bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–01–18
fifty-nine papers selected by
Cédric Chaveroux, CNRS
  1. Eukaryotic initiation factor eIF3 facilitates loading of eukaryotic release factor eRF1 or suppressor tRNA to the ribosome.
  2. A bacterial translation activator with an intrinsically disordered RNA-binding region.
  3. Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.
  4. Atypical tetracyclines promote longevity and ferroptotic neuroprotection via translation attenuation.
  5. Fibrillarin: bridging ribosome biogenesis and apoptosis in cellular stress and disease.
  6. Chronic stress disrupts the network among stress granules, P-bodies, and motor proteins.
  7. Bridging single-molecule and genome-wide studies of cellular mRNA translation.
  8. tRNA synthetase activity is required for stress granule and P-body assembly.
  9. Mechanistic insights into E. coli recovery from growth arrest.
  10. TlyA is a 23S and 16S 2'-O-methylcytidine methyltransferase important for ribosome assembly in Bacillus subtilis.
  11. The ribosomal landscape in influenza A virus infection: from molecular mechanisms to clinical relevance.
  12. PolyA tail segmentation improves the stability of the template DNA and increases the translatability of in vitro transcribed mRNA.
  13. RNA Polymerase III subunit Polr3a is required for craniofacial cartilage and bone development.
  14. Inhibitor screening identifies Entecavir as a promising candidate targeting human eIF4E to block cap-dependent translation in cancer: an integrated in silico and in vitro study.
  15. Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4.
  16. iTP-seq: a scalable profiling workflow to characterize bacterial translation landscapes in vitro.
  17. Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.
  18. Structural analysis of uridine modifications in solved RNA structures.
  19. Noc1 downregulation induces nucleolar stress and upregulates p53 isoforms, with a robust increase of the truncated p53E isoform in Drosophila wing discs.
  20. Tho1 and MOS11 promote nucleic acid double-strand unwinding by facilitating DEAD-box helicase oligomerization.
  21. LOTUS-domain proteins activate Vasa to drive germ granule assembly.
  22. The Ubiquitin-Proteasome Pathway Mediates Selective Degradation of Unloaded Argonaute Proteins in C. elegans.
  23. CNOT10 is involved in TTP-mediated AU-rich element containing mRNA metabolism, independent of mRNA decay regulation.
  24. m6A modification and its clinical applications in gynaecological cancer.
  25. A long non-coding RNA, afu-254 , is required for the oxidative stress response, cell wall stress response, azole susceptibility and virulence in Aspergillus fumigatus.
  26. Strategic variations in sarbecovirus and merbecovirus Nsp1 linker regions for translation inhibition.
  27. RNA-binding proteins and ribonucleoproteins as determinants of immunity.
  28. Recent advances in protein synthesis inhibitors.
  29. What Are the Roles of Mitochondrial Stress Responses and Mitohormesis in Neurodegenerative Disorders?
  30. Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
  31. Nucleolar targeting of lyssavirus P-protein is isoform- and phylogroup-specific.
  32. Targeted TP53 and KRAS Modulation Via AuNP-Mediated RNA Delivery Suppresses Cancer Progression.
  33. Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.
  34. Template nicking suppresses promoter-independent antisense transcription in IVT via R-loop-mediated strand displacement.
  35. METTL3 safeguard cancer cells from programmed cell death during detachment from their surrounding extracellular matrix.
  36. N1-Methylpseudouridine directly modulates translation dynamics.
  37. Multilayer Host Engineering of Saccharomyces cerevisiae to Enhance Cricket Paralysis Virus (CrPV) Internal Ribosome Entry Site Mediated Translation.
  38. The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation.
  39. WTAP Interferes With Ferroptosis by Regulating the m6A Modification of SF3B1 to Mediate the Malignant Progression of Endometrial Cancer.
  40. RNA Methylation in Cancer Metabolism: from Mechanisms to Therapeutic Opportunities.
  41. Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.
