huang, Xianglong Guo, Shiqi Sun, Huichen Guo.
      The internal ribosome entry site (IRES) is a cis-acting structural element found in many viral mRNAs, which mediates cap-independent translation by recruiting various RNA-binding proteins and IRES trans-acting factors (ITAFs). Foot-and-mouth disease virus (FMDV), a significant member of the Picornaviridae family, contains a functional IRES element that contributes to viral protein translation and RNA synthesis. Here, we uncover a previously unrecognized mechanism in which DEAD-box RNA helicase 5 (DDX5) functions as a novel ITAF, inhibiting FMDV translation and viral RNA synthesis through two distinct strategies. First, DDX5 binds to the D4 domain of the IRES, suppressing FMDV IRES-driven translation by blocking the assembly of 80S ribosome. Second, DDX5 interacts with the viral RNA-dependent RNA polymerase 3Dpol and 3'UTR of FMDV, disrupting viral RNA synthesis. Conversely, the inhibitory effect of DDX5 was counteracted by viral precursor protein 3ABCD-mediated proteolysis of 3Cpro. Furthermore, the functional importance of DDX5 in FMDV pathogenicity was further validated in vivo experiments. These findings enhance our understanding of how viruses exploit or antagonize cellular factors to regulate IRES-driven translation and provide new insights into translational control during viral infection.
    IMPORTANCE: Picornaviruses have evolved various strategies to compete and dominate host protein synthesis machinery, often bypassing cap-dependent mRNA translation. Foot-and-mouth disease virus (FMDV), a highly contagious member of the Picornaviridae family, is a globally significant pathogen responsible for severe epidemics in cloven-hoofed animals, posing substantial economic and agricultural threats. In this study, we identified DEAD-box RNA helicase 5 (DDX5) as a novel IRES trans-acting factor that plays a critical role in the translational regulation of FMDV. Specifically, DDX5 was found to negatively modulate FMDV IRES-driven translation and suppress viral RNA replication during infection. Furthermore, we elucidated a novel viral counteraction mechanism in which DDX5 is cleaved by the viral precursor molecule 3ABCD through proteolytic activity. These findings provide new insights into the complex interplay between viral and host factors, advancing our understanding of translational control during picornavirus infection and offering potential avenues for the development of antiviral strategies.
    Keywords:  DDX5; IRES-driven translation; foot-and-mouth disease virus (FMDV); internal ribosome entry site (IRES); replication
    DOI:  https://doi.org/10.1128/jvi.01731-25
  9. mBio. 2026 Jan 26. e0271725
    Nucleocapsid protein captures DDX5 and RNMT facilitating viral RNA synthesis and viral protein translation for coronavirus replication.
    Yuchang Liu, Ning Kong, Xinyu Yang, Wenzhen Qin, Yahe Wang, Chen Wang, He Sun, Jiarui Wang, Ao Gao, Dongfang Zheng, Wu Tong, Hai Yu, Hao Zheng, Guangzhi Tong, Tongling Shan.
      Coronaviruses (CoVs) hijack host RNA-binding proteins (RBPs) to facilitate their replication, but the viral proteins and host RBDs that participate in the synthesis of viral RNA and protein are unclear. In this study, we revealed that DEAD-box helicase (DDX5) and staphylococcal nuclease domain-containing protein (SND1) facilitate viral RNA synthesis and that RNA guanine-7 methyltransferase (RNMT) enhances viral protein translation to promote viral replication via coronaviral subgenomic RNA-protein interactomes. DDX5 and SND1 positively regulate PEDV replication by promoting viral RNA synthesis via the binding of DDX5 to positive-sense viral RNA, whereas SND1 specifically detects negative-sense viral RNA. The interaction of DDX5/SND1 and N/nsp9/nsp12 promotes the formation of replication-transcription complexes for viral RNA synthesis to facilitate viral replication. We found that RNMT captures the host protein translation system to cyclize viral mRNA to assist in viral protein translation to promote viral replication. We also found that DDX5 broadly interacts with the N protein of CoVs and promotes the RNA synthesis of bovine coronavirus and porcine delta-coronavirus to promote viral replication. These results indicate that CoVs use host proteins to assist in the synthesis of viral RNA and protein to facilitate viral replication.
    IMPORTANCE: The synthesis of viral RNA and proteins is a crucial process in the life cycle of CoVs. Our observations indicate that DDX5 and SND1 facilitate the assembly of viral replication-transcription complexes and enhance viral RNA synthesis, with DDX5 binding to positive-sense RNA and SND1 binding to negative-sense RNA. Meanwhile, RNMT promotes viral protein translation by hijacking the host translation machinery and mediating the circularization of viral mRNA. These findings offer new insights into the mechanisms through which coronaviruses exploit both viral and host proteins to synthesize viral RNA and proteins.
    Keywords:  RNA synthesis; RNA-binding proteins; coronaviruses; protein translation; virus-host interaction
    DOI:  https://doi.org/10.1128/mbio.02717-25
  10. RNA. 2026 Jan 28. pii: rna.080775.125. [Epub ahead of print]
    Structure-informed mutagenesis identifies combinatorial contributions to mouse insulin receptor IRES function.
    William B Dahl, Tammy C T Lan, Silvi Rouskin, Michael T Marr.
      Cells under stress shift their proteome by repressing cap-dependent translation initiation. RNA elements called internal ribosome entry sites (IRES) can allow key cellular transcripts to remain efficiently translated to support an effective stress response. We previously determined that the 5' untranslated region (5'UTR) of the insulin receptor mRNA possesses a capacity for IRES activity that is conserved from insects to mammals. Well-characterized IRESes depend on RNA structures that reduce the protein requirements for translation initiation, thus circumventing translation inhibition. While there are several examples of viral IRES structures solved in vitro, the RNA secondary structures of cellular IRESes remain elusive and little information exists about the secondary structures of these RNAs in vivo. Here we probe the secondary structure of the Insr 5'UTR IRES along with two well-studied viral IRESes from hepatitis C virus and encephalomyocarditis virus using dimethyl sulfate mutational profiling by sequencing (DMS-MaPseq) in vitro and in cells. We find that the structures of viral IRESes in a cellular environment are largely consistent with their known in vitro structures. Using DMS-MaPseq probing as a constraint, we generated a model of the RNA secondary structure of the mouse insulin receptor 5'UTR. With this model as a guide, we employed a mutation strategy which allowed us to identify a conserved segment of RNA, distal from the translation start codon, that is critical for Insr IRES function. This knowledge informed the design of a minimal IRES element with equivalent activity to the full-length Insr 5'UTR across translation contexts.
    Keywords:  5’ untranslated region; RNA structure; insulin receptor; internal ribosome entry sites; non-canonical translation initiation
    DOI:  https://doi.org/10.1261/rna.080775.125
  11. Biomolecules. 2026 Jan 07. pii: 97. [Epub ahead of print]16(1):
    Identification of Key Sequence Motifs Essential for the Recognition of m6A Modification in RNA.
    Aftab Mollah, Rushdhi Rauff, Sudeshi Abedeera, Chathurani Ekanayake, Chamali Thalagaha Mudiyanselage, Minhchau To, Helen Piontkivska, Sanjaya Abeysirigunawardena.
      N6-methyladenosine (m6A) constitutes the most prevalent nucleotide modification within eukaryotic messenger RNA (mRNA). Variations in m6A levels are associated with numerous human diseases and health conditions, including various forms of cancer, diabetes, neurological disorders, male infertility, and obesity. Nevertheless, the molecular mechanisms underpinning the recognition of m6A by different 'reader' proteins remain incompletely elucidated. In this study, we used phage display to identify key sequence features that methyl readers recognize in m6A. This study shows that m6A modifications affect the mRNA interactome. A peptide motif recognizing m6A in DRACH sequences suggests a common recognition mechanism, though proteins may use different methods to detect m6A in less accessible areas. The sequence of the hnRNP A1 RRM domain that aligns with the newly discovered m6A-binding peptide, m1p1, is crucial for the binding of m6A-modified RNAs, indicating a strong link between the m1p1 sequence and m6A recognition, which is key for recognizing m6A-modified, unstructured RNAs. Gaining a comprehensive understanding of the evolutionary influence of m6A on its reader proteins may facilitate the identification of additional m6A readers. These signature peptides could enhance theranostic approaches across cancers, enabling more targeted therapies.
    Keywords:  RNA–protein interactions; epitranscriptomic regulation; m6A modification; phage display; post-transcriptional RNA modifications
    DOI:  https://doi.org/10.3390/biom16010097
  12. Nucleic Acids Res. 2026 Jan 22. pii: gkag006. [Epub ahead of print]54(3):
    Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity?
    Cristina Gutierrez-Vargas, Swastik De, Suvrajit Maji, Zheng Liu, Zhonghe Ke, Martina Nieß, Andrei Seluanov, Vera Gorbunova, Joachim Frank.
      Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco, display fragmented 28S ribosomal RNA (rRNA), coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here, we show, by single-particle cryo-electron microscopy, that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved density for certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to the human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation.
    DOI:  https://doi.org/10.1093/nar/gkag006
  13. Nucleic Acids Res. 2026 Jan 22. pii: gkag030. [Epub ahead of print]54(3):
    Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33.
    Jutta Hafner, Ingrid Zierler, Hussein Hamze, Sébastien Favre, Matthias Thoms, Natalia Kunowska, Sarah Rimser, Benjamin Albert, Tomas Caetano, Marion Aguirrebengoa, Roland Beckmann, Ulrich Stelzl, Dieter Kressler, Anthony K Henras, Brigitte Pertschy.
      Eukaryotic ribosome synthesis is a highly complex, multistep process that is best characterized in the yeast Saccharomyces cerevisiae. It is orchestrated by >200 ribosome assembly factors and 75 small nucleolar ribonucleoproteins (snoRNPs), which guide site-specific chemical modifications of precursor rRNA (pre-rRNA). While canonical box C/D snoRNPs guide 2'-O-methylation, the atypical box C/D snoRNPs snR4 and snR45 guide acetylation of 18S rRNA residues C1280 and C1773, respectively, catalyzed by the acetyltransferase Kre33. Here, we identify and characterize Ynl050c/Sni445 as a novel ribosome assembly factor and previously unrecognized auxiliary component of the snR4 and snR45 box C/D snoRNPs. Sni445 associates with snR4 and snR45 in their free form and is required for their stable incorporation into 90S pre-ribosomes. Genetic interactions link Sni445 and the snR4 and snR45 snoRNAs to ribosomal proteins Rps20 (uS10) and Rps14 (uS11), which are positioned near the respective acetylation sites in the 40S subunit. Moreover, Sni445 physically interacts with Kre33 within the 90S pre-ribosome, and its absence abolishes acetylation of C1280 and C1773. Our findings suggest that Sni445 facilitates the recruitment of snR4 and snR45 snoRNPs to 90S particles and might promote their interaction with Kre33, thereby enabling the site-specific acetylation of 18S rRNA by Kre33.
    DOI:  https://doi.org/10.1093/nar/gkag030
  14. Nucleic Acids Res. 2026 Jan 22. pii: gkaf1420. [Epub ahead of print]54(3):
    Constant trouble with prolines-navigating a global translation dilemma.
    Jürgen Lassak, Jingzhi Stritzel, Andreas Schlundt, Tess Brewer.
      Proline is a paradox in biology-integral to protein structure and functionality, yet exceptionally challenging during translation. This review examines what sets proline apart from the other proteinogenic amino acids, detailing its unique chemical and structural characteristics that hinder efficient peptide bond formation. Although proline's impact is evident across all domains of life, our focus is primarily on bacteria, where the evolutionary pressure to overcome proline-induced ribosomal stalling has led to a sophisticated suite of specialized translation factors. Ultimately, we discuss how the interplay between proline and its translational rescue systems not only ensures protein synthesis but also drives the evolution of bacterial proteomes.
    DOI:  https://doi.org/10.1093/nar/gkaf1420
  15. Microbiol Spectr. 2026 Jan 26. e0256125
    Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis.
    Mateusz A Maździarz, Katarzyna Krawczyk, Ewa Lepiarczyk, Łukasz Paukszto, Jakub Sawicki, Marta Majewska.
      RNA modifications represent a critical layer of post-transcriptional gene regulation, shaping RNA fate and function through modulation of splicing, stability, translation, and immune signaling. Their role in viral infections remains insufficiently explored. We applied direct RNA sequencing to profile three key RNA modifications, 5-methylcytosine (m5C), N6-methyladenosine (m6A), and pseudouridine (psU), in whole blood samples from COVID-19 patients and healthy controls. Using CHEUI and NanoSPA, we identified condition-specific modification sites, their positional distribution, and associated functions. We detected 689 m5C, 738 m6A, and 1,201 psU sites, many uniquely enriched in infected individuals. These modifications localized predominantly to 3' UTRs and final exons. Codon-level and motif analysis revealed distinct enrichment patterns. Functional annotation indicated involvement in immune response, viral defense, inflammation, and stress. Several immune-regulatory genes, including CSF3R, PIK3CD, and CAPZB, exhibited co-occurring modifications. Pathway analysis revealed convergence on processes such as endocytosis, Fc receptor-mediated phagocytosis, and phagosome maturation, mechanisms central to viral entry and immune activation. Our findings show that RNA modifications are dynamically regulated during infection and may serve as biomarkers and therapeutic targets in COVID-19.
    IMPORTANCE: RNA modifications are increasingly recognized as critical regulators of host-virus interactions, yet their specific roles in human viral infections remain largely unexplored. Here, we provide the first comprehensive epitranscriptomic map of 5-methylcytosine (m5C), N6-methyladenosine (m6A), and pseudouridine (psU) in the host transcriptome during SARS-CoV-2 infection. By combining direct RNA sequencing with advanced modification-calling algorithms, we identify hundreds of condition-specific sites, reveal their positional preferences within transcripts, and uncover their functional association with immune defense and viral entry pathways. These findings demonstrate that host RNA modifications are dynamically remodeled during infection and define molecular signatures with potential diagnostic and therapeutic value. Our work establishes RNA modification profiling as a powerful tool for dissecting viral pathogenesis and opens new avenues for targeted antiviral strategies.
    Keywords:  COVID-19; SARS-CoV-2; m5C; m6A; psU
    DOI:  https://doi.org/10.1128/spectrum.02561-25
  16. FASEB J. 2026 Feb 15. 40(3): e71491
    RNA Processing in Cardiac Hypertrophy: Coordinating Physiological Adaptation and Pathological Remodeling.
    Mengling Peng, Yu Fu, Cong Qin, Jingpeng Jin, Shanshan Zhou.
      Cardiac hypertrophy represents a complex remodeling process involving extensive reprogramming of gene expression. While transcriptional regulation has been well characterized, post-transcriptional RNA processing has recently emerged as a crucial determinant of cardiac homeostasis. This review summarizes current knowledge of RNA modifications, alternative splicing, mRNA stability, and RNA editing in physiological and pathological hypertrophy. We highlight key epitranscriptomic marks such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G), as well as the functions of RNA-binding proteins and adenosine deaminases acting on RNA (ADAR1/2). In exercise-induced hypertrophy, RNA processing contributes to adaptive remodeling by supporting sarcomere organization, calcium handling, and survival pathways, exemplified by RBFOX2-dependent splicing of CACNA1C, RBM20-directed regulation of titin isoforms, and METTL14-mediated m6A signaling that enhances Akt activity. Conversely, pathological stress leads to dysregulated RNA programs that promote maladaptive remodeling through aberrant splice variants, perturbation of circular RNAs, and persistent pro-inflammatory signaling, thereby facilitating contractile dysfunction and progression to heart failure. Context-dependent regulators, including METTL3, YTHDF2, RBM24, and ADAR2, orchestrate the balance between adaptive and maladaptive responses. Targeting specific nodes, such as METTL3-driven m6A methylation or RBM24-dependent splicing fidelity, may provide innovative therapeutic strategies. Advances in RNA-targeted interventions, including ADAR-mediated editing and small molecule inhibitors of methyltransferases, highlight the translational potential of RNA processing as a novel avenue for precision cardiovascular therapy.
    Keywords:  RNA editing; RNA modification; RNA processing; alternative splicing; cardiac hypertrophy; mRNA stability
    DOI:  https://doi.org/10.1096/fj.202503525R
  17. Biophys Rev. 2025 Oct;17(5): 1215-1231
    EPR spectroscopy in the study of ribosomal complexes.
    Olesya Krumkacheva, Alexey Malygin, Dmitri Graifer, Mikhail Kolokolov, Elena Bagryanskaya.
      Protein synthesis is a fundamental biological process universally mediated by ribosomes-complex ribonucleoprotein assemblies responsible for translating genetic information into functional proteins. Despite significant structural information provided by X-ray crystallography and cryo-electron microscopy (cryo-EM), certain dynamic features of ribosomal function, particularly those involving RNA conformational flexibility and transient interactions, remain challenging to characterize. Electron Paramagnetic Resonance (EPR) spectroscopy, combined with site-directed spin labeling (SDSL), has emerged as a robust complementary approach for probing structural dynamics and conformational heterogeneity in ribosomal complexes. This review summarizes recent advances in applying EPR spectroscopy, particularly pulse dipolar EPR (DEER/PELDOR), to investigate human ribosomal complexes. We discuss methodological aspects of spin-labeling strategies for mRNA, comparing various nitroxide-based labels and highlighting their specific advantages for probing ribosomal interactions. Through representative examples, we illustrate how different EPR techniques yield complementary structural information in studying ribosome-RNA interactions. Key findings include the identification of alternative mRNA conformations within ribosomal complexes, characterization of labile RNA binding sites near the mRNA entry channel, and elucidation of stabilization effects mediated by tRNA interactions. Furthermore, we demonstrate how the integration of EPR data with molecular modeling facilitates accurate interpretation of distance distributions, enabling the correlation of experimental findings with atomic-level structural models. Finally, we address current methodological limitations of EPR spectroscopy, outlining promising perspectives and anticipated advancements in this evolving field.
    Keywords:  Conformational heterogeneity; DEER/PELDOR; EPR spectroscopy; Pulse dipolar EPR; RNA; Ribosome; Translation; mRNA dynamics
    DOI:  https://doi.org/10.1007/s12551-025-01348-0
  18. Brief Bioinform. 2026 Jan 07. pii: bbag009. [Epub ahead of print]27(1):
    Decoding RNA triple helices: identification from sequence and secondary structure.
    Margherita A G Matarrese, Michela Quadrini, Nicole Luchetti, Federico Di Petta, Daniele Durante, Monica Ballarino, Letizia Chiodo, Luca Tesei.
      The discovery of long non-coding RNAs (lncRNA) has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; e.g. a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here, we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established triple helices (8 RNAs), TripleMatcher localized all annotated regions (structure-wise detection 8/8); geometric filtering removed most spurious candidates and improved precision (positive predictive value from 0.42 to 0.81) and overall accuracy (F$_{1}$ from 0.42 to 0.62) while maintaining sensitivity. Benchmarking eight predictors showed that pseudoknot-aware methods most reliably reproduce the local architecture required for detection, aligning secondary-structure quality with downstream triple-helix recovery. Applied prospectively, the framework identified candidate regions directly from predicted secondary structures and scaled to a screen of 4160 RNAs, where distance filtering reduced 150 990 (median per molecule: 108 [20-270]) raw candidates to 97 geometrically feasible regions across seven molecules, including human telomerase complexes. Together, the notation and TripleMatcher provide a concise route from secondary structure to a small, interpretable set of triple-helix candidates suitable for targeted experimental validation.
    Keywords:  RNA pattern search; RNA secondary structure; RNA structure prediction; long non-coding RNA; non-coding RNA
    DOI:  https://doi.org/10.1093/bib/bbag009
  19. Mol Cell. 2026 Jan 27. pii: S1097-2765(26)00022-5. [Epub ahead of print]
    Why m⁶A? An RNA surveillance model.
    D Dierks, S Schwartz.
      N6-methyladenosine (m⁶A) is the most abundant internal modification of mRNA and is most strongly linked to promoting mRNA decay. Why transcripts are born with a death-promoting mark has remained unclear. A previously proposed "fast-track" model posited regulated, gene-specific modulation of m⁶A to coordinate translation and turnover. However, emerging evidence reveals that m⁶A is broadly and mostly constitutively installed at all DRACH motifs except in the vicinity of splice sites, all of which challenge a fast-track model. We propose an "m⁶A surveillance model": properly spliced transcripts mostly evade methylation, while unspliced, transposon-derived, viral, or aberrant RNAs are hypermethylated and selectively degraded. This model reframes m⁶A as a default quality-control mark that flags undesirable unspliced RNAs for removal. We discuss literature supporting and challenging this model as well as experimental priorities that could allow for a more thorough investigation of this model.
    Keywords:  DRACH motifs; N6-methyladenosine; RNA surveillance; YTH readers; aberrant RNAs; exon-junction complex; gene expression regulation; m6A; mRNA stability and decay; methyltransferase complex; splicing-dependent methylation
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.002
  20. RNA. 2026 Jan 26. pii: rna.080864.125. [Epub ahead of print]
    MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.
    Taiya Jarva, Chris Baugh, Jialin Zhang, Eric Lai, Alex Flynt.
      Argonaute proteins mediate gene silencing via small regulatory RNAs that are generated by distinctive biogenesis pathways. In animals, three main classes are recognized: ~21-24 nucleotide (nt) microRNAs (miRNAs), ~21-24 nt small-interfering RNAs (siRNAs) and ~24-32 nt Piwi-interacting RNAs (piRNAs). Mechanistic understanding of these pathways was gained from genetic, biochemical and genomic studies in a handful of model systems, where key ribonucleolytic events were identified that specify stereotyped positioning of small RNAs relative to their precursor transcripts. With burgeoning availability of assembled genomes and small RNA data, there are abundant opportunities to characterize the diversity of small RNAs across non-model organisms. While several tools are well-suited to analyze specific small RNA pathways, an integrated package that can help classify and interpret all three major classes of small RNAs is wanting. To address this need, we developed a simple and efficient R package (MiSiPi.Rna) that can generate a variety of plots and statistics for pre-selected loci, which enable the characterization of diverse biogenesis features of miRNAs, siRNAs and piRNAs. MiSiPi.Rna requires minimal computational expertise to run, and will facilitate efforts to annotate and analyze the major classes of Argonaute-based small regulatory RNAs in arbitrary species of choice.
    Keywords:  AI annotation; Dicer processing; Phasing biogenesis; small RNA
    DOI:  https://doi.org/10.1261/rna.080864.125
  21. J Mol Biol. 2026 Jan 23. pii: S0022-2836(26)00026-4. [Epub ahead of print] 169653
    The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis.
    Nima Sarfaraz, Ranjit Kaur, Sky Harper, Lilly Oni, Srinivas Somarowthu, Michael J Bouchard.
      Primary liver cancer represents a significant global health burden, with limited therapeutic options for advanced disease. Long non-coding RNAs (lncRNAs) are increasingly found to play crucial roles in hepatic biology and disease progression. Here, we identify FAM99A as a highly liver-enriched lncRNA that is systematically downregulated across liver malignancies, with reduced expression correlating with poor clinical outcomes. FAM99A exhibits remarkable tissue specificity with minimal expression outside the liver, and its levels rapidly decline during primary hepatocyte dedifferentiation in culture. Through isoform analysis, we establish FAM99A-203 as the predominant transcript in normal liver tissue and observe altered isoform distribution in liver cancers. Functionally, FAM99A overexpression inhibits anchorage-independent growth in liver cancer cell lines. Transcriptomic analysis reveals that FAM99A negatively regulates translation-related pathways in both liver cancer cells and primary hepatocytes. This is corroborated by protein synthesis assays showing that FAM99A overexpression substantially reduces global translation rates. Targeted RNase H-mediated extraction coupled with mass spectrometry identifies multiple components of the translation machinery as direct FAM99A binding partners, including eukaryotic translation initiation factors and RNA helicases involved in ribosome biogenesis. Clinical data analysis demonstrates significant inverse correlations between FAM99A expression and ribosomal protein genes in liver cancer patients. Additionally, hepatitis B virus appears to downregulate FAM99A expression, potentially contributing to its oncogenic properties. Our findings establish FAM99A as a liver-enriched translational regulator that exerts tumor-suppressive effects by restraining protein synthesis rates, offering insights into hepatocarcinogenesis and the potential of FAM99A as both a biomarker and agent in new therapeutic avenues.
    Keywords:  FAM99A; Hepatocellular Carcinoma; Liver Cancer; LncRNA; Ribosome; Translation; Tumor Suppressor
    DOI:  https://doi.org/10.1016/j.jmb.2026.169653
  22. RNA. 2026 Jan 28. pii: rna.080839.125. [Epub ahead of print]
    Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.
    Shira Fisher, Hanah Margalit.
      Bacterial small RNAs (sRNAs) play crucial roles in gene regulation by base pairing with their target mRNAs, modulating mRNA stability and translation. While sRNA binding sites were initially identified in 5' untranslated regions of mRNAs, consistent with their role as regulators of translation initiation, recent large-scale studies have revealed sRNA binding sites within protein-coding sequences, suggesting additional regulatory mechanisms. It is intriguing to explore how the latter sRNA binding sites are adjusted with the reading frame and what selection forces maintain them within the coding sequence through evolution. Using RIL-seq data, we determined prime sRNA binding positions within coding sequences, which are positions within the inferred binding-site motif that show exceptionally high conservation across target sequences (≥95%), indicating their putative functional importance for sRNA-mRNA base pairing. We found that these positions are mostly adjusted with the reading frame and correspond to the most frequent codons, high above random expectation. This coincidence may suggest that frequent codons in the binding sites increase the probability of sRNA-mRNA encounter, and that the establishment of the binding sites is influenced by codon usage bias and evolutionary pressures. Conservation analysis across genomes in the Enterobacterales order revealed that prime positions show relatively high conservation of base pairing interactions, but, on the other hand, in some genomes base pairing in these positions may be hampered due to the degeneracy of the genetic code. This is often compensated for by other positions that conserve the base pairing interactions, ensuring the maintenance of a requisite number of base pairs for sustaining the sRNA-target interaction. Our findings highlight the importance of distinct interacting positions as well as an adequate number of base pairs for sustaining sRNA-target interactions.
    Keywords:  Base pairing; Codon Usage; Small RNAs
    DOI:  https://doi.org/10.1261/rna.080839.125
  23. Biology (Basel). 2026 Jan 14. pii: 142. [Epub ahead of print]15(2):
    Molecular Insights into Widespread Pseudouridine RNA Modifications: Implications for Women's Health and Disease.
    Qiwei Yang, Ayman Al-Hendy, Thomas G Boyer.
      Pseudouridine (Ψ), the most abundant RNA modification, plays essential roles in shaping RNA structure, stability, and translational output. Beyond cancer, Ψ is dynamically regulated across numerous physiological and pathological contexts-including immune activation, metabolic disorders, stress responses, and pregnancy-related conditions such as preeclampsia-where elevated Ψ levels reflect intensified RNA turnover and modification activity. These broad functional roles highlight pseudouridylation as a central regulator of cellular homeostasis. Emerging evidence demonstrates that Ψ dysregulation contributes directly to the development and progression of several women's cancers, including breast, ovarian, endometrial, and cervical malignancies. Elevated Ψ levels in tissues, blood, and urine correlate with tumor burden, metastatic potential, and therapeutic responsiveness. Aberrant activity of Ψ synthases such as PUS1, PUS7, and the H/ACA ribonucleoprotein component dyskerin alters pseudouridylation patterns across multiple RNA substrates, including rRNA, tRNA, mRNA, lncRNAs, snoRNAs, and ncRNAs. These widespread modifications reshape ribosome function, modify transcript stability and translational efficiency, reprogram RNA-protein interactions, and activate oncogenic signaling programs. Advances in high-resolution, site-specific Ψ mapping technologies have further revealed mechanistic links between pseudouridylation and malignant transformation, highlighting how modification of distinct RNA classes contributes to altered cellular identity and tumor progression. Collectively, Ψ and its modifying enzymes represent promising biomarkers and therapeutic targets across women's cancers, while also serving as sensitive indicators of diverse non-cancer physiological and disease states.
    Keywords:  RNA modification; epitranscriptomics; female cancers; gynecological diseases; pseudouridine; pseudouridine synthases; reproductive biology; sex-specific regulation; women health
    DOI:  https://doi.org/10.3390/biology15020142
  24. Front Cell Dev Biol. 2025 ;13 1681555
    The epitranscriptome meets non-coding RNA: m6A-mediated regulation in oncogenesis and therapy.
    Prasanna Srinivasan Ramalingam, Mokhtar Rejili, Faouzi Haouala, Md Sadique Hussain, Yumna Khan, Mudasir Maqbool, Janaki Ramaiah Mekala, Sivakumar Arumugam.
      The field of epitranscriptomics discovered N6-methyladenosine (m6A) modifications, which function as fundamental elements that control RNA metabolism properties that powerfully affect cancer biology. This review examines the way m6A modifications shape RNA stability while regulating translation, together with their eraser and reader proteins. We demonstrate that m6A modifications guide oncogene and tumor suppressor transcript outcomes, which promote tumor growth, metastasis, and therapeutic resistance. The regulatory function of m6A depends significantly on its relationship with ncRNAs that mainly include miRNAs, lncRNAs, and circRNAs. The review examines the effects of m6A on ncRNA production, stability, export, and degradation, as well as the regulation of m6A protein expression by ncRNAs, highlighting intricate reciprocal feedback loops that drive cancer progression. The interplay between m6A RNA modifications and ncRNAs provides emerging evidence on how they collectively influence the tumor microenvironment, modulate immune system responses, and contribute to resistance. Harnessing ncRNA-m6A interactions for managing drug resistance offers promising therapeutic avenues. However, advancing our understanding of the context-specific roles of m6A modifications and translating these insights into clinical applications remains a significant challenge. This review synthesizes recent findings on ncRNA-m6A crosstalk to lay the groundwork for developing epitranscriptomic strategies in precision oncology.
    Keywords:  RNA metabolism; RNA modifications; epigenesis; oncology; tumor microenvironment
    DOI:  https://doi.org/10.3389/fcell.2025.1681555
  25. Wiley Interdiscip Rev RNA. 2026 Jan-Feb;17(1):17(1): e70035
    3' Processing of Animal Replication-Dependent Histone mRNAs.
    William F Marzluff.
      Each time a eucaryotic cell divides, it replicates its DNA and packages the DNA into chormatin. Large amounts of all five histone proteins are co-ordinately synthesized to assemble the newly replicated chromatin. The metazoan replication-dependent (RD) histone mRNAs differ from all other cellular mRNAs. They are not polyadenylated, but end instead in a conserved stem-loop (SL). The genes encoding all five RD-histone mRNAs are clustered, and localized to a subdomain of the nucleus, the histone locus body (HLB). Factors required for transcription and 3' processing are concentrated in the HLB, allowing coordinate expression of the five histone mRNAs, which are synthesized inside the HLB. Since RD-histone genes lack introns, capping and 3' end formation are the only processing reactions required for their biosynthesis. A set of factors involved only in histone mRNA metabolism; NPAT, FLASH, U7 snRNP, and SLBP are required for synthesis of histone mRNAs. The HLB is present throughout the cell cycle. Histone mRNA expression is restricted to S-phase by phosphorylation of NPAT by cyclin E/cdk2. Like cleavage/polyadenylation, histone pre-mRNA processing requires recognition of a 5' signal, the SL, by SLBP, and a 3' signal, the histone downstream element (HDE) by U7 snRNP, with cleavage occurring between them. A subcomplex of CPSF, the cleavage module for cleavage/polyadenylation, is a component of the active U7 snRNP, which assembles in the HLB only in S-phase. CPSF73 catalyzes the cleavage of the nascent transcript to produce mature histone mRNA.
    Keywords:  RNA processing; cell cycle regulation; histone mRNAs; nuclear bodies; snRNP
    DOI:  https://doi.org/10.1002/wrna.70035
  26. Zhonghua Wai Ke Za Zhi. 2026 Jan 26. 64(3): 276-280
    [The function and application of nucleolar small RNAs in digestive tract tumors].
    Y Y Qin, Z Z Quan.
      Small nucleolar RNAs (snoRNAs) are a class of important non-coding RNAs traditionally involved in the modification and processing of ribosomal RNA. Recent studies have revealed that snoRNAs are aberrantly expressed in various gastrointestinal malignancies-including gastric cancer, colorectal cancer, and esophageal cancer-and contribute to tumorigenesis and progression by regulating gene expression and modulating key biological processes such as tumor cell proliferation, apoptosis, invasion, migration, metabolism, drug resistance, and stemness maintenance. Although extensive research has focused on the roles of snoRNAs in cancer, their precise molecular mechanisms and clinical utility remain incompletely understood. This review summarizes the expression profiles and functional mechanisms of snoRNAs in gastrointestinal cancers and discusses their potential as biomarkers or therapeutic targets, aiming to provide new insights for early diagnosis and precision therapy of these malignancies.
    DOI:  https://doi.org/10.3760/cma.j.cn112139-20251125-00545
  27. Biochemistry. 2026 Jan 26.
    Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease.
    Chia Yi Yao, Simpson Joseph.
      RNA-binding proteins (RBPs) are essential regulators of posttranscriptional gene expression, influencing mRNA processing, translation, and stability. Defining their binding sites on RNA is key to understanding how they assemble into functional ribonucleoprotein (RNP) complexes, but existing footprinting and cross-linking approaches often yield low signal-to-noise, variable efficiency, or require highly purified complexes. To address these limitations, we developed Tethered Micrococcal Nuclease Mapping (TM-map), a sequencing-based strategy that determines the three-dimensional binding sites of RBPs on RNA in vitro. In TM-map, the RBP is fused to micrococcal nuclease (MNase), which upon Ca2+ activation cleaves proximal RNA regions, producing fragments whose 3' termini report the spatial proximity of the fusion. We first validated TM-map using the bacteriophage MS2 coat protein bound to its cognate RNA stem-loop engineered into the Escherichia coli ribosome. Cleavage sites mapped proximal to the engineered stem-loop, confirming that tethered MNase reliably reports local protein-RNA proximity on the ribosome surface. We then applied TM-map to the Drosophila Fragile X Mental Retardation Protein (FMRP), a translational regulator with an unresolved ribosome-binding site. Both N- and C-terminal MNase-FMRP fusions produced reproducible cleavage clusters on the 18S rRNA localized to the body and head of the 40S subunit. The similar profiles suggest that FMRP's termini are conformationally flexible and sample multiple orientations relative to the ribosome, consistent with a dynamic interaction rather than a fixed binding mode. TM-map thus provides a simple, proximity-based, and generalizable in vitro approach for visualizing RBP-RNA interactions within native RNP assemblies.
    DOI:  https://doi.org/10.1021/acs.biochem.5c00660
  28. Mol Neurobiol. 2026 Jan 30. 63(1): 409
    4E-BP2-dependent translational control in GABAergic interneurons is required for long-term memory.
    Ziying Huang, Niaz Mahmood, Konstantina Psycharis, Kevin Lister, Mehdi Hooshmandi, Nikhil Nageshwar Inturi, Diana Tavares-Ferreira, Shane Wiebe, Arkady Khoutorsky, Nahum Sonenberg.
      mRNA translational repression by eukaryotic initiation factor 4E-binding proteins (4E-BPs), plays a critical role in synaptic plasticity and the formation of long-term memory (LTM). Among the three 4E-BP paralogs, 4E-BP2 is the predominant form expressed in neurons, and its full-body deletion in mice causes memory deficits. Mice lacking 4E-BP2 in GABAergic inhibitory interneurons, but not excitatory neurons, display autistic-like behaviors and deficits in object location and recognition. The specific mRNAs translationally regulated by 4E-BP2 in GABAergic interneurons, and how they contribute to spatial and associative memory, are unknown. Here, we show that conditional knockout (cKO) mice lacking 4E-BP2 selectively in GABAergic interneurons exhibit impairments in long-term spatial and contextual fear memory formation. We further demonstrate that 4E-BP2 deletion controls the translation of selective mRNAs in interneurons without increasing general protein synthesis. One of the mRNAs is Gal, which encodes a neuropeptide that modulates memory. Our findings provide evidence that 4E-BP2 selectively controls the translation of a subset of mRNAs in inhibitory neurons that are required for LTM formation.
    Keywords:  4E-BP2; GABAergic interneurons; Long-term memory; TRAP; Translation
    DOI:  https://doi.org/10.1007/s12035-026-05684-4
  29. Acta Biochim Pol. 2025 ;72 15819
    RNA splicing in bone diseases: mechanisms, pathogenesis and therapeutics.
    Linlin Zheng, Hui Sun, Ning Li, Lianqing Wang, Tianchu Li, Qiaoli Zhai.
      RNA splicing is a fundamental post-transcriptional mechanism that enables the generation of diverse mRNA isoforms from a single gene, thereby expanding proteomic complexity and regulating cell fate decisions. Emerging evidence highlights that dysregulated splicing contributes to the onset and progression of various bone-related diseases, including osteoporosis, osteoarthritis, and skeletal malignancies. In this review, we summarize current knowledge on the core mechanisms of pre-mRNA splicing, with emphasis on alternative splicing events that modulate bone cell differentiation, matrix formation, and tissue homeostasis. We further discuss how aberrant splicing impacts signaling pathways involved in bone metabolism and disease pathogenesis, and we explore the epigenetic and RNA-binding protein networks that fine-tune these processes. Finally, we examine the therapeutic potential of targeting splicing machinery or correcting mis-splicing events using small molecules, antisense oligonucleotides, and RNA-based approaches. This comprehensive overview provides mechanistic insights and highlights splicing regulation as a promising avenue for the diagnosis and treatment of skeletal disorders.
    Keywords:  alternative splicing; gene regulation; mechanisms; skeletal disorders; therapy
    DOI:  https://doi.org/10.3389/abp.2025.15819
  30. iScience. 2026 Jan 16. 29(1): 114556
    Chronic stress antagonizes formation of stress granules.