  42. Valine availability controls oncogenic cell-cycle progression through translation of D-type cyclins.
  43. Translating the green code: Ribo-Seq for photosynthetic eukaryotes in focus.
  44. Single-molecule experiments reveal NusG displaces transcription initiation factor σ70 from mature elongation complexes.
  45. Mapping of CELF1-RNA interactions reveals post-transcriptional control of lens development.
  46. Foliar-applied double-stranded RNA is mobile, transfers to plant pathogens, and triggers RNAi.
  47. Short-term hypoxia and nutrient deprivation stress induced shifts in p53 isoform expression in HepG2 tumourspheres.
  48. Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.
  49. TGFβ pathway represses hepatic ribosome biogenesis and protein synthesis by regulating p70S6K-S6RP proteins.
  50. Introduction of the Ribo-BiFC method to plants using a split mVenus approach.
  51. Regulation of trehalose biosynthesis and thermotolerance by the Cryptococcus neoformans HECT E3 ubiquitin ligase Rsp5.
  52. Mechanism of RNA Oxidation and Its Inhibitor Involved in Ang II-Induced Cardiomyocyte Hypertrophy.
  53. Structural basis of long non-coding RNA PVT1 interactions with select mRNAs universal in pan-cancer system: A computational study.
  54. Metal ions govern coronavirus endoribonuclease activity.
  55. EIF2AK2 Globally Binds and Regulates the Expression and Alternative Splicing of T2D-Related Genes in INS1 Cell.
  56. A Novel Mechanism of Berberine Targeting EIF2AK2 Dimerization Attenuates Methylglyoxal-Induced Endothelial Senescence and Apoptosis.
  57. Dilated cardiomyopathy-associated RNA-binding motif protein 20 regulates long pre-mRNAs in neurons.
  58. Biologics for bone regeneration: advances in cell, protein, gene, and mRNA therapies.
  59. Regulation of stress tolerance by CREB1 sustains multiple myeloma cell survival.
  1. Nucleic Acids Res. 2026 Jan 05. pii: gkaf1372. [Epub ahead of print]54(1):
    Eukaryotic initiation factor eIF3 facilitates loading of eukaryotic release factor eRF1 or suppressor tRNA to the ribosome.
    Ekaterina Shuvalova, Alexey Shuvalov, Walaa Al Sheikh, Alexandr Klishin, Nikita Biziaev, Elena Alkalaeva.
      Eukaryotic translation initiation factor eIF3 plays a pivotal role in 48S preinitiation complex assembly and ribosomal scanning. It binds simultaneously to the 40S ribosomal subunit and the eIF4F cap-binding complex, which, through its interaction with poly(A)-binding protein (PABP), facilitates closed-loop mRNA structure formation. PABP also interacts with the eukaryotic release factor eRF3, thereby co-localizing initiation and release factors, and suggesting potential functional crosstalk. Using a reconstituted mammalian translation system, we demonstrate that eIF3 significantly enhances translation termination. Specifically, eIF3 promotes the loading of eRF1 into the ribosomal A site, accelerating the GTPase activity of eRF3 and the rate of peptide release. We also show that eIF3 facilitates the binding of suppressor or near-cognate tRNAs to stop codons to enable readthrough and continued elongation. These findings establish a conserved, direct role of eIF3 in regulation both translation termination and stop codon readthrough, a mechanism particularly relevant within closed-loop mRNA structures and during upstream open reading frame translation.
    DOI:  https://doi.org/10.1093/nar/gkaf1372
  2. Proc Natl Acad Sci U S A. 2026 Jan 20. 123(3): e2519770123
    A bacterial translation activator with an intrinsically disordered RNA-binding region.
    Pallabi Basu, Elizabeth A Farland, James C Charity, Kade A Townsend, Simon L Dove.