    Yuichiro Adachi, Allison M Williams, Masashi Masuda, Yutaka Taketani, Paul J Anderson, Pavel Ivanov.
      Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates formed in response to stress-induced inhibition of mRNA translation and polysome disassembly. Despite the broad interest in SG assembly and disassembly in response to acute stress, SG dynamics under chronic stress has not been extensively investigated. We show that cells pre-conditioned with low-dose chronic (24 h exposure) stresses of various natures fail to assemble SGs in response to acute stress. While protein synthesis is drastically decreased by acute stress in pre-conditioned cells, polysome profiling analysis reveals the partial preservation of polysomes. Mechanistically, chronic stress slows down the rate of mRNA translation at the elongation phase, and triggers phosphorylation of translation elongation factor eEF2. These events further promote ribosome stalling, which is distinct from ribosome collisions known to trigger ribosome-associated quality-control pathways. In summary, chronic stress triggers ribosome stalling, which prevents efficient polysome disassembly and SG formation by subsequent acute stress.
    Keywords:  biochemistry; cell biology
    DOI:  https://doi.org/10.1016/j.isci.2025.114556
  31. Cells. 2026 Jan 07. pii: 105. [Epub ahead of print]15(2):
    Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.
    Mihyun Oh, Bo Lim Lee, Srinivas Somarowthu.
      Recent advances in sequencing technologies have highlighted long non-coding RNAs (lncRNAs) as key regulators that perform essential biological functions without encoding proteins. Despite growing interest, the molecular mechanisms of most lncRNAs remain poorly understood, with only a few characterized in detail. A promising strategy to elucidate these mechanisms is to explore their structure-function relationships. Such studies require advanced biophysical and biochemical methods due to the large size and structural complexity of lncRNAs. Equally important is the analysis of lncRNA interactomes, which reveal how lncRNAs engage RNA-binding proteins and other biomolecules to drive conformational and functional changes underlying diverse biological pathways. Ultimately, integrative approaches combining structural and interactome analyses will yield deeper insight into lncRNA function and uncover new therapeutic opportunities. This review highlights recent advances in elucidating lncRNA structure-function relationships by integrating biophysical, biochemical, and sequencing-based approaches to overcome challenges of size and heterogeneity, identify functional binding partners, and inform therapeutic target development.
    Keywords:  RNA structure; chemical probing; lncRNAs
    DOI:  https://doi.org/10.3390/cells15020105
  32. J Comput Biol. 2026 Jan;33(1): 134-167
    Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs.
    Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H Mathews, Liang Huang.
      RNA design aims to find a sequence that folds into a designated target structure under a specific RNA folding model, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to search for sequences capable of folding into a target structure under the default (Turner) RNA folding model, little attention has been given to the identification of undesignable structures. This work bridges the gap between RNA design and undesignability by introducing a series of theorems and algorithms aimed at identifying both undesignable structures and their causative local structural components, which we define as minimal undesignable motifs. We first present theorems that provide sufficient conditions for recognizing undesignability structures and propose efficient, theorem-guided algorithms to verify whether an RNA structure is undesignable. While such global undesignability sheds light on the limits of RNA design, identifying the specific motifs responsible for undesignability is critical for understanding RNA folding models and advancing design methodologies. To this end, we develop a new theoretical framework for motif undesignability and propose scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identified 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Last but not least, we demonstrate that our theory and algorithms can handle motifs with external loops-a critical advancement given the substantial impact of external loops on the quantity, diversity, and designability of RNA structure motifs.
    Keywords:  RNA design; designability; inverse folding; structural motif; undesignability
    DOI:  https://doi.org/10.1177/15578666251398551
  33. Stress Biol. 2026 Jan 27. 6(1): 9
    Molecular gatekeepers: eukaryotic translation factors decoding plant-virus dynamics for resistance engineering.
    Pankhuri Singhal, Shubham Saini, Oshin Saini, Ankit Bishnoi, Rashmi E R, Bharat Raj Meena, Jitender Singh, Kalenahalli Yogendra.
      Plant viruses are among the most significant biotic stressors, posing a severe threat to crop productivity and global food security. Their success largely depends on the exploitation of host eukaryotic translation factors (eTFs), including initiation factors (eIFs) and elongation factors (eEFs), which act as molecular gatekeepers of the viral life cycle. Key members such as eIF4E, eIF(iso)4E, eIF4G, eEF1A, and eEF1B have been identified as susceptibility factors that mediate viral translation, replication, and systemic movement. Viruses have co-evolved specialized proteins and RNA elements, including VPg and IRES structures, to hijack these host factors and circumvent plant defense barriers. This review synthesizes current understanding of the mechanistic roles of eTFs in virus-host dynamics and highlights strategies to mitigate viral stress. Approaches such as natural allele mining, induced mutagenesis, TILLING/EcoTILLING, RNA interference, and precise genome editing with CRISPR/Cas systems are explored as practical tools for reducing susceptibility. Targeted manipulation of eTFs offers a promising avenue to reprogram plants for resistance while maintaining essential cellular functions. By integrating molecular biology with applied strategies, we propose an eTF-centered framework for resistance breeding within a broader stress biology perspective. Future research combining functional genomics, synthetic biology, and breeding innovation will be pivotal in delivering broad-spectrum, durable, and environmentally sustainable resistance to plant viral stress.
    Keywords:  Eukaryotic translation elongation factors; Eukaryotic translation initiation factors; Movement; Replication; Virus translation
    DOI:  https://doi.org/10.1007/s44154-025-00273-2
  34. J Biol Chem. 2026 Jan 23. pii: S0021-9258(26)00066-9. [Epub ahead of print] 111196
    A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response.
    Han Gao, Rasangi Tennakoon, Felicia Pais Araújo, Jolie M Miller, Samuel Protais Nyandwi, Qingyu Shi, Juan Pablo Padilla-Martínez, Hui Peng, Haissi Cui.
      Aminoacyl-tRNA synthetases are key enzymes in protein synthesis, as they catalyze the attachment of amino acids to their designated, cognate tRNAs. As such, mutations in aminoacyl-tRNA synthetases are associated with severe diseases, such as neurodevelopmental disorders. Many of these mutations occur in the catalytically active site or tRNA binding domains, however, others can affect domains associated with multisynthetase complex formation. Here, we investigate a disease-causing mutation in the UNE-I domain of Isoleucyl-tRNA synthetase (IARS1, IleRS), which mediates IleRS interactions within the multisynthetase complex. Interestingly, levels of the resulting protein were severely reduced in comparison to wildtype IleRS. While bulk protein synthesis and cell proliferation were not affected, the integrated stress response signaling pathway was altered. This change was exacerbated in low glucose medium, suggesting that mutant cells could respond differently to cellular stress. Our study hints at a possible underlying disease mechanism, where catalytic activity might not be affected but instead complex formation and protein stability.
    Keywords:  aminoacyl-tRNA synthetase; integrated stress response; mulitsynthetase complex; neurodevelopmental disorder; tRNA
    DOI:  https://doi.org/10.1016/j.jbc.2026.111196
  35. Biotechnol Prog. 2026 Jan 30. e70109
    Enhancing mRNA vaccine production: Optimization of in vitro transcription for improved yield and purity.
    Kaixi Zhao, Jessica Raffaele, David A Holland, Kristen Feibelman, Kathleen Lengel, Jon Shanter, Emily Wen.
      In vitro transcription (IVT) is a powerful method to generate RNA which not only facilitates RNA research but also plays a key role in the development and manufacture of RNA-based vaccines. mRNA is produced via the IVT process with a DNA template that contains information for the target antigen. However, as many disease-causing viruses mutate quickly and the cost of raw materials is high for the IVT reaction, there is a need for a system to develop a cost-effective and efficient IVT process platform. In this paper, we showed how total nucleoside-5'-triphosphates (NTPs) input, Mg2+ concentration and NTP preparation methods can influence IVT reaction yield and purity level of the final RNA constructs of different lengths and sequences. We propose an IVT design that will result in high RNA yield, high RNA integrity and low double-stranded RNA (dsRNA) concentrations for multiple RNA sequences. The approach presented here could significantly contribute to the development of a cost-effective, easy-to-adopt IVT process platform for RNA manufacturing.
    Keywords:  T7 RNA polymerase; dsRNA; in vitro transcription (IVT); messenger RNA (mRNA)
    DOI:  https://doi.org/10.1002/btpr.70109
  36. Wiley Interdiscip Rev RNA. 2026 Jan-Feb;17(1):17(1): e70036
    MiRNA Stability and Degradation: Dynamic Regulators of Cellular Regulatory Networks.
    Ziqi Lin, Weijie Wen, Muhammad Irfan, Tielong Xu, Xianfeng Zhou.
      MicroRNAs (miRNAs) are pivotal post-transcriptional regulators of gene networks in development and disease, with their functional output critically dependent on dynamic turnover. Dysregulation of miRNA turnover disrupts signaling fidelity and contributes to pathologies such as cancer and infection. This review synthesizes recent advances in understanding miRNA turnover, focusing on key degradation pathways-including ZSWIM8-mediated target-directed miRNA decay (TDMD), TUT4/7-DIS3L2-driven uridylation, and nuclease cleavage-and how they integrate with stability factors such as AGO association, terminal modifications, and sequence features to orchestrate global miRNA abundance and health status. From these insights, critical unresolved questions are delineated, such as identifying nucleases responsible for degrading TDMD-liberated miRNAs and elucidating compartment-specific degradation mechanisms in physiological contexts like the gut lumen and circulation. Addressing these questions will facilitate innovative strategies for targeting miRNA stability within precision medicine. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
    Keywords:  Argonaute; RNA modification; TDMD; gene regulation; miRNA degradation; miRNA stability; signaling networks; therapeutic targeting
    DOI:  https://doi.org/10.1002/wrna.70036
  37. Front Immunol. 2025 ;16 1686490
    Catalogue of LPS-induced transcriptional changes across vertebrates identifies syntenically conserved human long non-coding RNAs that regulate the innate immune response.
    Marina R Hadjicharalambous, Richard R Ryder, Peter S Fenwick, Louise E Donnelly, Mark A Lindsay.
       Background: Innate immunity involves the detection and removal of pathogens and is an ancient physiological response observed across all living organisms. Long non-coding RNAs (lncRNAs) are a novel family of RNA transcripts that regulate the innate immune response. Although the identification of functional lncRNAs has been hindered by their poor evolutionary sequence conservation, it has been speculated that syntenic conservation (position relative to protein coding genes) might provide an alternative approach. To examine this hypothesis, we have produced a catalogue containing the LPS-induced transcriptional changes across 27 vertebrate species, which was employed to identify syntenically conserved and functional LPS-induced human lncRNAs.
    Methods: Transcriptomics was employed to compare differential lncRNA expression, as well as mRNA expression, between LPS-stimulated human cells and 26 vertebrate species, including 7 primates, 10 mammals, 4 birds and 5 fish. The function of manually annotated syntenically conserved human lncRNAs was examined in LPS-stimulated monocytic THP-1 cells using antisense mediated knockdown.
    Results: Sequencing data from 9 LPS-stimulated human cell studies was analysed to produce a high confidence catalogue of 1036 mRNAs and 71 lncRNAs that were differentially expressed in 4 or more cell types. Examination of the mRNAs involved in the LPS signaling pathway showed evolutionary conservation across human, primates, mammals, birds and fish, one notable exception being the absence of the LPS sensing complex (MD2/TLR4/CD14) in fish. To overcome poor sequence conservation amongst lncRNAs, we employed syntenic position to show that many of the 71 lncRNAs identified in humans were conserved and induced across vertebrates, the most common being MITA1 (IL7AS) and LINC02541. Knockdown studies showed that MITA1 (IL7AS) and LINC02541 negatively regulate the human LPS-induced inflammatory response in monocytic THP-1 cells. Significantly, we have identified regions/domains of MITA1 (IL7AS) and LINC02541 that are conserved across vertebrates.
    Conclusion: This report provides a comprehensive catalogue of the transcriptional response following activation of the LPS-induced innate immune response across 9 human cell types and 26 vertebrate species. We show that many of the LPS-induced human lncRNAs are syntenically conserved and induced across vertebrate species and that this can predict a functional role in the human innate immune response.
    Keywords:  LPS; evolution; innate immunity; long non-coding RNAs; transcriptomics; vertebrate
    DOI:  https://doi.org/10.3389/fimmu.2025.1686490
  38. Biol Open. 2026 Feb 15. pii: bio062148. [Epub ahead of print]15(2):
    Meeting Review on India EMBO lecture course on RNA-protein complexes: from molecular assembly to physiological functions and disease.
    Debleena Mukhopadhyay, Nasrin Banu Mohammad Faisal, Chloe Leray, Sania Sultana.
      The India EMBO lecture course 'RNA-protein complexes: from molecular assembly to physiological functions and disease' was held at The National Centre for Cell Science, Pune, India, from February 24 to 28, 2025. The major theme of the lecture series centred on the recent advances in RNA-protein interactions and their role in regulating complex assembly or condensation as well as cellular functions and plasticity. Additionally, the course highlighted the impact of dysregulated post-transcriptional processes in various diseases. Speakers from various biological disciplines presented their research on both the fundamental architecture of RNA and protein complexes and their contributions to higher-order cellular functions. The course also featured flash talks and poster presentations selected from abstract submissions, alongside special methodological workshops on omics and phase separation. This Meeting Review reflects on the event's key discussions, drawing attention to the overarching themes and main conclusions.
    Keywords:  India EMBO lecture course; Meeting report; RBPs; RNA and RBPs
    DOI:  https://doi.org/10.1242/bio.062148
  39. Exp Biol Med (Maywood). 2025 ;250 10784
    Beginning of a new era of synthetic messenger RNA therapeutics: Comprehensive insights on mRNA drug design, development and applications.
    Saumya Nishanga Heendeniya, Suxiang Chen, Saadia Bhatti, Qurat Ul Ain Zahra, Kamal Rahimizadeh, Bal Hari Poudel, Stephen D Wilton, Rakesh N Veedu.
      Messenger RNA (mRNA) therapeutics have significantly transformed contemporary medicine, particularly through their role as the active component in the SARS-CoV-2 vaccine. This remarkable achievement is the culmination of extensive research conducted over many years by scientists. The widespread administration of the COVID-19 vaccine has further accelerated research into the precise therapeutic potential of mRNA technologies. Since mRNA doesn't integrate with the host genome, the safety and versatility of mRNA-based therapeutics make them an iconic candidate in targeted therapies. Due to a surge in innovation efforts, biomodification of the molecular signatures of mRNAs like the 5'cap, untranslated regions (UTRs), and the poly(A) tail are being developed to increase translation efficacy. Recent advancements in chemical modifications, codon optimization techniques, and targeted delivery methods have significantly enhanced the stability of synthetic mRNAs while concurrently reducing their immunogenicity. Various mRNA manufacturing and synthesizing methods are investigated in this review, focusing on their scalability and limitations. mRNA therapeutic strategies can be divided into protein replacement, immune modulation, and cellular modulation. This review explores mRNA's molecular landscape and comprehensive utility, including applications in both clinical trials and commercial sectors.
    Keywords:  mRNA delivery; mRNA design and synthesis; mRNA patents and clinical trials; mRNA therapeutics; mRNA vaccine; protein replacement therapy
    DOI:  https://doi.org/10.3389/ebm.2025.10784
  40. Viruses. 2026 Jan 13. pii: 105. [Epub ahead of print]18(1):
    Mechanism of SARS-CoV-2 Nucleocapsid Protein Phosphorylation-Induced Functional Switch.
    Megan S Sullivan, Michael Morse, Kaylee Grabarkewitz, Dina Bayachou, Ioulia Rouzina, Vicki Wysocki, Mark C Williams, Karin Musier-Forsyth.
      The SARS-CoV-2 nucleocapsid protein (Np) is essential for viral RNA replication and genomic RNA packaging. Phosphorylation of Np within its central Ser-Arg-rich (SRR) linker is proposed to modulate these functions. To gain mechanistic insights into these distinct roles, we performed in vitro biophysical and biochemical studies using recombinantly expressed ancestral Np and phosphomimetic SRR variants. Limited-proteolysis showed minor cleavage differences between wild-type (WT) and phosphomimetic Np, but no major structure or stability changes in the N- and C-terminal domains were observed by circular dichroism spectroscopy and differential scanning fluorimetry, respectively. Mass photometry (MP) revealed that WT Np dimerized more readily than phosphomimetic variants. Crosslinking-MP showed that WT Np formed discrete complexes on viral 5' UTR stem-loop (SL) 5 RNA, whereas phosphomimetic Np assembled preferentially on SL1-4. WT Np bound non-specifically to all RNAs tested primarily via hydrophobic interactions, whereas phosphomimetic Np showed selectivity for SARS-CoV-2-derived RNAs despite binding more electrostatically. A major difference was observed in the binding kinetics; WT Np compacted and irreversibly bound single-stranded DNA, whereas phosphomimetic Np displayed reduced compaction and fast on/off binding kinetics. These mechanistic insights support a model where phosphorylated Np functions in RNA replication and chaperoning, while non-phosphorylated Np facilitates genomic RNA packaging. The findings also help to explain infectivity differences and clinical outcomes associated with SRR linker variants.
    Keywords:  RNA binding; RNA chaperone; RNA packaging; SARS-CoV-2; coronavirus; nucleocapsid; phosphorylation
    DOI:  https://doi.org/10.3390/v18010105
  41. Front Cell Infect Microbiol. 2025 ;15 1731808
    The DEAD-box RNA helicase eIF4A is a crucial factor for stem-cell activity and reproduction of the parasite Schistosoma mansoni.
    Sophie Welsch, Oliver Puckelwaldt, Sagar Ajmera, Francesca Magari, Simone Haeberlein, Arnold Grünweller, Christoph G Grevelding.
       Introduction: The parasite Schistosoma mansoni has a unique reproductive biology, because female maturation depends on constant pairing with a male. Paired females produce each up to 300 eggs per day, which are the pathogenic factors of schistosomiasis, a neglected tropical disease that affects > 240 million people worldwide. Due to the importance of egg production for life-cycle maintenance and pathology, molecular mechanisms controlling schistosome reproduction are in the focus of research. Among the candidates involved in regulating the reproductive biology of this parasite are DEAD-box RNA helicases. These enzymes are associated with various cellular processes, including ribosome biogenesis and post-transcriptional regulation. In platyhelminths, helicases are largely unexplored. One member of the DEAD-box helicase family is the eukaryotic translation initiation factor 4A (eIF4A), which unwinds stable RNA structures in the 5'-untranslated region of selected mRNAs.
    Objectives: We functionally characterized two eIF4A isoforms of S. mansoni (SmeIF4A-a and SmeIF4A-b), which are potentially involved in translation initiation like their human orthologs, to evaluate their importance for parasite vitality and reproduction.
    Methodologies/findings: Transcripts of both SmeIF4A isoforms were localized in female ovaries as shown by whole mount in situ hybridization. RNA-interference (RNAi) experiments revealed a decisive role of SmeIF4A-a in gonad maintenance and egg production. Stem-cell proliferation assays and confocal laser scanning microscopy uncovered the loss of proliferation activity in germinal and somatic stem cells after Smeif4a-a RNAi. No distinct function was found for SmeIF4A-b.
    Conclusion: Our results suggest that SmeIF4A-a is a key factor in stem-cell proliferation and gonad maintenance, and thus also in egg production.
    Keywords:  RNA helicase; Schistosoma mansoni; eIF4A; ovary; reproduction; stem cell; testis
    DOI:  https://doi.org/10.3389/fcimb.2025.1731808
  42. Biomolecules. 2025 Dec 24. pii: 30. [Epub ahead of print]16(1):
    The RNA-Binding Protein KSRP Is a Negative Regulator of Innate Immunity.
    Vanessa Bolduan, Andrea Pautz, Matthias Bros.
      KSRP (KH-type splicing regulatory protein) has emerged as a pivotal regulator of gene expression at multiple levels, acting as a transcription and splicing factor in the nucleus, and mediating AU-rich element (ARE)-dependent mRNA decay, translational silencing, and microRNA (miRNA) maturation in the cytoplasm. We and others have shown that KSRP acts as a regulator of immune responses, e.g., by dampening the expression of proinflammatory cytokines such as TNF-α, IL-6, IL-8, but also of NOS2, and facilitating the maturation of regulatory miRNAs, including let-7a, miR-129, and miR-155. This review aims to present current knowledge on the regulation of KSRP activity as conferred by miRNAs, phosphorylation, ubiquitination, SUMOylation, and interactions with long non-coding RNAs to enable dynamic responses towards inflammatory stimuli, and the effects of KSRP on innate immune reactions. Here, KSRP acts as an inhibitor by attenuating RIG-I-mediated antiviral signaling, cytokine production, and phagocytosis. In vivo, KSRP deficiency reduced arthritis severity but heightened inflammatory responses in sepsis and enhanced pathogen clearance in invasive pulmonary aspergillosis. These findings position KSRP as a dual regulator that limits tissue damage while constraining antimicrobial immunity. As a perspective, modulation of KSRP activity by applying pharmacological inhibitors may provide strategies to either suppress hyperinflammation in autoimmunity and sepsis or enhance host defense in immunocompromised states.
    Keywords:  KSRP; RNA-binding protein; innate immunity
    DOI:  https://doi.org/10.3390/biom16010030
  43. Biogerontology. 2026 Jan 30. 27(1): 43
    The role of circular RNAs in mediating the protective effects of exercise against muscle degeneration and aging.
    Bo Li, Ling Chen, Yiping Su, Junyan Meng, Zhanguo Su.
      A newly identified specific category of non-coding RNA (ncRNA), circRNAs, is drawing interest for their role in controlling several biological processes including muscle regeneration, aging, and adaptation to physical activity. Unlike linear RNAs, circRNAs are very stable and can have long-lasting regulatory impact since they create a covalently closed loop structure. Emerging evidence indicates that circRNAs play a pivotal role in skeletal muscle biology by regulating myogenesis, satellite cell activation, protein synthesis, and cellular senescence-processes significantly influenced by aging. These molecules are crucial for muscle function and regeneration, acting as microRNA sponges, interacting with RNA-binding proteins, and modulating gene expression and translation. Exercise-especially resistance and endurance training-has been shown to change circRNA expression in skeletal muscle, therefore possibly reducing age-related muscle loss and improving regenerative capacity. Though encouraging, much of the circRNA in muscle biology research is still in its early stages, with few functional studies and varying outcomes across various species and exercise models. Moreover, the exact ways circRNAs affect muscular adaptation to exercise and stop aging-related degeneration are still not completely known. This review addresses the existing knowledge gaps regarding the potential therapeutic applications of circRNAs in combating muscle degeneration and sarcopenia, as well as their role in muscle health and aging.
    Keywords:  Aging; CircRNA; Exercise; Muscle
    DOI:  https://doi.org/10.1007/s10522-026-10390-8
  44. Prog Mol Biol Transl Sci. 2026 ;pii: S1877-1173(25)00162-0. [Epub ahead of print]218 49-64
    Development of cell-free transcription translation.
    Ajay Kumar, Juveriya Israr, Shabroz Alam.
      Cell-free transcription-translation (TXTL) systems provide a robust platform for in vitro protein synthesis, transforming molecular biology, synthetic biology, and biotechnology by replicating natural protein synthesis outside of living cells with exceptional control and flexibility. Initially developed by Nirenberg and Matthaei in the 1960s using E. coli extracts, these systems have undergone substantial evolution, and now incorporate extracts from bacteria, yeast, and eukaryotes to construct comprehensive TXTL platforms. A cell-free extract comprises essential components, such as ribosomes, RNA polymerase, and tRNAs, enabling protein synthesis directed by DNA templates through transcription and translation. TXTL systems, offer distinct advantages, including rapid, efficient, and accurate synthesis of natural and non-natural proteins, enhanced chemical resistance, and streamlined labeling-often surpassing cell-based techniques. Their extensive application span synthetic biology and biopharmaceutical production. Despite this promise, challanges remain, including high cost, limited protein yield, lack of complex post-translational modifications, and extract instability. Future efforts will focus on overcoming these challenges by reducing costs, improving yields, expanding post-translational modification capabilities, enhancing stability, and developing continuous-flow systems. Ultimately, cell-free systems are poised to deepen our understanding of biological processes and drive the development of innovative biotechnological tools.
    Keywords:  Cell-free extract; Cell-free transcription-translation; Protein engineering; Synthetic biology; in vitro protein synthesis
    DOI:  https://doi.org/10.1016/bs.pmbts.2025.08.003
  45. Genes (Basel). 2026 Jan 09. pii: 78. [Epub ahead of print]17(1):
    Interdependent Regulation of Alternative Splicing by Serine/Arginine-Rich and Heterogeneous Nuclear Ribonucleoprotein Splicing Factors.
    Megan E Holmes, Klemens J Hertel.
       BACKGROUND: Alternative pre-mRNA splicing is a combinatorial process involving serine/arginine-rich (SR) and heterogeneous nuclear ribonucleoprotein (hnRNP) splicing factors. These proteins can silence or enhance splicing based on their expression levels and binding positions.
    OBJECTIVES: To better understand the combinatorial and interdependent regulation between SR and hnRNP splicing factors during alternative splicing.
    METHODS: Computational analyses were performed using cell knockdown and binding datasets from available databases.
    RESULTS: Analyses of differential splicing data for 9 SR proteins and 21 hnRNP knockdowns revealed statistically significant interdependent regulation among several RNA-binding protein (RBP) combinations, albeit at different levels. Neither SR proteins nor hnRNPs showed strong preferences for collaborating with specific RBP classes in mediating exon inclusion. While SRSF3, hnRNPK, hnRNPC, and hnRNPL stand out as major influencers of alternative splicing, they do so predominantly independent of other RBPs. Minor influencers of alternative splicing, such as hnRNPDL and hnRNPR, predominantly regulate exon inclusion in concert with other RBPs, indicating that exon inclusion can be mediated by both single and multiple RBPs. Interestingly, the higher the number of RBPs that regulate the inclusion of an exon, the more variable exon inclusion preferences become. Interdependently regulated exons are more modular and can be characterized by weaker splice sites compared to their independently regulated counterparts. A comparison of RBP interdependence between HeLa and other cell lines provides a framework that explains cell-type-specific alternative splicing.
    CONCLUSIONS: Our study highlights the importance of the interdependent regulation of alternative exons and identifies characteristics of interdependently regulated exons that differ from independently regulated exons.
    Keywords:  SR proteins; alternative splicing; exon inclusion; hnRNPs
    DOI:  https://doi.org/10.3390/genes17010078
  46. Genes Cells. 2026 Mar;31(2): e70075
    Carboxyl-Terminal Region of the Maturation Protein of RNA Coliphage Qβ Mediates Host Attachment, Virion Formation, and Cell Lysis.
    Masayuki Kajitani, Noriko Hakoshima, Yoshio Inokuchi.
      The single-stranded RNA coliphage Qβ infects Escherichia coli by attaching to the host F-pilus and entering the host cells. The maturation protein (A2) within the virion is thought to mediate these events in the host cell. In this study, we investigated the functional domains of A2 by isolating infectious and noninfectious particles produced in cells harboring Qβ cDNAs with mutations in the distal region of the A2 gene. Noninfectious particles with capsids lacking A2 failed to adsorb to the F-pilus, and A2 protein missing the C-terminal region was not incorporated into the capsid. Several A2 mutants also exhibited reduced cell lysis. These findings demonstrate that the conserved C-terminal region of A2 is involved in several functions, including host binding, complete virion formation, and cell lysis by A2. This study provides a foundation for elucidating the mechanism by which the viral genome enters the host.
    Keywords:  Qβ phage; adsorption; cell lysis; maturation protein; virion formation
    DOI:  https://doi.org/10.1111/gtc.70075
  47. Anim Genet. 2026 Feb;57(1): e70073
    Assessing the effect of bovine MSTN variants on pre-mRNA splicing.
    Nicolas Gaiani, Dominique Rocha, Arnaud Boulling.
      The myostatin protein is a potent negative regulator of skeletal muscle growth encoded by the MSTN gene. MSTN loss-of-function variants lead to a particular cattle phenotype characterized by an increase in skeletal muscle mass, known as "double muscling" or "double muscled". However, most of the MSTN causal variants that have been linked to this phenotype lack experimental validation. This is the case, for example, for the five missense MSTN variants reported to be causal according to the Online Mendelian Inheritance in Animals. RNA splicing plays a major role in regulating gene expression; therefore, exploring the effects of variants on RNA splicing may provide relevant information on their functional impact. Here, we have set up a full-length gene assay (FLGA) to functionally assess MSTN splicing variants, and we have used it to test the five missense variants plus a well-described deep intronic splicing variant as a positive control. We also evaluated the performances of SpliceAI and Pangolin, two deep learning-based splice predictors, to identify potential splicing effects of these six variants. Our FLGA system performed well and showed that none of the missense variants has an effect on splicing, unlike the positive control. For each variant, splicing program predictions were perfectly concordant with the effect observed in the FLGA. We have produced a relevant and powerful assay to analyze MSTN splicing variants in cattle. SpliceAI and Pangolin may be efficiently used to screen large datasets of MSTN variants and sort the best candidates prior to experimental validation using an FLGA.
    Keywords:  functional analysis; splicing prediction; splicing variant
    DOI:  https://doi.org/10.1002/age.70073
  48. Nat Commun. 2026 Jan 27. 17(1): 1064
    Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.
    Wenqian Chen, Gabriel C Lander, Jie Yang.
      The human ClpXP complex (hClpXP) orchestrates mitochondrial protein quality control through targeted degradation of misfolded and unnecessary proteins. While bacterial ClpXP systems are well characterized, the assembly and regulation of human ClpXP remain poorly understood. In this study, we elucidate the complete assembly pathway of hClpXP through high-resolution cryo-electron microscopy (cryo-EM) structures. Our findings confirm that hClpP exists as a single-ring heptamer in isolation and reveal a previously undocumented initial assembly complex in which hexameric hClpX first engages with heptameric hClpP. We further demonstrate how this interaction drives substantial conformational rearrangements that facilitate the formation of tetradecameric hClpP within the fully assembled complex. Notably, we characterize a unique eukaryotic sequence in hClpX, termed the E-loop, which plays a critical role in stabilizing hexamer assembly and maintaining ATPase activity. Additionally, we show that peptide binding at the hClpP active site triggers further structural changes essential for achieving full proteolytic competence. Together, these structures provide unprecedented mechanistic insights into the stepwise assembly and activation of hClpXP, significantly advancing our understanding of this essential mitochondrial protein degradation machinery.
    DOI:  https://doi.org/10.1038/s41467-025-67010-1
  49. Nucleic Acids Res. 2026 Jan 22. pii: gkag027. [Epub ahead of print]54(3):
    NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes.
    Marie B A Peters, Richard Lindqvist, Priyanka Madhu, Richard Lundmark, Ylva Ivarsson, Anna K Överby.
      The nuclear pore complex (NPC) is composed of multiple nucleoporins (NUPs) and enables the exchange of RNA and proteins between the nucleus and cytoplasm. NUP98 is one of the major components of the NPC, being involved in the RNA export pathway by interacting with several transport factors. Previous studies have suggested both proviral and antiviral functions of NUP98 in viral infection, yet little is known about its function in orthoflavivirus infection. In this study we show that NUP98 is a proviral cellular protein that is recruited to the cytoplasm during orthoflavivirus infection. We observe that NUP98 is found specifically in the vicinity of the replication vesicles during infections with tick-borne encephalitis virus, Japanese encephalitis virus, and yellow fever virus. Furthermore, using surface plasmon resonance, cross-link immunoprecipitation, and cross-link immunoprecipitation-sequencing we observe that the C-terminal domain of NUP98 directly interacts with a conserved site of the viral RNA (vRNA) in the E coding region promoting viral replication. We identified a peptide that binds to NUP98 that is antivirally active against several orthoflaviviruses by outcompeting the binding between NUP98 and vRNA, making NUP98 an attractive target for antiviral development.
    DOI:  https://doi.org/10.1093/nar/gkag027
  50. Signal Transduct Target Ther. 2026 Jan 29. 11(1): 29
    Deciphering the regulatory landscape of enhancer RNAs in health and disease.
    Qian Wang, Peter Ten Dijke, Chuannan Fan.
      Enhancers are distal cis-regulatory elements that orchestrate spatiotemporal gene expression patterns in response to developmental cues and environmental stimuli. Genetic and epigenetic alterations in enhancers are associated with the initiation and progression of human diseases, including cancers. Over the past few decades, accumulating evidence has revealed that a class of nascent RNA transcripts, known as enhancer RNAs (eRNAs), is broadly transcribed from active enhancers. These eRNA species contribute to complex and dynamic gene regulatory networks under both physiological and pathological conditions through diverse mechanisms. Notably, dysregulated eRNA expression has been reported across various cancer types and is often correlated with patient survival outcomes. Consequently, eRNAs are emerging as promising biomarkers and therapeutic targets for cancer treatment. This review provides a comprehensive summary of the current understanding of eRNAs and their mechanisms of action in gene regulation. We discuss the critical roles of eRNAs in both health and disease and highlight their diagnostic and prognostic value, as well as their therapeutic potential in cancer. Additionally, we review current strategies for targeting RNA transcripts, including eRNAs, and discuss the major challenges in developing eRNA-targeted therapies. Finally, we propose future directions for advancing eRNA-based interventions in the treatment of human diseases, including cancer.
    DOI:  https://doi.org/10.1038/s41392-025-02436-z
  51. Biomolecules. 2025 Dec 19. pii: 5. [Epub ahead of print]16(1):
    RNAa-Mediated Gene Activation in the Regulation of Stem Cell Fate.
    Hyohi Lee, Jiin Moon, Seung-Kyoon Kim.
      Stem cell fate is governed by complex transcriptional networks and dynamic chromatin architectures, with RNA molecules acting as critical regulators. Traditionally, small RNAs have been associated with gene silencing; however, growing evidence reveals that certain RNA species can also activate transcription, a phenomenon termed RNA activation (RNAa). This evolutionarily conserved mechanism functions through both synthetic small activating RNAs (saRNAs) and endogenous RNA molecules, including promoter-targeting microRNAs, small modulatory double-stranded RNAs, and circular RNAs. By modulating chromatin accessibility and engaging the transcriptional machinery, these RNAs orchestrate gene expression programs that control pluripotency maintenance and lineage-specific differentiation in stem cells. This review integrates emerging mechanistic insights and functional evidence to provide a comprehensive perspective on RNAa-mediated gene activation in stem cell biology and highlights its potential as a precise tool for controlling cell fate through epigenetic modulation.
    Keywords:  RNA activation (RNAa); differentiation; endogenous RNA activator; epigenetic regulation; small activating RNA (saRNA); stem cell pluripotency
    DOI:  https://doi.org/10.3390/biom16010005
  52. Iran Biomed J. 2025 11 01. 29(6): 397-404
    Transcriptional Control of PI3K/AKT/mTOR by piRNA-651 in Breast Carcinoma.
    Sena Köstü, Baturalp Bakırcı, Ece Bilge Şimşek, Defne Dumanlı, Ahmetcan Çelik, Alara Kaya, Damla Kolcuoğlu, Ertuğrul Çolak, Çağrı Öner.
       Background: Breast cancer (BC) is among the most prevalent malignancies in women worldwide, yet early diagnosis is associated with a high survival rate. The proliferation of BC is linked to the overexpression of genes within the PI3K/AKT/mTOR signaling pathway. piR-651 has been reported to be effective in the proliferation and metastasis of BC. This research sought to evaluate the impact of piR-651 inhibition on the PI3K/AKT/mTOR pathway in HUVEC, MCF-7, and MDA-MB-231 cells.
    Methods: Anti-piR-651 and non-target sequences were introduced into HUVEC, MCF-7, and MDA-MB-231 BC cells by lipofectamine transfection. After 48 hours, total RNA was extracted, and qRT-PCR assessed the gene expression of PI3K, AKT, and mTOR.
    Results: Anti-piR-651 treatment significantly increased PI3K, AKT, and mTOR gene expression in HUVECs (p < 0.001). In contrast, PI3K and mTOR expression decreased in MCF-7 and MDA-MB-231 cells (p < 0.001), while AKT expression remained unchanged in MDA-MB-231 cells (p > 0.05). Correlations between these genes varied by cell type, with significant associations observed at p < 0.05 or p < 0.01, depending on the group.
    Conclusion: piR-651 inhibition causes AKT to behave independently of PI3K and mTOR, particularly in MCF-7 cells, suggesting limited gene therapy potential for estrogen receptor-positive BC. Preliminary data indicate that piR-651 inhibition may reduce BC cell proliferation through effects on PI3K and mTOR.
    Keywords:  Epigenetics; Piwi-interacting RNA; Triple negative breast neoplasms
    DOI:  https://doi.org/10.61882/ibj.5229
  53. Curr Issues Mol Biol. 2026 Jan 22. pii: 123. [Epub ahead of print]48(1):
    Spermatogenesis Beyond DNA: Integrated RNA Control of the Epitranscriptome and Three-Dimensional Genome Architecture.
    Aris Kaltsas, Maria-Anna Kyrgiafini, Zissis Mamuris, Michael Chrisofos, Nikolaos Sofikitis.