      Bacterial RNA-binding proteins (RBPs) that control the translation of multiple transcripts act largely as negative regulators. Here, we report the identification and characterization of a positive regulator of translation (called PhaF) in the opportunistic pathogen Pseudomonas aeruginosa. Using CLIP-seq and CLAP-seq we identify upward of 50 transcripts targeted by PhaF. We demonstrate that PhaF acts to stimulate the translation of target mRNAs by binding upstream of the Shine-Dalgarno sequence using one or more of the multiple KPAA motifs located in an intrinsically disordered region of the protein. Importantly, we show that PhaF plays a key physiological role in P. aeruginosa through its translational control of the pslA transcript required for exopolysaccharide synthesis and biofilm formation. Our findings uncover an activator of translation in bacteria that binds target transcripts using an RNA-binding region reminiscent of those that are prominent in eukaryotic RBPs.
    Keywords:  IDR; PhaF; Pseudomonas aeruginosa; PslA; post-transcriptional regulator
    DOI:  https://doi.org/10.1073/pnas.2519770123
  3. RNA. 2026 Jan 14. pii: rna.080908.125. [Epub ahead of print]
    Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.
    Aaron M Fleming, Cynthia J Burrows.
      Nanopore direct RNA sequencing (DRS) is revolutionizing our ability to analyze the epitranscriptome to evaluate nucleoside modifications in both cellular and synthetic RNA. The process involves minimal handling of fragile RNA strands, one round of reverse transcription to provide a DNA:RNA duplex, and library preparation to directly read nucleotides with their modifications as the pass through a protein nanopore embedded in a membrane. Simultaneous sequencing of hundreds of strands on a chip provides unprecedented access to whole transcriptome information. A key advantage is the long read length that permits, for example, operon-specific epitranscriptomics of ribosomal RNA modifications as a function of cellular stress. By analyzing the entire transcriptome, the interplay of different modifications on the same RNA, or the correlation of changes in different RNAs in the same cell type can be monitored. This review presents several recent examples of the types of experiments that are suitable for nanopore DRS as well as some of the current challenges and future expectations.
    Keywords:  Epitranscriptomics; Nanopore sequence; RNA modifications; Ribosomal RNA
    DOI:  https://doi.org/10.1261/rna.080908.125
  4. bioRxiv. 2026 Jan 11. pii: 2026.01.09.698733. [Epub ahead of print]
    Atypical tetracyclines promote longevity and ferroptotic neuroprotection via translation attenuation.
    Khalyd J Clay, Manuel Sanchez-Alavez, Ian Newman, Na Na, Ana P Verduzco Espinoza, Alan To, Shannon Saad, Hollis T Cline, Michael Petrascheck.
      Preclinical and clinical studies have reported neuroprotective and geroprotective effects of tetracyclines that are independent of their antibiotic activity, but the underlying mechanisms remain unclear. Here, we systematically profile widely used tetracyclines, including impurities and degradation products, and identify translation attenuation as the shared driver of their neuroprotective and longevity-promoting effects, independent of classical tetracycline mechanisms. Instead, we uncover two mechanistically distinct classes of tetracyclines. Mitochondrial-targeting tetracyclines (MitoTets), exemplified by doxycycline, inhibit the mitochondrial ribosome and attenuate cytosolic translation through activation of the Integrated Stress Response (ISR). In contrast, atypical tetracyclines such as 4-epiminocycline and 12-aminominocycline act as cytosolic-targeting tetracyclines (CytoTets), directly inhibiting the cytosolic ribosome, bypassing the ISR, and protecting neurons from ferroptotic cell death. CytoTets are non-antibiotic, brain-penetrant, and neuroprotective in mouse and human neurons, establishing the tetracyclines as a tunable chemical scaffold for selectively targeting translation in aging and neurodegeneration.
    Highlights: The tetracyclines broadly attenuate translation in multiple eukaryotic modelsTranslation attenuation results from both ISR-dependent and ISR-independent mechanismsDiscovery of atypical, cytosolic targeting tetracyclines (CytoTETs) that protect from ferroptosis ISR-independentlyCytoTETs inhibit translation and are neuroprotective in human-derived neurons and mouse hippocampus.