      Spermatogenesis is a tightly coordinated differentiation program that sustains male fertility while transmitting genetic and epigenetic information to the next generation. This review consolidates mechanistic evidence showing how RNA-centered regulation integrates with the epitranscriptome and three-dimensional (3D) genome architecture to orchestrate germ-cell fate transitions from spermatogonial stem cells through meiosis and spermiogenesis. Recent literature is critically surveyed and synthesized, with particular emphasis on human and primate data and on stage-resolved maps generated by single-cell and multi-omics technologies. Collectively, available studies support a layered regulatory model in which RNA-binding proteins and RNA modifications coordinate transcript processing, storage, translation, and decay; small and long noncoding RNAs shape post-transcriptional programs and transposon defense; and dynamic chromatin remodeling and 3D reconfiguration align transcriptional competence with recombination, sex-chromosome silencing, and genome packaging. Convergent nodes implicated in spermatogenic failure are highlighted, including defects in RNA metabolism, piRNA pathway integrity, epigenetic reprogramming, and nuclear architecture, and the potential of these frameworks to refine molecular phenotyping in male infertility is discussed. Finally, key gaps and priorities for causal testing in spatially informed, stage-specific experimental systems are outlined.
    Keywords:  3D genome architecture; RNA-binding proteins; chromatin remodeling; epitranscriptome; male infertility; noncoding RNAs; piRNA; single-cell multi-omics; spermatogenesis
    DOI:  https://doi.org/10.3390/cimb48010123
  54. J Biochem Mol Toxicol. 2026 Feb;40(2): e70700
    Multi-Omics and Functional Analyses Identify let-7b-3p as a Negative Regulator of EMT in Lung Adenocarcinoma.
    Donghong Zhang, Mengyao Wang, Li Li, Haitao Wei.
      Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer (NSCLC), and its malignant progression involves complex molecular mechanisms. While microRNAs (miRNAs) play a crucial regulatory role in LUAD development, their specific mechanisms remain unclear. This study used bioinformatics analysis to identify key miRNA-mRNA interaction axes in LUAD, revealing that let-7b-3p was significantly downregulated. Functional analyses demonstrated that let-7b-3p regulates LUAD cell proliferation, migration, and invasion by targeting High Mobility Group AT-Hook 2 (HMGA2) and Lin-28 Homolog A (LIN28A). Dual-luciferase reporter assays confirmed that let-7b-3p directly binds to HMGA2 and LIN28A, suppressing their expression. Furthermore, Western blot and immunofluorescence (IF) assays showed that let-7b-3p inhibits the Wnt/TGF-β signaling pathway and epithelial-mesenchymal transition (EMT) via the HMGA2-LIN28A axis. In vivo, experiments using a nude mouse model further demonstrated that let-7b-3p overexpression significantly suppressed LUAD tumor growth and lung metastasis while reducing the expression of EMT-related molecules. Importantly, this study is the first to reveal the inhibitory role of let-7b-3p in LUAD through the HMGA2-LIN28A axis in regulating the Wnt/TGF-β signaling pathway and EMT. These findings highlight the originality of this work and underscore the potential clinical translational value of targeting let-7b-3p or the HMGA2-LIN28A axis as novel therapeutic strategies for LUAD.
    Keywords:  High Mobility Group AT‐Hook 2; Lin‐28 Homolog A; TGF‐β signaling pathway; Wnt signaling pathway; let‐7b‐3p; lung adenocarcinoma
    DOI:  https://doi.org/10.1002/jbt.70700
  55. Nucleic Acids Res. 2026 Jan 22. pii: gkag055. [Epub ahead of print]54(3):
    Cleavage of host tRNAs by mycoplasma membrane-associated nuclease.
    Yasutoshi Akiyama, Yoshika Takenaka, Nana Kunii, Katsuki Aoyama, Asuka Yamada, Takaaki Abe, Yoshihisa Tomioka, Pavel Ivanov.
      Mycoplasmas are pathogens causing infectious diseases in various animals, including humans. They are also common contaminants of cell culture. Although it is suggested that mycoplasmas alter nucleic acid metabolism of host cells through their nucleases, the actual impact of the nucleases on host cell RNAs is unknown. Here we report that Mycoplasma hyorhinis, a common laboratory contaminant species, promotes cleavage of host cell transfer RNAs (tRNAs) through a membrane-associated nuclease. When infected by M. hyorhinis, scraping of cells as well as cell lysis induced a marked cleavage of host RNAs. Further analysis suggested that the protein encoded by the membrane nuclease A (mnuA) gene is responsible for the host RNA cleavage. MnuA protein demonstrates DNase and RNase activities dependent on Ca2+/Mg2+ ions. Purified MnuA protein acts as an atypical sugar non-specific nuclease: while it possesses broad DNase activities, its RNase activity is highly specific to tRNAs in live cells. Mutational analysis shows that the nuclease activity is mediated by a domain which is highly similar to DNase I. Furthermore, M. hyorhinis promoted cleavage of host tRNAs under amino acid deprivation, suggesting that M. hyorhinis infection may alter RNA metabolism in host cells under certain physiological stress. As mnuA genes are conserved in various mycoplasma species, our findings provide novel insights into the effects of MnuA nucleases on host cell RNAs under mycoplasma infection.
    DOI:  https://doi.org/10.1093/nar/gkag055
  56. Front Genet. 2025 ;16 1756452
    Ribosome plasticity in glioblastoma: a multi-omics framework for future investigation.
    Dario Benelli, Christian Barbato, Carlo Cogoni.
      Glioblastoma (GBM) remains a challenging tumour to mechanistically dissect, in part because of its capacity to adapt to hypoxia, metabolic imbalance and therapeutic pressure. Across cancer biology more broadly, attention has increasingly turned to ribosomal proteins (RPs). Although long regarded as stable structural components of the ribosome, several RPs show variation across tumour regions, stress states and differentiation trajectories. In some cancers, specific RPs have been mechanistically linked to selective translation or cell-state transitions, whereas in others the evidence remains largely associative. Overall, current observations leave open the question of whether RP variation reflects active regulatory roles or instead mirrors the broader physiological pressures experienced by malignant cells. In this mini review, we summarise what multi-omics approaches-including transcriptomics, proteomics and translatomics-currently reveal about RP regulation in GBM. Rather than making firm causal claims, we outline the main interpretations proposed so far, the uncertainties that complicate them and the conceptual gaps that keep the field open. Our aim is to provide a balanced and cautious overview that may help frame future work on how ribosomal components and the translational machinery could contribute to GBM plasticity.
    Keywords:  glioblastoma; multi-omics; ribosomal proteins; ribosome biogenesis; ribosome heterogeneity; translational regulation; tumour plasticity
    DOI:  https://doi.org/10.3389/fgene.2025.1756452
  57. Cancers (Basel). 2026 Jan 14. pii: 260. [Epub ahead of print]18(2):
    Stress Granule-Driven Resistance in Cancer: Mechanisms and Emerging Strategies.
    Abirami Rajendiran, Gayathri Ramakrishnan, Takbum Ohn, Aravinth Kumar Jayabalan.
      Stress granules (SGs) are dynamic, membraneless organelles that form in response to stress and play pivotal roles in translational control, RNA metabolism, and cell survival. In cancer, SGs are increasingly recognized as central mediators of therapy resistance, enabling malignant cells to evade apoptosis, reprogram metabolism, and modulate immune responses. Understanding the mechanistic and clinical insights into SG kinetics in healthy versus cancer cells holds significant potential for targeting them in precision oncology. This review integrates current knowledge on how chemotherapeutic agents, oncogenic signaling pathways, and tumor microenvironmental stressors promote SG formation, as well as evidence of altered SG kinetics across tumor types. We further highlight how the upregulation of SG components within the tumor microenvironment shapes cancer cell behavior and adaptability, and how crosstalk between SGs and other biomolecular condensates could contribute to resistance. Finally, we discuss emerging therapeutic strategies targeting SGs, including kinase inhibitors and modulators of SG dynamics, and propose that SGs represent tractable vulnerabilities in precision oncology. By bridging mechanistic insights with clinical implications, this review positions SGs as a promising frontier in overcoming cancer therapy resistance.
    Keywords:  biomolecular condensates; cell survival; drug resistance; metastasis; stress granules; stress response
    DOI:  https://doi.org/10.3390/cancers18020260
  58. Front Cell Dev Biol. 2025 ;13 1686025
    Regulation of RNA methylation linked to drug resistance in gastric cancer.
    Zihan Yang, Yanpin Ma, Ziyi Xu, Hongyan Liu, Xinyu Gu, Jiachun Sun.
      In global terms, gastric cancer (GC) represents one of the most commonly occurring malignancies. It is positioned as the fifth most frequent cancer in terms of incidence and stands as the third primary contributor to cancer-related mortality. As per the latest global cancer report from 2020, there were approximately 1.1 million new cases of GC and about 800,000 new deaths in that year, making up 5.6% of new cases and 7.7% of deaths related to cancer. In recent years, as bioinformatics technology and high-throughput sequencing have advanced rapidly, our comprehension of the genetic and epigenetic alterations associated with GC has also progressed considerably. Among these alterations, RNA methylation, as one of the common modifications within RNA molecules, has been regarded as a key factor in the development and progression of GC. Research indicates that the dysregulation of RNA methylation influences GC development through various pathways. Therefore, understanding the pathogenic mechanisms of RNA methylation in GC is of great significance for the diagnosis, treatment and prognostic assessment of affected patients. In this review, we discuss various types of RNA methylation, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), and N1-methyladenosine (m1A), and how they might affect the mechanism of GC. We also look at how RNA methylation impacts chemotherapy, targeted therapy, and immune resistance in gastric cancer, as well as the potential uses of RNA methylation in treating gastric cancer, setting the stage for more detailed research on RNA methylation in gastric cancer.
    Keywords:  GC; RNA methylation; drug resistance; epigenetic modification; immunotherapy
    DOI:  https://doi.org/10.3389/fcell.2025.1686025
  59. Int J Biol Macromol. 2026 Jan 27. pii: S0141-8130(26)00502-7. [Epub ahead of print] 150576
    Aptamer-mediated targeted approach to disrupt oncogenic HSP90α.
    Jaskirat Kaur, Sakshi Nautiyal, Ipsita Roy.
      Among the cytosolic isoforms of HSP90, HSP90α (the inducible isoform) has been observed to be significantly upregulated in both cancer and stress conditions. HSP90α client proteins are required for the proliferation of cancer cells. The inability of HSP90 inhibitors to recognize and bind to specific isoforms of the protein is a major reason for their failure to reach the clinic. In this work, RNA aptamers were selected from a diverse, randomized oligonucleotide library. These were able to bind to HSP90α with significantly higher affinity than HSP90β and inhibit ATPase activity. The two isoforms differ in just two amino acids in their ATP-binding domains. The presence of the aptamers led to decrease in migration of MCF7 breast cancer cells. Significant reduction in the expression of an HSP90α- but not HSP90β-specific client protein was also observed. Aptamers showed significant lethality only on cancer cells, but not on healthy cells. Cell death occurred by apoptosis. Unlike traditional anti-cancer drugs which are inherently toxic and cannot be administered regularly, aptamers offer a promising alternative for prevention of metastasis.
    Keywords:  Cancer cell migration; Cancer cell proliferation; HSP90 isoforms; Protein specificity; RNA aptamers
    DOI:  https://doi.org/10.1016/j.ijbiomac.2026.150576
  60. Annu Rev Plant Biol. 2026 Jan 29.
    Extracellular Vesicles and Extracellular RNAs in Plant-Microbe Interactions.
    Benjamin L Koch, Meenu Singla-Rastogi, Roger W Innes.
      Plants and microbes exchange macromolecules such as RNA and proteins. How this exchange is accomplished is poorly understood, but extracellular vesicles (EVs) have been proposed as likely vehicles. Here, we review recent work on the biogenesis and functions of plant EVs and the current evidence in support of and against their role in cross-kingdom RNA interference. Plant EVs, like EVs from other kingdoms of life, are released in part by the fusion of multivesicular bodies with the plasma membrane, a complex and conserved mechanism involving lipid-modifying proteins, the exocyst complex, and Rab GTPases. Though some plant EV subpopulations are involved in immunity, it appears unlikely that plant EVs contribute to cross-kingdom RNA interference. Recent work has shown that plants secrete extravesicular RNA, including small RNAs and long noncoding RNAs, into the leaf apoplast and onto leaf surfaces, while very little RNA is found inside of EVs. We propose that these free extracellular RNAs play a central role in maintaining a healthy leaf microbiome.
    DOI:  https://doi.org/10.1146/annurev-arplant-063025-110704
  61. Front Endocrinol (Lausanne). 2025 ;16 1705600
    The latest progression of N6-methyladenosine (m6A) RNA modification in diabetes mellitus and diabetic complications.
    Guangyang Yin, Jiajing Hong, Guohui Shan, Cuizhu Xu, Bailin Li, Dongyu Yang.
      The increasing global prevalence of diabetes mellitus and its complications continues to encourage exploration of novel molecular mechanisms for their prevention and treatment. N6-methyladenosine (m6A) is a methylation modification that occurs at the N6 position of adenosine in most RNAs and represents the most prevalent internal modification of eukaryotic messenger RNA. This dynamic and reversible modification is involved in regulating nearly all aspects of RNA metabolism and therefore plays important roles in various diseases, including diabetes mellitus and its complications. The present review summarizes recent advances in understanding the functions of m6A modification, its regulators, and potential downstream targets in diabetes mellitus and diabetic complications. Notably, different-and sometimes opposite-expression patterns and regulatory roles of m6A regulators have been reported within the same disease or among diabetes-related disorders. The heterogeneity of patient tissues, cell lines, and experimental models used across studies highlights the need for further comprehensive evaluation of the roles of m6A modification in diabetes mellitus and its complications. This review provides a valuable reference for tracking recent research progress in the field of m6A modification in diabetes mellitus.
    Keywords:  diabetes complications; diabetes mellitus; m6A; m6A regulators; methyladenosine
    DOI:  https://doi.org/10.3389/fendo.2025.1705600
  62. PLoS Genet. 2026 Jan 26. 22(1): e1011743
    Oculopharyngeal muscular dystrophy (OPMD) associated alanine expansion impairs the function of the nuclear polyadenosine RNA binding protein PABPN1 as revealed by proximity labeling and comparative proteomics.
    Allison T Mezzell, Yu Zhang, Alexandra M Perez, Katherine E Vest.
      Oculopharyngeal muscular dystrophy (OPMD) is a late-onset disease caused by modest alanine expansion at the amino terminus of the nuclear polyadenosine RNA binding protein PABPN1. PABPN1 is expressed ubiquitously and is involved in multiple steps in RNA processing including optimal cleavage and polyadenylation, polyadenylation signal selection, and export of polyadenylated RNAs from the nucleus. Expanded PABPN1 forms aggregates in a subset of muscle nuclei, but PABPN1 levels are paradoxically low in muscle compared to other tissues. Despite several studies in model systems and patient tissues, it remains unclear whether alanine expansion directly impairs PABPN1 function. The molecular mechanisms leading to OPMD pathology are poorly understood. Here we used a proximity labeling approach to better understand the effect of alanine expansion on PABPN1 function in a cell culture model of skeletal muscle. To avoid the confounding factor of overexpression, PABPN1 constructs containing a carboxy-terminal TurboID tag were expressed in skeletal myotubes at near native levels using an inducible promoter. Although non-expanded PABPN1-TurboID was able to complement RNA export and myoblast differentiation defects caused by deficiency of endogenous PABPN1, alanine expanded PABPN1-TurboID was not. Comparative proteomics revealed increased interaction between expanded PABPN1 and RNA splicing and polyadenylation machinery and follow-up studies identified a dominant negative effect of expanded PABPN1 on RNA export in differentiated myotubes. These data indicate that alanine expansion can impair PABPN1 function regardless of the presence of wild type PABPN1 and support a model wherein both loss function and dominant negative effects of expanded PABPN1 contribute to OPMD pathology.
    DOI:  https://doi.org/10.1371/journal.pgen.1011743
  63. Int J Mol Sci. 2026 Jan 09. pii: 672. [Epub ahead of print]27(2):
    Dissecting the Interaction Domains of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicase DDX3X and Search for Potential Inhibitors.
    Camilla Lodola, Maria Michela Pallotta, Fabrizio Manetti, Paolo Governa, Emmanuele Crespan, Giovanni Maga, Massimiliano Secchi.
      The SARS-CoV-2 nucleocapsid protein (Np) plays multifunctional roles in the viral life cycle. By interacting with host cellular proteins, Np regulates viral RNA transcription, replication, and immune evasion. It controls genome packaging and counteracts host RNA interference mediated antiviral responses through its RNA binding activity. Previous studies revealed a physical interaction between Np and DDX3X, a human DEAD-box RNA helicase that facilitates the replication of several viruses. This interaction enhances Np affinity for double-stranded RNA and inhibits DDX3X helicase activity. Since Np-RNA binding activity promotes ribonucleoprotein complex formation, targeting this interaction is a promising antiviral strategy. We generated truncated protein variants to define interaction regions between Np and DDX3X. Using AlphaFold modelling, we identified RecA2 as the key DDX3X domain involved in Np binding. Finally, to disrupt Np-RNA complex formation, we screened a small molecule library of putative binders of Np N-terminal region and identified two candidate inhibitors for further development.
    Keywords:  DDX3X; SARS-CoV-2; antiviral drugs; dead-box RNA helicase; nucleocapsid
    DOI:  https://doi.org/10.3390/ijms27020672
  64. Adv Exp Med Biol. 2026 ;1497 33-50
    Mutagenesis-Centered Integrative Approaches for Identifying Binding Sites in Ion Channels and Uncovering Modulatory Mechanisms.
    Avia Rosenhouse-Dantsker.
      Recent advances in structural techniques have provided unprecedented insights into protein structure and function. Yet, obtaining insights into the structure and function of transmembrane proteins, whether alone or in complex with modulators or other proteins, remains challenging. The aim of this chapter is to demonstrate how mutagenesis studies, in conjunction with sequence, structural, and computational information, can assist in identifying binding regions in ion channels and provide mechanistic insights into their modulation. The examples presented comprise various potassium channels and include the identification of binding sites for ions such as sodium and for lipids, including PI(4,5)P2 and cholesterol, as well as the characterization of channel-protein interactions involving the βγ subunits of G proteins. Further examples focus on elucidating modulatory mechanisms, such as the reversal of the effect of cholesterol on an ion channel from enhancement to suppression. Additionally, recent advances in double-mutant cycle analysis and deep learning are enabling more detailed mapping of interaction surfaces, quantification of interaction strengths, and more precise identification of key residues. Together, these studies exemplify the utility of mutagenesis as a powerful perturbation approach for probing ion channel function and modulation.
    Keywords:  Binding site; Double-mutant cycle analysis; Interaction homology; Ion channel; Protein-protein interactions; Site-directed mutagenesis
    DOI:  https://doi.org/10.1007/978-3-032-07523-9_3
  65. Blood. 2026 Jan 29. 147(5): 476-478
    Ribosomal RNA methylation in HSCs: it's so "good for you".
    Judith López, Konstantinos Tzelepis.
      
    DOI:  https://doi.org/10.1182/blood.2025032073
  66. mBio. 2026 Jan 30. e0376225
    Regulation of ribosome hibernation controls Legionella survival, infection, antibiotic tolerance, and phenotypic heterogeneity.
    Camille Schmid, Selina Natalie Trinkler, Elizabeth Teresa Vittori, Michaela Oborská-Oplová, Vikram Govind Panse, Hubert Hilbi.
      Bacterial virulence is regulated by the growth phase and ribosome activity, implicating the formation of translationally silent ("hibernating") ribosomes. Legionella pneumophila, the causative agent of Legionnaires' disease, is a facultative intracellular bacterium that grows in both environmental amoebae and mammalian macrophages. Thus far, ribosome hibernation factors of L. pneumophila have not been characterized. Here, we show that L. pneumophila encodes homologs of the ribosome hibernating factors LhpF (Lpg1206), RaiA (Lpg0467), RsfS (Lpg1377), and the GTPase HflX (Lpg0010), which define the ribosome populations by mediating 100S ribosome dimerization, 70S inactivation, ribosome assembly inhibition, and ribosome splitting, respectively. Exceptional among γ-proteobacteria, L. pneumophila forms 100S ribosome dimers during exponential growth. Functional studies show that the hibernation factors support survival upon starvation, regrowth, efficient host infection, and virulence factor production of L. pneumophila. Furthermore, they enhance antibiotic tolerance and shape intracellular heterogeneity of bacterial growth and motility. Our findings identify ribosome hibernation as a central mechanism by which L. pneumophila orchestrates survival, persistence, and infection, highlighting its critical role in bacterial physiology and pathogenesis.IMPORTANCEDue to nutrient limitation and adverse conditions in the environment, bacteria mostly do not grow exponentially but adopt a resting ("dormant") state. Bacterial dormancy usually coincides with the formation of translationally silent ("hibernating") ribosomes; however, the role of ribosome hibernation in intracellular pathogens is poorly understood. The facultative intracellular bacterium Legionella pneumophila is virulent in the stationary but not in the exponential growth phase, and therefore, an in-depth characterization of the pathogen's physiological states and ribosome profiles is crucial for understanding its virulence. Using bioinformatics, bacterial genetics, biochemical, and cell biological approaches, in this study, we reveal that the L. pneumophila ribosome hibernation factors LhpF, RaiA, RsfS, and HflX determine distinct ribosome subpopulations and are implicated in starvation survival and regrowth, as well as in host cell infection, intracellular replication, and phenotypic heterogeneity. Collectively, our data highlight the critical importance of ribosome hibernation for the physiology and virulence of L. pneumophila.
    Keywords:  Acanthamoeba; Legionella; amoeba; antibiotics; intracellular pathogens; macrophage; pathogen vacuole; persistence; phenotypic heterogeneity; ribosome hibernation; starvation; stress response; virulence
    DOI:  https://doi.org/10.1128/mbio.03762-25
  67. J Biochem Mol Toxicol. 2026 Feb;40(2): e70709
    Transfer RNA-Derived Small RNAs: Novel Predictive Biomarkers for Diagnosis and Prognosis of Breast Cancer.
    Lihan Bie, Minhua Wu, Zhouhong Xiang, Xin Lei, Xiudi Jiang.
      tRNA-derived small RNAs (tsRNAs) have emerged as important regulators in cancer biology, yet their role in breast cancer remains insufficiently understood. This study identifies tRF-30-PW5SVP9N15WV as a tsRNA consistently upregulated in breast cancer, supported by analyses of TCGA-BRCA and independent clinical cohorts. Elevated expression was an independent predictor of poor overall survival (HR = 20.83, 95% CI 2.76-157.35; p < 0.001) and displayed superior prognostic power compared with TNM stage. A nomogram integrating tRF-30-PW5SVP9N15WV achieved a C-index of 0.78, with time-dependent ROC AUCs of 0.882, 0.733, 0.704, and 0.662 at 1, 3, 5, and 10 years, respectively, outperforming clinical parameters alone. Functional assays demonstrated that tRF-30-PW5SVP9N15WV promotes proliferation (CCK-8, colony formation) and invasion (Transwell migration) in vitro, while xenograft and tail-vein injection models confirmed its ability to accelerate tumor growth and lung metastasis (p < 0.01) in vivo. Subcellular fractionation revealed predominant cytoplasmic localization (67.1%), consistent with posttranscriptional regulatory activity. Clinically, tRF-30-PW5SVP9N15WV also exhibited diagnostic potential in differentiating malignant from benign tissues (AUC = 0.805). Together, these findings establish tRF-30-PW5SVP9N15WV as a clinically relevant tsRNA with diagnostic, prognostic, and therapeutic relevance in breast cancer.
    Keywords:  breast cancer; metastasis; prognostic biomarker; tsRNAs; tumor proliferation
    DOI:  https://doi.org/10.1002/jbt.70709
  68. Mol Biol Rep. 2026 Jan 30. 53(1): 336
    SUMOylation machinery protein, PIAS4 role in breast cancer cell proliferation and drug sensitivity.
    Mohammed A M Salih, Mohamed M A E L Salem, Muhammad Ali Shahid, Hussein A S Elrewey, Ritchie Williamson, Sriharsha Kantamneni.
       PURPOSE: Breast cancer is a significant global health issue, with resistance to doxorubicin (DOX) posing a major challenge to effective treatment. SUMOylation, a post-translational modification process, is linked to cancer progression and therapy resistance. PIAS4, a SUMO E3 ligase involved in maintaining genome stability and stress response, may play a role in these mechanisms. However, its function in breast cancer progression and DOX resistance remains uncertain. This study investigates the potential role of PIAS4 in mediating DOX resistance in breast cancer.
    METHODS AND RESULTS: Naked mole-rats (NMRs) are cancer-resistant rodents with improved genome maintenance, yet the role of SUMOylation in this trait remains unclear. SUMOylation machinery gene expression levels are investigated using qPCR in NMR tissue in comparison with carcinogenic breast cancer (MCF-7) cell line. Functional studies are performed in MCF-7 cells overexpressing PIAS4 to demonstrate effects on proliferation, invasion, drug sensitivity, and protein expression in the presence and absence of DOX treatment. While most SUMOylation genes were expressed at low levels in NMR intestinal tissues, PIAS4 showed higher expression compared to MCF-7 cells. PIAS4 overexpression in MCF-7 cells significantly decreases colony formation, invasiveness, and resistance to DOX. Western blot analysis showed downregulated Bcl-2 protein levels after DOX treatment, indicating a potential role in apoptosis evasion.
    CONCLUSION: PIAS4 expression level plays a role in breast cancer cell survival, invasiveness, and chemoresistance, partly by altering anti-apoptotic pathways. These findings position PIAS4 as a potential biomarker and therapeutic target for overcoming resistance to anthracycline-based therapies in breast cancer.
    Keywords:  Breast cancer; MCF-7; Naked mole-rat; PIAS4; SUMOylation
    DOI:  https://doi.org/10.1007/s11033-025-11423-0
  69. Viruses. 2026 Jan 20. pii: 128. [Epub ahead of print]18(1):
    Making Sense from Structure: What the Immune System Sees in Viral RNA.
    Benjamin J Cryer, Margaret J Lange.
      Viral RNA structure plays a critical regulatory role in viral replication, serving as a dual-purpose mechanism for encoding genetic information and controlling biological processes. However, these structural elements also serve as pathogen-associated molecular patterns (PAMPs), which are recognized by pattern recognition receptors (PRRs) of the host innate immune system. This review discusses the complex and poorly understood relationship between viral RNA structure and recognition of RNA by PRRs, specifically focusing on Toll-like receptor 3 (TLR3) and Retinoic acid-inducible gene I (RIG-I). While current interaction models rely upon data generated from use of synthetic ligands such as poly(I:C) or perfectly base-paired double-stranded RNA stems, this review highlights significant gaps in our understanding of how PRRs recognize naturally occurring viral RNAs that fold into highly complex three-dimensional structures. Furthermore, we explore how viral evolution and nucleotide variations, such as those observed in influenza viruses, can drastically alter local and distal RNA structure, potentially impacting immune detection. We conclude that moving beyond synthetic models to understand natural RNA structural dynamics is essential for elucidating the mechanisms of viral immune evasion and pathogenesis.
    Keywords:  RNA structure; innate immune; pattern recognition receptor; virus
    DOI:  https://doi.org/10.3390/v18010128
  70. Mol Cell. 2026 Jan 28. pii: S1097-2765(26)00026-2. [Epub ahead of print]
    Coordinating mRNA maturation: The U1 relay model.
    Yoseop Yoon, Cailyx Quan, Lindsey V Soles, Yongsheng Shi.
      mRNA maturation requires precise coordination among transcription, 5' capping, splicing, and 3' end formation. Recent biochemical, structural, and genomic studies demonstrate that these processes are tightly coupled through dynamic interactions among RNA polymerase II, the spliceosome, and cleavage-polyadenylation complexes. Here, we synthesize current mechanistic insights into how transcription elongation factors and RNA processing machineries communicate to ensure efficient and accurate transcript maturation. We propose a "U1 relay" model as a unified framework for understanding co-transcriptional splicing and 3' end formation. We further discuss how RNAs are sorted into nuclear retention/degradation or export pathways based on the RNA processing status. Importantly, RNA processing factors not only act downstream of transcription but also feed back to modulate transcriptional elongation, pausing, and termination, thereby reinforcing bidirectional coupling between RNA synthesis and processing.
    Keywords:  capping; cleavage and polyadenylation; degradation; export; nuclear retention; splicing
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.006
  71. Angew Chem Int Ed Engl. 2026 Jan 29. e20198
    DNA Flap-Mediated Control of Transcription for Programmable RNA Synthesis.
    Eun Sung Lee, Jisu Woo, Seokjoon Kim, Seok Hyeon Kim, Gun Haeng Lee, Ki Soo Park.
      The growing success of RNA-based therapeutics has emphasized the need for precise and programmable RNA synthesis platforms. T7 RNA polymerase (T7RP) is widely utilized for in vitro transcription; however, most existing regulatory strategies rely on auxiliary proteins or chemical modulators. Here, we investigated whether transcription can be regulated solely through nucleic acid sequences. Specifically, we evaluated the effects of single-stranded DNA flap sequences appended to the 3' end of the non-template strand of the T7 promoter, termed the flap promoter, on transcriptional efficiency. Remarkably, we observed a sequence-dependent inhibitory effect, wherein flaps enriched in pyrimidines (cytosine and thymine) significantly suppressed T7RP-mediated transcription. Leveraging this intrinsic sequence preference, we developed two novel transcription control platforms, D-FIT (DNAzyme-mediated Flap promoter Induced Transcription control) and M-FIT (MNAzyme-mediated Flap promoter Induced Transcription control) that enable precise regulation of T7RP activity without the need for auxiliary proteins or chemical agents. These findings uncover a previously unrecognized sequence-specific regulatory mechanism of T7RP and establish a new framework for the rational design of programmable RNA synthesis systems, with broad potential applications in RNA therapeutics and diagnostics.
    Keywords:  DNAzyme; T7 RNA polymerase; T7 promoter engineering; in vitro transcription; transcriptional regulation
    DOI:  https://doi.org/10.1002/anie.202520198
  72. J Microbiol Biotechnol. 2026 Jan 22. 36 e2510015
    Astragalus Polysaccharide Attenuates Breast Cancer Progression by Regulating METTL3-Mediated MAL2 m6A Modification.
    Youting Hu, Kongjun Zhu, Jing Zhang, Jianguo Zhao.
      Astragalus polysaccharide (APS) has recently emerged as a potent antitumor agent, however its impact on breast cancer (BC) remains inadequately understood. The current research aimed to examine the regulatory mechanism of APS in the pathogenesis of BC examining its influence on N6-methyladenosine (m6A) modification of MAL2. The effect of APS on the malignant phenotypes of BC was assessed by CCK8, EdU, transwell and tumor xenograft model assays. The differentially expressed genes (DEGs) in BC were identified by GEPIA-BC database, and their expression levels were determined by qRT-PCR in the BC cells. The role of MAL2 in BC malignancy was examined by EdU and transwell assays. Furthermore, bioinformatics analysis was first employed to explore the m6A modification site of MAL2 mediated by METTL3, which was then validated through MeRIP, western blotting, and qRT-PCR assays. APS was found to significantly reduce the cell proliferation, migration, as well as invasion of MCF-7 (IC50: 1014 μg/ml) and MDA-MB-231 (IC50: 685 μg/ml) cell lines. Additionally, it effectively suppressed tumor growth in vivo. The bioinformatics analysis revealed that among the five DEGs, MAL2 was significantly downregulated upon APS treatment both BC cell lines. Furthermore, the overexpression of MAL2 partially reversed the anti-tumor effects of APS. Notably, METTL3 modulates the m6A modification of MAL2 to regulate tumorigenesis in BC. APS prevents BC progression in association with reduced METTL3 expression and altered m6A modification of MAL2, suggesting that MAL2 may represent a potential therapeutic target to enhance the efficacy of APS.
    Keywords:  Astragalus polysaccharide; Breast cancer; MAL2; METTL3; m6A modification
    DOI:  https://doi.org/10.4014/jmb.2510.10015
  73. Redox Biol. 2026 Jan 16. pii: S2213-2317(26)00036-4. [Epub ahead of print]90 104038
    Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response.
    Shadi Al-Mesitef, Daisuke Ando, Tomoya Saigasaki, Yuki Sakaguchi, Shunya Akagi, Abdulrahman Mousa, Sherif Rashad, Kuniyasu Niizuma.
      Transfer RNA-derived small RNAs (tDRs) are emerging regulators of cellular stress response, yet their biogenesis and activities during mitochondrial dysfunction remain poorly understood. Here we profiled tDRs generated in HEK293T cells exposed to inhibitors of respiratory complexes I-V (rotenone, TTFA, antimycin A, KCN, oligomycin) or to arsenite and assessed the impact of CRISPR-mediated angiogenin (ANG) knockout, ANG over-expression and recombinant ANG supplementation on the stress response and tDRs production. tDR-seq revealed stress-specific, highly ordered tDR repertoires: rotenone and antimycin predominantly induced internal (i-tRF) and 3' tRNA (tRF3) fragments, whereas arsenite induced anticodon-cleaved tRNA halves (tiRNAs). mito-tDRs were mostly internal fragments and antimycin induced the strongest mitochondrial tDRs expression. ANG deletion markedly impaired stress-induced tDR biogenesis and sensitized cells to antimycin and oligomycin stress, whereas its overexpression selectively enhanced tDR biogenesis and conferred protection against these mitochondrial stressor. Synthetic tDR mimics failed to rescue viability, implying that native modification patterns or cooperative tDR pools are required. tDR motif enrichment analysis identified YBX1-binding sites among antimycin-induced tDRs, and genetic perturbation of YBX1 phenocopied aspects of enhanced mitochondrial bioenergetics and stress resistance. Together, these findings demonstrate that context-specific, ANG-directed tDR biogenesis forms a crucial arm of the mitochondrial stress response.
    Keywords:  Angiogenin; Mitochondrial stress; RNA binding proteins; YBX1; tRNA; tRNA derived fragments
    DOI:  https://doi.org/10.1016/j.redox.2026.104038
  74. Plant Cell Rep. 2026 Jan 30. 45(2): 47
    Let go or retain: role of calmodulin in orchestrating nuclear protein transport in eukaryotes.
    Vibha Verma, Neelima Boora, Meenu Kapoor, Sanjay Kapoor.
      Protein transport is a tightly regulated and complex cellular process fundamental to growth and development. A critical aspect of this process is the accurate and timely translocation of transcription factors and other components of the transcriptional machinery into the nucleus, which is indispensable for the regulation of gene expression. Calmodulin (CaM), a conserved calcium-sensing protein, binds 4 calcium ions and, upon activation, triggers a cascade of signaling events that fine-tune transcriptional outcomes. Notably, CaM exerts a dual regulatory role-facilitating or inhibiting the nuclear import of proteins depending on the cellular context. This review provides a detailed account of the structure and function of CaM, elucidates the molecular basis of its interactions with nuclear transport components, and presents case studies that substantiate its role as a modulator of nuclear protein trafficking across diverse organisms, including recent findings in plants. In addition, we have summarized the potential future applications and implications of CaM-mediated nuclear transport. This finding paves the way for further exploration of how calcium-signaling and CaM-mediated protein transport shape plant development and stress responses. Beyond elucidating the complex regulation of protein localization in plant cells, this insight may also offer new strategies for enhancing plant growth, development, and resilience under stress conditions.
    Keywords:  Calcium; Calmodulin; EGFR; HMGN1; NF-kB; Nuclear transport; OsMADS29; Protein transport; Signaling
    DOI:  https://doi.org/10.1007/s00299-026-03723-x
  75. Nucleic Acids Res. 2026 Jan 22. pii: gkag046. [Epub ahead of print]54(3):
    Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.
    Sélène Forget, Guillaume Stirnemann.
      Some naturally occurring ribozymes can catalyze self-cleavage reactions through a 2'-OH group. Consequently, experimental structures of pre-catalytic states often require chemical modifications of the 2'-OH, such as its removal or methylation. However, the impact of these chemical modifications on the active site structure remains largely unexplored, which raises important questions since methylated structures are often taken as being representative of pre-catalytic states. Here, we employ extensive atomistic simulations critically compared with and fine-tuned on experimental data, and we revisit experimental results to show that 2'-O-methylation critically affects reactant geometries and, therefore, the possible reaction mechanisms inferred from the structures. Our results also challenge the common assumption that 2'-O-methylation stabilizes the C3'-endo puckering conformation. Our findings, consistent with recent experimental data on ribosome structure, reveal that this effect is highly sensitive to the local secondary structure and is often overstated. For three investigated small-cleaving ribozymes, the C2'-endo conformation observed for chemically modified active site residues through 2'-O-methylation is not stable upon methyl group removal to obtain the catalytically relevant hydroxylated state. This suggests that these geometries arise primarily from a combination of steric hindrances and electrostatic interactions with the surrounding environment rather than intrinsic conformational preferences of the ribose upon methylation.
    DOI:  https://doi.org/10.1093/nar/gkag046
  76. Front Immunol. 2025 ;16 1699400
    An antibody uniquely binding short 2'-O-methyl RNA oligonucleotide duplexes: formation and recognition of target duplexes on cell surfaces.
    Ian S Dunn, Matthew M Lawler, Leah Fagundes, Milto Simoes Junior, April Mangold, Domenic Rinaldi, Lenora B Rose, James T Kurnick.
      With the primary aim of generating antibody tools useful for diagnostic and therapeutic applications relevant to oligonucleotide-templated reactions, an scFv filamentous phage library was screened using a specific 2'-O-methyl RNA template:oligonucleotide click reaction complex as the target structure. Such an antibody would not be expected to recognize any naturally occurring biological molecules. Two promising candidate scFv clones were converted into human IgG1 antibodies for further characterization. Surprisingly, although the best antibody (IgG1-DS5) was bound to the original selection complex, its recognition preference was shown to be directed toward short 2'-O-methyl RNA duplexes without click modifications. The IgG1-DS5 antibody showed no binding to the separate single strands comprising the recognized duplex, nor to the corresponding duplexes with RNA or DNA template strands. Versions of the target 2'-O-methyl RNA duplex with divergent sequences were also not recognized by IgG1-DS5. The unexpected binding properties of the IgG1-DS5 antibody were directed toward potential applications based on the molecular proximity of tethered single strands. Initially, SKBr3 cells were coated with biotins by means of surface azide metabolic labeling with peracetylated N-azidoacetylmannosamine, followed by treatment with a click-reactive DBCO-PEG4-biotin compound. Subsequent cell treatment with the tetravalent biotin-binding protein neutravidin (NAV), carrying subsaturating levels of biotinylated 2'-O-methyl RNA target duplexes, showed strong IgG1-DS5 staining on cell surfaces. These observations were extended with biotinylated anti-EGFR antibody linked with biotinylated 2'-O-methyl RNA single strands, also by means of the NAV protein as an adaptor. Flow cytometry analysis showed that DS5 antibody binding was only obtained when combinations of separate preparations of antibodies carrying top and bottom target strands were applied sequentially to EGFR-positive cells. These results show that proximity-based surface annealing of the IgG1-DS5 antibody target single strands can act to define cell populations with a surface marker of sufficient density. Where IgG1-DS5 is derivatized with either a fluorescent moiety or a cytotoxic drug, this antibody may find application in diagnostic or therapeutic tumor targeting.
    Keywords:  2’-O-methyl RNA binding; cancer diagnosis and therapy; cell surface targets; short duplex recognition; surface annealing; unique monoclonal antibody
    DOI:  https://doi.org/10.3389/fimmu.2025.1699400
  77. Front Biosci (Landmark Ed). 2026 Jan 16. 31(1): 47597
    Long Non-Coding RNA RAB11B-AS1 Suppresses Cervical Cancer Progression by Upregulating RPL26 Expression.
    Xuemin Gu, Yuanyuan Yang, Zhixia Zhang, Yiqin Ouyang, Xiaowen Tong.
       BACKGROUND: Cervical cancer (CC) is one of the most prevalent gynecological malignancies. The expression and functional role of the long non-coding RNA (lncRNA) Ras-related protein Rab-11B antisense RNA 1 (RAB11B-AS1) in CC remain poorly understood.
    METHODS: The expression profile of lncRNA RAB11B-AS1 across multiple cancer types was initially assessed using data from The Cancer Genome Atlas. Its expression in CC tissues and lesions of varying pathological grades was subsequently validated via RNA in situ hybridization. To investigate its functional role in CC, a combination of transcriptomic, proteomic, and functional assays was employed to delineate the molecular role of RAB11B-AS1. The effects of alterations in RAB11B-AS1 expression on cervical cancer growth were ultimately validated in vivo.
    RESULTS: LncRNA RAB11B-AS1 was downregulated in CC and associated with a favorable patient prognosis. Functionally, RAB11B-AS1 promoted apoptosis while suppressing proliferation, migration, and invasion of CC cells in vitro, and inhibited tumor growth in vivo. Mechanistically, RAB11B-AS1 upregulated ribosomal protein L26 (RPL26) expression. Notably, RAB11B-AS1 suppressed cervical cancer progression by activating the p53 pathway via RPL26. Critically, in vitro and in vivo experiments confirmed that RPL26 knockdown abrogates the tumor-suppressive functions of RAB11B-AS1, establishing RPL26 as a pivotal downstream effector of RAB11B-AS1 in CC.
    CONCLUSIONS: Our findings demonstrate that lncRNA RAB11B-AS1 suppresses cervical cancer progression primarily through upregulation of RPL26 and suggest that RAB11B-AS1 may serve as a potential biomarker and therapeutic target in cervical cancer.
    Keywords:   RAB11B-AS1 ; apoptosis; cell proliferation; cervical cancer; metastasis; ribosomal protein L26
    DOI:  https://doi.org/10.31083/FBL47597
  78. J Virol. 2026 Jan 28. e0216225
    The ability of alphavirus replicases to synthesize non-viral type I interferon-inducing RNAs correlates with viral RNA synthesis and has a diverse impact on virus replication and pathogenicity.
    Ailar Omler, Anna Rutmane, Suresh Mahalingam, Andres Merits.
      Alphaviruses have positive-strand RNA genomes that mimic cellular mRNAs, and their translation results in the synthesis of nonstructural (ns) polyprotein, the precursor of viral replicase. The ns polyprotein is processed by its protease activity to form an early replicase complex, responsible for the synthesis of negative-strand RNA that forms a double-stranded RNA (dsRNA) replication intermediate with the RNA genome. The following processing results in the formation of a late replicase complex responsible for the synthesis of positive-strand RNAs. Replication complexes are anchored to membranes, and dsRNA is shielded from cellular pattern recognition receptors. Nevertheless, alphavirus infection triggers a type I interferon response; this is partly due to the ability of replicases to utilize cellular RNAs as templates for synthesis of specific dsRNAs (rPAMPs). Here, we demonstrate that replicases of 11 alphaviruses, representing most of the antigenic complexes of alphaviruses, are all capable of rPAMP synthesis in human cells and that some replicases also do the same in mosquito cells. The levels of rPAMPs generally correlate with the efficiency of viral RNA synthesis and are increased by mutations slowing down the processing of the ns polyprotein. For different strains of Semliki Forest virus, the elevated synthesis of rPAMPs correlates with a previously reported virulent phenotype, while for mutants of chikungunya virus, the situation is reversed. Thus, synthesis of rPAMPs is a universal property of alphavirus replicases; these molecules are used to regulate virus infection, and their functional impact depends on their amount as well as the virus species.IMPORTANCEAlphaviruses are important mosquito-borne emerging pathogens. Their ability to interact with cellular defenses, including type I IFN, is crucial for infection. Here, we found that alphavirus replicases have a universal ability to synthesize type I IFN-inducing RNAs using non-viral templates, and that their synthesis varies greatly among viruses and their strains. Production of these RNAs was increased by mutations slowing down the maturation of the viral replicase. The abundance of non-viral type I IFN-inducing RNAs correlated with neurovirulence of Semliki Forest virus, indicating their role in virus pathogenicity; however, for chikungunya virus, their excess correlated with virus attenuation. These data are important to promote the understanding of mechanisms of alphavirus pathogenesis and virus interactions with the host immune system. As alphaviruses represent promising platforms for development of advanced mRNA vaccines, the data can also be used for rational optimization of alphavirus-based vaccine candidates.
    Keywords:  Semliki Forest virus; alphavirus; chikungunya virus; double-stranded RNA; innate immune sensing; interferons; self-amplifying RNA vaccines; type I interferon; viral RNA replicase
    DOI:  https://doi.org/10.1128/jvi.02162-25
  79. Viruses. 2025 Dec 30. pii: 57. [Epub ahead of print]18(1):
    Transcriptomic and Epitranscriptomic Landscape of Integrated HTLV-1 in MT2 Cells.
    Shuanglong Wei, Bohan Zhang, Jingwan Han, Hanping Li, Yongjian Liu, Lei Jia, Jingyun Li, Xiaotian Huang, Lin Li.
      Human T-lymphotropic virus type 1 (HTLV-1), the first human retrovirus identified, is linked to adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. However, its post-transcriptional regulation remains poorly understood. Here, we used Oxford Nanopore direct RNA sequencing to profile the HTLV-1 transcriptome and epitranscriptome in MT2 cells. We identified 23 transcript isoforms, encompassing canonical and novel splice variants. Polyadenylation analysis revealed a predominant poly(A) tail length of around 50-100 nucleotides with transcript-specific variations. Distinct RNA modifications, including pseudouridine, N6-methyladenosine, and 5-methylcytidine, were enriched near the 3' end and varied among transcript classes, with generally lower modification ratios in viral transcripts. These findings provide a more comprehensive map of HTLV-1 RNA splicing, polyadenylation, and modifications in MT2 cells, offering new insights into viral gene regulation and pathogenic mechanisms.
    Keywords:  DRS; HTLV-1; modifications; polyadenylation; splice
    DOI:  https://doi.org/10.3390/v18010057
  80. Biomolecules. 2025 Dec 24. pii: 33. [Epub ahead of print]16(1):
    Heterogeneous Folding Intermediates Govern the Conformational Pathway of the RNA Recognition Motif Domain of the Ewing Sarcoma Protein.
    Priyanka Kataria, Vishakha Chaudhary, Chandra Bhushan Mishra, Vijay Kumar, Ravi Datta Sharma, Amresh Prakash.
      The RNA Recognition Motif (RRM) domain of the Ewing sarcoma (EWS) protein plays a pivotal role in RNA binding and gene regulation, being crucial for its function. However, its structural dynamics are yet to be revealed. Herein, we performed 5.5 μs cumulative molecular dynamics (MD) simulations to investigate the unfolding pathways of the EWS-RRM domain in urea and DMSO across 300-500 K. The unfolding process was characterized by using free-energy landscape (FEL) analysis, hydrogen-bond occupancy, and Gaussian Mixture Model (GMM) clustering. At lower temperatures (300-350 K), the RRM largely retained its native conformation, while extensive unfolding occurred between 400 and 450 K. Results revealed multiple conformational ensembles: native (N), native-like intermediate (IN), intermediate (I), and unfolded (U) states, underlying the unfolding pathway of RRM. In urea at 400 K, a long-lived I-state dominated, with transient N and IN-populations, whereas in DMSO, the IN-state appeared more stable, that transitioned into tightly packed I-states, reflecting a stepwise unfolding via compact intermediates. At 450 K, the protein reached the U-state in both solvents, though unfolding occurred more readily in urea. This study highlights the solvent-dependent unfolding mechanisms and heterogeneous I-states of EWS-RRM, providing insight into its stability, misfolding, and potential relevance to Ewing sarcoma pathogenesis.
    Keywords:  DMSO; EWS; GMM; MD simulation; RRM; free-energy landscape; urea
    DOI:  https://doi.org/10.3390/biom16010033
  81. Plant Commun. 2026 Jan 29. pii: S2590-3462(26)00050-7. [Epub ahead of print] 101742
    Emerging roles of mRNA acetylation in plants.
    Jie Zhao, Changhua Zhu, Xiaoyun Song, Mingjia Chen.
      N4-acetylcytidine (ac4C) is a conserved acetylation modification on messenger RNA (mRNA) recently identified in plants. It is deposited by the N-ACETYLTRANSFERASE FOR CYTIDINE IN RNA (ACYR) protein, which is homologous to mammalian N-ACETYLTRANSFERASE (NAT10) (Wang et al., 2023; Li et al., 2023). Here, we describe the defining features and functional landscape of ACYR-dependent ac4C marks, their effects on mRNA expression, stability, splicing, and translation, and their roles in leaf development (Wang et al., 2023), photosynthesis (Zhao et al., 2025; Cai et al., 2025), thermosensory flowering (Wu et al., 2025), and plant defense (Lu et al., 2024). We highlight current methods for ac4C profiling and discuss future directions in ac4C research.mRNA acetylation occurs in plants.
    DOI:  https://doi.org/10.1016/j.xplc.2026.101742
  82. J Microbiol Biotechnol. 2026 Jan 21. 36 e2510047
    Discovery of the MELK-Nucleostemin Axis in Glioblastoma: Implications for p53 Regulation and Tumor Progression.
    Songyi Baek, Hyojin Jeon, Jae-Su Moon, Young Eun Kim, Dukjin Kang, Sunghwan Kim, Kwang-Rok Kim, Kyung-Sun Heo.
      Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor, classified as a World Health Organization (WHO) grade IV astrocytoma. Despite multimodal therapies, the prognosis of patients with GBM remains poor, with a median survival of only 12-16 months. The highly invasive nature and therapeutic resistance of GBM underscore the need to identify novel molecular targets. Maternal embryonic leucine zipper kinase (MELK), a serine/threonine kinase of the Snf1/AMPK family, is highly expressed in GBM and regulates cell proliferation, cell cycle progression, and stemness; however, its downstream mechanisms are unclear. Nucleostemin (NS, GNL3) is a nucleolar GTP-binding protein involved in cell proliferation and p53 regulation; however, its regulation in GBM has not been fully elucidated. In this study, we identified NS as a novel MELK substrate in glioblastoma U87MG cells. MELK directly interacts with and phosphorylates NS, promoting its proteasomal degradation. MELK overexpression decreased NS expression, leading to enhanced p53 activation and G1 cell cycle arrest. Conversely, MELK knockdown restored NS stability and attenuated p53 activation. These findings define a previously unrecognized MELK-NS-p53 signaling axis that links kinase activity to the regulation of the cell cycle. Our fundings provide mechanistic insights into glioblastoma pathogenesis and suggest that targeting the MELK-NS pathway may be a potential therapeutic strategy for high-grade gliomas.
    Keywords:  Glioblastoma; MELK-NS axis; Proteasomal degradation; p53 Signaling
    DOI:  https://doi.org/10.4014/jmb.2510.10047
  83. Front Immunol. 2025 ;16 1729362
    Expression and clinical value of key m6A RNA modification regulators in tuberculosis.
    Hongfei Du, Hang Wang, Yan Yang, Qiao Yu, Zhongyong Jiang, Ying Xu.
       Background: N6-methyladenosine (m6A), the most prevalent and reversible post-transcriptional RNA modification, is involved in the progression of various diseases. Nonetheless, the role of m6A modification in Tuberculosis (TB) pathogenesis remains unknown. Here, we investigated the general expression patterns and potential functions of m6A regulators in TB.
    Methods: The differentially expressed m6A genes between the healthy and TB groups were evaluated using the public Gene Expression Omnibus (GEO) database, and quantitative real-time PCR (qRT-PCR) was used to test the expression of key m6A regulators in our collected human TB and healthy samples. Random forest and LASSO regression analysis were performed to determine the prognostic performance of m6A regulators in TB patients. The relationship between m6A regulators and immune cells and immune reaction activity was analyzed through single-sample gene set enrichment analysis (ssGSEA). Unsupervised clustering was used to confirm that m6A regulators induced m6A modification patterns. The relationship between m6A modification patterns and the immune microenvironment, biological function, and TB subtype construction was evaluated by using Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) analysis and KEGG pathway analysis.
    Results: Our data revealed seven differentially expressed m6A -related genes-METTL3, VIRMA, YTHDF1, YTHDC1, YTHDC2, ELAVL1and LRPPRC mRNA-confirmed as critical m6A regulators in TB. The excellent diagnostic significance of these genes was further supported by the random forest, LASSO regression and clinical samples, which achieved a high area under the ROC (0.97). Unsupervised clustering classified patients into two m6A patterns with different immune microenvironment and biological feature.
    Conclusions: Our study provides an overview of the expression patterns and potential roles of key m6A regulatory genes as diagnostic biomarkers and immunotherapy targets for TB, revealing their functions in TB pathogenesis. Our data may offer a valuable resource to guide both mechanistic and therapeutic analyses of key m6A regulators in TB.
    Keywords:  N6-methyladenosine; immune cell; immune process; immunemicroenvironment; m6A RNA modification; pulmonarytuberculosis; tuberculosis
    DOI:  https://doi.org/10.3389/fimmu.2025.1729362
  84. Genes (Basel). 2025 Dec 28. pii: 26. [Epub ahead of print]17(1):
    Identification and Validation of Tissue-Specific Housekeeping Markers for the Amazon River Prawn Macrobrachium amazonicum (Heller, 1862).
    Gabriel Monteiro de Lima, Mônica Andressa Leite Rodrigues, Rômulo Veiga Paixão, Ítalo Lutz, Manoel Alessandro Borges Aviz, Janieli do Socorro Amorim da Luz Sousa, Bruna Ramalho Maciel, Luciano Domingues Queiroz, Carlos Murilo Tenório Maciel, Iracilda Sampaio, Eduardo Sousa Varela, Cristiana Ramalho Maciel.
      Background/Objectives: The selection and validation of species-specific housekeeping genes (HKGs) have become increasingly common in functional genomics, with application of quantitative Polymerase Chain Reaction (qPCR) or cDNA-based qPCR (RT-qPCR). Despite the Macrobrachium amazonicum having RNA-seq studies available, there are still no data on the most stable and consistent HKGs for use in relative gene expression analyses. Therefore, the present study aimed to identify and validate seven HKGs in M. amazonicum: Eukaryotic Translation Initiation Factor (EIF), 18S ribosomal RNA (18S), Ribosomal Protein L18 (RPL18), β-actin, α-tubulin (α-tub), Elongation Factor 1-α (EF-1α), and Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH). Methods: The HKGs were identified in the M. amazonicum transcriptome, characterized for identity confirmation, and compared against public databases. Subsequently, RT-qPCR assays were prepared using muscle, hepatopancreas, gills, testis, androgenic gland, and ovary to assess the stability of the HKG markers, employing the comparative ∆Ct, BestKeeper, NormFinder, and GeNorm methods. Results: All candidate HKGs identified showed high similarity with other decapods. Reactions performed with these markers demonstrated high specificity, PCR efficiency, and elevated coefficients of determination. The comprehensive ranking, indicated that no single HKG was stable across all tissues, with HKGs showing the best stability being tissue-specific. The most stable HKGs were RPL18 and 18S. GAPDH, historically used as an HKG, showed the poorest performance in stability ranking for most tissues tested, whereas β-actin was most suitable only for ovarian. Conclusions: These data reinforce the need for species-specific HKG validation and provide an appropriate panel of reference markers for gene expression studies in the M. amazonicum.
    Keywords:  RT-qPCR; gene expression normalization; stability
    DOI:  https://doi.org/10.3390/genes17010026
  85. Biomedicines. 2026 Jan 08. pii: 126. [Epub ahead of print]14(1):
    Directional Modulation of the Integrated Stress Response in Neurodegeneration: A Systematic Review of eIF2B Activators, PERK-Pathway Agents, and ISR Prolongers.
    Isabella Ionela Stoian, Daciana Nistor, Mihaela Codrina Levai, Daian Ionel Popa, Roxana Popescu.
      Background and Objectives: The integrated stress response (ISR) is a convergent node in neurodegeneration. We systematically mapped open-access mammalian in vivo evidence for synthetic ISR modulators, comparing efficacy signals, biomarker engagement, and safety across mechanisms and disease classes. Methods: Following PRISMA 2020, we searched PubMed (MEDLINE), Embase, and Scopus from inception to 22 September 2025. Inclusion required mammalian neurodegeneration models; synthetic ISR modulators (eIF2B activators, PERK inhibitors or activators, GADD34-PP1 ISR prolongers); prespecified outcomes; and full open access. Extracted data included model, dose and route, outcomes, translational biomarkers (ATF4, phosphorylated eIF2α), and safety. Results: Twelve studies met the criteria across tauopathies and Alzheimer's disease (n = 5), prion disease (n = 1), amyotrophic lateral sclerosis and Huntington's disease (n = 3), hereditary neuropathies (n = 2), demyelination (n = 1), and aging (n = 1). Among interpretable in vivo entries, 10 of 11 reported benefit in at least one domain. By class, eIF2B activation with ISRIB was positive in three of four studies, with one null Alzheimer's hAPP-J20 study; PERK inhibition was positive in all three studies; ISR prolongation with Sephin1 or IFB-088 was positive in both studies; and PERK activation was positive in both studies. Typical regimens included ISRIB 0.1-2.5 mg per kg given intraperitoneally (often two to three doses) with reduced ATF4 and phosphorylated eIF2α; oral GSK2606414 50 mg per kg twice daily for six to seven weeks, achieving brain-level exposures; continuous MK-28 delivery at approximately 1 mg per kg; and oral IFB-088 or Sephin1 given over several weeks. Safety was mechanism-linked: systemic PERK inhibition produced pancreatic and other exocrine toxicities at higher exposures, whereas ISRIB and ISR-prolonging agents were generally well-tolerated in the included reports. Conclusions: Directional ISR control yields consistent, context-dependent improvements in behavior, structure, or survival, with biomarker evidence of target engagement. Mechanism matching (down-tuning versus prolonging the ISR) and exposure-driven safety management are central for translation.
    Keywords:  drug effects; drug therapy; endoplasmic reticulum; eukaryotic metabolism; neurodegenerative diseases; protein kinase; protein response physiology
    DOI:  https://doi.org/10.3390/biomedicines14010126
  86. Neurobiol Dis. 2026 Jan 22. pii: S0969-9961(26)00028-8. [Epub ahead of print]220 107284
    Distinct Argonaute2-associated small RNA profiles in microglia and neurons drive cell-specific responses in a mouse model of temporal lobe epilepsy.
    Leticia Villalba-Benito, Justine Mathoux, Theresa Auer, Kaushik Narasimhan, Ruth Colbert, James P Reynolds, Elizabeth Brindley, Aasia Batool, Thomas D M Hill, Mairead Diviney, Morten T VenØ, Marco Prinz, Niamh M C Connolly, Dearbhaile Dooley, David C Henshall, Gary P Brennan.
      Small RNAs including microRNAs (miRNAs) and tRNA fragments (tRFs) are key post-transcriptional regulators of gene expression in temporal lobe epilepsy (TLE), but the cellular origin of these changes is often unclear. Here, we dissected the cell-type specific small RNA landscape, focussing on miRNA and tRFs, during epileptogenesis and in chronic epilepsy by profiling the RNA-induced silencing complex (RISC) using novel, transgenic mice with inducible expression of a FLAG-tagged Argonaute 2 protein driven specifically in neurons (Thy1-Ago2) or microglia (Cx3cr1-Ago2). We induced epilepsy in male mice via intra-amygdala microinjection of kainic acid and tracked miRNA expression over time in the hippocampus. Microglia and neurons displayed distinct and largely non-overlapping small RNA profiles across disease. Shortly following the epileptogenic insult, we detected a rapid microglial miRNA and tRF response which was sustained in chronic stages of the disease whereas small RNA changes in neurons displayed a delayed but sustained wave of unique changes as the disease progressed. Interestingly, our data reveals selective loading and incorporation of miRNAs into Ago2/RISC complexes, independent of overall abundance, in a cell- and disease-stage specific manner as well as differential processing of tRNAs in microglia compared to neurons. Additionally we found that certain epilepsy-associated miRNAs, previously considered ubiquitous, display dysregulation in multiple cell types while exhibiting cell-specific activity. Together our results demonstrate the cell-specific small RNA responses and functions to epileptogenic insults and shed further light on the complexity of post-transcriptional gene dysregulation in TLE. The findings indicate the potential advantages of targeted, cell-specific therapeutic strategies to effectively modulate miRNA pathways in epilepsy.
    Keywords:  Argonaute2; Epileptogenesis; Microglia; Temporal lobe epilepsy; microRNA
    DOI:  https://doi.org/10.1016/j.nbd.2026.107284
  87. Cells. 2026 Jan 06. pii: 94. [Epub ahead of print]15(2):
    miRNAs in Glomerular Diseases: From Pathogenic Insight to Therapeutic Potential: A Narrative Review.
    Mugurel Apetrii, Alexandru Dan Costache, Irina Iuliana Costache Enache, Luminita Voroneanu, Andreea Simona Covic, Mehmet Kanbay, Dragos Viorel Scripcariu, Adrian Covic.
      This article explores the multifaceted role of micro-ribonucleic acids (RNAs) (miRNAs) as critical posttranscriptional regulators in renal physiology and disease, with a focus on their emerging significance in glomerulopathies. miRNAs, small endogenous noncoding RNAs, modulate gene expression by promoting messenger RNA degradation or inhibiting translation, thereby orchestrating essential cellular processes such as proliferation, differentiation, apoptosis, and stress responses. Recent advances have revealed that aberrant miRNA expression profiles are intricately linked to the pathogenesis and progression of various renal diseases, including acute kidney injury, chronic kidney disease, alloimmune injury in solid organ transplantation and glomerulonephritis. This review summarizes the pathogenic and protective roles of miRNAs in major glomerulopathies, discusses their potential as diagnostic and prognostic biomarkers, and outlines future directions for their integration into personalized therapeutic strategies. At the moment, it is not fully established whether some of these mechanisms are the primary pathogenic driver or a secondary response. Combining miRNAs with other molecular markers may further enhance diagnostic and predictive accuracy, facilitating clinical translation, while selective targeting of specific miRNAs at different stages of disease progression could offer promising therapeutic opportunities.
    Keywords:  diabetic nephropathy; glomerulopathies; lupus nephritis; microRNA
    DOI:  https://doi.org/10.3390/cells15020094
  88. Dose Response. 2026 Jan-Mar;24(1):24(1): 15593258261418854
    The Roles and Implications of m6A Methylation in Radiotherapy for Gastrointestinal Tumors.
    Jinling Bi, Wentao Hu, Huahui Bian, Wei Cheng.
      Gastrointestinal malignancies, which arise from multiple etiological factors, are a global health burden due to their high incidence and mortality rates. Nearly all gastrointestinal cancers present genomic and epigenomic alterations that play a critical role in initiating and driving tumor progression. N6-methyladenosine (m6A) methylation, a key epigenetic modification in eukaryotic messenger RNA (mRNA), is pivotal for regulating various cellular biological processes and influences both the progression and prognosis of diverse diseases. In gastrointestinal cancers, m6A methylation is closely associated with tumor proliferation, invasion, metastasis, and radiosensitivity. This review aims to uncover the translational regulatory mechanisms mediated by m6A methylation in gastrointestinal cancers and to clarify its role in radiotherapy, as well as to identify potential molecular targets for improving the efficacy of radiotherapy in treating gastrointestinal tumors.
    Keywords:  epigenetics; gastrointestinal cancers; m6A methylation; radioresistance; radiotherapy
    DOI:  https://doi.org/10.1177/15593258261418854
  89. J Orthop. 2026 Apr;74 195-204
    METTL14 regulate LRIG1 expression via m6A to affect nucleus pulposus cell senescence in intervertebral disc degeneration.
    Ruihai Xiao, Qunying Yang, Yingqun Yin, Shanshan Peng, Xigao Cheng.
       Objectives: This study aims to explore the role of METTL14, a key m6A "writer" in regulating LRIG1 expression and its involvement in IVDD pathogenesis.
    Methods: METTL14 expression was evaluated in nucleus pulposus (NP) tissues from IVDD patients at different degeneration stages using immunohistochemistry. In vitro experiments were conducted with METTL14 knockdown and TNF-α-induced cellular degeneration in NP cells. The effects on cellular senescence markers, ECM components, and m6A RNA methylation were examined. m6A RNA immunoprecipitation was employed to assess m6A modification levels. Bioinformatics tools predicted potential m6A sites on LRIG1 mRNA, which were further validated by luciferase reporter assays.
    Results: METTL14 expression was significantly upregulated in NP tissues from patients with severe IVDD. METTL14 knockdown in NP cells led to reduced m6A enrichment on LRIG1 mRNA, destabilizing LRIG1 transcripts and increasing cellular senescence marker P21. TNF-α stimulation further induced METTL14 expression, exacerbated ECM degradation, and accelerated cellular senescence. Restoration of LRIG1 expression through overexpression mitigated the degenerative changes caused by METTL14 knockdown. Luciferase assays confirmed that METTL14 regulates LRIG1 mRNA stability via specific m6A sites, establishing a METTL14-LRIG1 axis in cellular senescence.
    Conclusions: This study identifies METTL14 as a critical regulator of LRIG1-mediated ECM stability and cellular senescence in IVDD pathogenesis. The METTL14-LRIG1 axis, driven by m6A modifications, provides new mechanistic insights into the inflammatory and degenerative processes underlying IVDD. Targeting METTL14 or the associated m6A pathway may offer novel therapeutic strategies for IVDD.
    Keywords:  Intervertebral disc degeneration (IVDD); METTL14; Nucleus pulposus (NP) cells; TNF-α; m6A RNA methylation
    DOI:  https://doi.org/10.1016/j.jor.2026.01.004
  90. Cancer Cell Int. 2026 Jan 28. 26(1): 50
    Unresolved questions on the GADD45GIP1-RPL35 axis in osteosarcoma: mechanistic links to ER stress and therapeutic targeting.
    LiSheng Qi, QinWen Gu, DuJiang Yang, Zhijun Ye, DongDong Li.
      In their recent study, Li et al. (2025) propose a novel signaling axis in which GADD45GIP1 promotes osteosarcoma progression by stabilizing RPL35, thereby alleviating endoplasmic reticulum (ER) stress through the PERK/eIF2α pathway. While this work identifies a potentially significant oncogenic mechanism, our analysis highlights several critical aspects that require further elucidation. The central claim-that stabilization of a single ribosomal protein, RPL35, directly and specifically alleviates ER stress-presents a conceptual paradox, as enhanced ribosome biogenesis would typically be expected to increase the proteotoxic load. We explore alternative explanations, including the potential for selective mRNA translation or non-ribosomal functions of RPL35. Furthermore, the therapeutic promise of targeting this pathway is tempered by the challenges of inhibiting protein-protein interactions and the risk of on-target toxicity given the pervasive role of the PERK pathway in normal secretory cells. The model also necessitates validation across the spectrum of osteosarcoma's genetic heterogeneity. This letter critically examines these mechanistic ambiguities and proposes essential experiments to validate the model, assess its therapeutic viability, and define its clinical relevance within the complex landscape of osteosarcoma biology.
    DOI:  https://doi.org/10.1186/s12935-025-04145-7
  91. Biomedicines. 2026 Jan 08. pii: 129. [Epub ahead of print]14(1):
    Circuitous Ways of EWS::FLI1 Using Circular RNA ZNF609 to Evade Translational Repression by miR-145 in Ewing's Sarcoma.
    Aakash Koppula, Ahmed Abdelgawad, Brigette Romero, Victoria Beringer, Vijay Parashar, Mona Batish.
      Background: Ewing's sarcoma (EwS) is a pediatric bone and soft tissue cancer driven by the oncogenic fusion protein EWS::FLI1. Currently, EwS lacks targeted therapies, necessitating the identification of novel regulatory mechanisms. While the role of microRNAs and long non-coding RNAs has been explored in EwS, the presence and functional significance of circular RNAs (circRNAs) in EwS is not reported. This is the first study to report the presence and role of oncogenic circRNA, circZNF609 in EwS tumor progression. Methods: Expression of circZNF609 was validated in 5 different EwS cell lines using qPCR. Cellular localization of circZNF609 was identified using circFISH. Functional assays for proliferation, migration and apoptosis were performed in wild type and circZNF609 knocked down (KD) cell lines to confirm its oncogenic role. The impact of circZNF609 on EWS::FLI1 protein levels was confirmed using western blots, immunofluorescence, and polysome fractionation. Mechanistic insights were gained utilizing bioinformatic, dual-luciferase reporter assays, rescue experiments, and microscopy to identify and validate the circRNA-miRNA-mRNA regulatory axis. Results: We report the first identification of circZNF609 in EwS, demonstrating that its expression is EWS::FLI1-dependent. Functional analysis reveals that circZNF609 promotes cell proliferation and metastasis while inhibiting apoptosis. Mechanistically, circZNF609 acts as a molecular sponge for miR-145-5p. By sequestering this miRNA, circZNF609 prevents the translational repression of EWS::FLI1, thereby sustaining oncogenic signaling. Conclusions: These findings identify circZNF609 as a novel post-transcriptional regulator of EWS::FLI1 and establish its critical role in EwS pathogenesis. Our results suggest that targeting the circZNF609/miR-145-5p/EWS::FLI1 axis may offer a promising therapeutic strategy for EwS.
    Keywords:  EWS:: FLI1; EwS; Ewing’s Sarcoma; circRNA; circZNF609; circular RNA; miR145; miRNA; microRNA
    DOI:  https://doi.org/10.3390/biomedicines14010129
  92. Foods. 2026 Jan 15. pii: 318. [Epub ahead of print]15(2):
    Yeast Efficiently Utilizes Ribosomal RNA-Derived Oligonucleotides as Bioavailable Nutrient Sources.
    Xinmei Du, Qitao Chen, Jingyun Zhuang, Mingqi Zhao, Yixin Duan, Shuang Wang, Ran An, Xingguo Liang.
      Nucleic acids are essential dietary components with diverse physiological functions. Numerous studies have focused on the biological functions of nucleotides, nucleosides, and functional RNAs such as microRNAs. However, the nutritional value of ribosomal RNA (rRNA)-derived oligonucleotides, which are likely the predominant nucleic acid-derived components in foods, remains largely unexplored. Here, yeast was used as a food-associated eukaryotic model organism to investigate the uptake and utilization of rRNA-derived oligonucleotides. Yeast efficiently utilized short RNA oligonucleotides (approximately 5-30 nt) as nutrient sources, supporting robust cell growth. Confocal microscopy confirmed rapid uptake of Cy5-labeled RNA oligonucleotides by yeast cells. Proteomic analysis further revealed marked upregulation of proteins involved in endocytosis and autophagy in yeast cultured with RNA oligonucleotides. Collectively, these findings demonstrate that yeast can internalize and metabolize rRNA-derived oligonucleotides as efficient nutrient sources, likely through coordinated endocytic and autophagic pathways. This study highlights the nutritional potential of rRNA-derived oligonucleotides and provides a foundation for their future application in functional foods and fermentation systems.
    Keywords:  autophagy; endocytosis; oligonucleotide nutrient sources; proteomics; rRNA-derived oligonucleotides; yeast
    DOI:  https://doi.org/10.3390/foods15020318
  93. Biomolecules. 2025 Dec 26. pii: 45. [Epub ahead of print]16(1):
    Design of Anti-Tumor RNA Nanoparticles and Their Inhibitory Effect on Hep3B Liver Cancer.
    Shuyi Sun, Ling Yan, Zhekai Liu, Weibo Jin.
      RNA interference (RNAi) holds promise as a gene-silencing therapy for liver cancer but faces challenges related to siRNA instability, short half-life, and inefficient cellular uptake. In this study, we designed a self-assembling RNA nanoparticle targeting three oncogenes-hTERT, BIRC5, and FGFR1-key drivers of cancer progression. These RNA nanoparticles demonstrated enhanced stability and specificity, eliminating the need for conventional toxic delivery carriers. Functional assays revealed that the nanoparticles effectively suppressed the proliferation, migration, tumor growth and apoptosis of a Hepatocellular carcinoma cell line, Hep3B. The nanoparticles exhibited excellent safety and efficacy in xenograft model mice, without off-target toxicity. This work introduces a scalable, biocompatible RNA nanoparticle platform with multi-targeting capability, paving the way for improved RNAi-based therapeutics. Our findings offer a promising strategy for advancing personalized cancer therapies and underscore the broader potential of RNA nanotechnology in addressing complex malignancies.
    Keywords:  BIRC5; FGFR1; RNA nanoparticles; RNAi therapy; hTERT; liver cancer
    DOI:  https://doi.org/10.3390/biom16010045
  94. Front Immunol. 2025 ;16 1717319
    METTL3 inhibition alleviates neuroinflammation and apoptosis by reducing ETV4 m6A modification.
    Dong He, Xiaokun Jiang, Gengyin Guo, Jinfeng Ma, Jinyan Chen, Yongfei Zhang, Jianfeng Zhuang, Ping Xie, Zhen Zhang.
      Intracerebral hemorrhage (ICH) triggers devastating secondary brain injury driven by maladaptive microglial activation and neuroinflammation. While N6-methyladenosine (m6A) RNA methylation influences inflammation, its spatiotemporal regulation in ICH microglia remains unclear. Here, we identified METTL3 as a key epigenetic driver that promotes neuropathology post-ICH. Our analyses revealed that upregulated METTL3 expression in activated microglia in ICH model mice was correlated with increased global m6A levels. Functional studies have demonstrated that METTL3 depletion attenuates the release of proinflammatory cytokines (TNF-α, IL-1β, and IL-6), suppresses NF-κB activation, and reduces apoptosis in microglia. Mechanistically, MeRIP-seq and RNA-seq identified the transcription factor ETV4 as a METTL3 target, where METTL3-mediated m6A modification of the ETV4 3'-UTR recruits the reader IGF2BP2 to increase mRNA stability. This axis drives NF-κB-mediated inflammation and caspase-3-dependent apoptosis. Overall, our work reveals the role of METTL3 in sustaining neuroinflammation and inducing apoptosis via m6A/ETV4 stabilization and suggests that METTL3 inhibition is a promising strategy for ameliorating ICH injury.
    Keywords:  Etv4; METTL3; apoptosis; m6A modification; neuroinflammation
    DOI:  https://doi.org/10.3389/fimmu.2025.1717319
  95. RNA. 2026 Jan 26. pii: rna.080764.125. [Epub ahead of print]
    Identification of 3D motifs in Rfam with JAR3D.
    James E Roll, Craig L Zirbel.
      Many non-protein-coding RNAs have been discovered and more are being discovered each year. At first we know them only by their sequences in a few organisms, but to understand their function and interactions, we need to understand what 3D structures they may form, in whole or in part. Many hairpin and internal loops are known to form structured 3D motifs, many of which are recurrent across different non-coding RNAs, for example, kink turn and sarcin-ricin internal loops, and GNRA, UNCG, and T-loop hairpin loops. As such, a new non-protein-coding RNA may well have one or more known structured 3D loop motifs. The goal of this paper is to introduce a tool which can identify loops in Rfam seed alignments that match well to known 3D loop motifs, and which makes those identifications easily accessible. JAR3D was developed to map sequences of hairpin and internal loops to known 3D motifs, and was extended for this work to 3-way and 4-way junction motifs. We applied JAR3D to 4,166 Rfam seed alignments from Rfam 15.0 and made the results accessible on the JAR3D web page, which makes it easy to inspect and evaluate the possible matches for each loop in each Rfam family. We provide several examples which validate JAR3D's ability to identify the correct loop motif, using 3D structures of RNAs outside of the training set. We created a new page to search for instances of a particular loop motif across all Rfam families, to facilitate studies of how widespread the occurrence of each motif is. We provide statistics on how many Rfam loops appear to match well to a known 3D motif. Match rates are much higher for internal loops than for hairpins or multi-helix junctions.
    Keywords:  3D structure prediction; RNA motif; Rfam; non-coding RNA; secondary structure
    DOI:  https://doi.org/10.1261/rna.080764.125
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