    DOI:  https://doi.org/10.64898/2026.01.09.698733
  5. Apoptosis. 2026 Jan 10. 31(1): 11
    Fibrillarin: bridging ribosome biogenesis and apoptosis in cellular stress and disease.
    Zhuoyuan Zhang, Min Zhang, Zixuan Cao, Haoyan Zhao, Xin Li, Peng Luo.
      Nucleolar stress has emerged as a critical regulatory mechanism linking ribosome biogenesis defects to apoptotic cell death in various pathological conditions. Fibrillarin (FBL), the catalytic component of box C/D small nucleolar ribonucleoproteins, participates in multiple forms of programmed cell death through both p53-dependent and p53-independent pathways across diverse disease contexts including cancer and neurodegeneration. In malignancies including breast cancer, colorectal cancer, and hepatocellular carcinoma, FBL overexpression promotes apoptosis resistance, whereas in Alzheimer's disease and ALS/FTD, FBL dysfunction contributes to pathological neuronal death. Dysregulation of FBL can lead to excessive apoptosis or apoptosis resistance depending on cellular context and disease state. Various cellular stressors trigger aberrant FBL function, disrupting rRNA processing and ribosome assembly, which then activates nucleolar stress responses that culminate in cell death through ribosomal protein-MDM2-p53 axis activation or selective translational control of survival factors in a context-dependent manner. Therefore, targeting FBL-mediated apoptotic pathways is considered an important avenue for the treatment of various cancers and neurodegenerative diseases. In this review, we summarize the major and recent findings focusing on the mechanisms of FBL-regulated apoptosis in disease pathogenesis and provide a systematic overview of current therapeutic strategies targeting nucleolar stress pathways, including RNA polymerase I inhibitors and precision medicine approaches based on p53 status, which may provide important therapeutic targets that merit further investigation.
    Keywords:  Apoptosis; Fibrillarin; Nucleolar stress; Precision therapeutics; Ribosome biogenesis; p53-independent pathways
    DOI:  https://doi.org/10.1007/s10495-025-02220-y
  6. bioRxiv. 2026 Jan 11. pii: 2026.01.09.698697. [Epub ahead of print]
    Chronic stress disrupts the network among stress granules, P-bodies, and motor proteins.
    Yuichiro Adachi, Masashi Masuda, Yutaka Taketani, Paul J Anderson, Pavel V Ivanov.
      Stress granules (SGs) are dynamic RNA granules that rapidly form in response to various stresses concurrent with mRNA translation shutdown, contributing to cellular adaptation and disease pathogenesis. While SG assembly and disassembly under acute stress have been extensively characterized, how SGs behave under chronic stress remains poorly understood. We previously reported that chronic stress preconditioning inhibits the earliest steps of SG assembly via translation-dependent mechanisms. In contrast, the regulation of SG maturation under chronic stress has not yet been investigated. Here, we show that chronic stress decreases SG size by disrupting the MYH9-dependent myosin crosstalk with core SG nucleator G3BP1. This defect leads to impaired SG and processing body (PB) docking as well, limiting the biogenesis of early SGs. Furthermore, chronic stress reduces expression of the SG nucleator UBAP2L, required for SG-PB docking, thus exacerbating these deficiences. In summary, chronic stress disrupts the myosin-SG-PB network and inhibits SG maturation in a translation-independent manner.
    Summary: Chronic stress disrupts the MYH9 network with G3BP1, which inhibits stress granule (SG) assembly. It also decreases UBAP2L levels, which inhibits SG and processing body docking. Disrupted MYH9 network further inhibits this docking, thus blocking maturation of SGs.
    DOI:  https://doi.org/10.64898/2026.01.09.698697
  7. RNA. 2026 Jan 12. pii: rna.080824.125. [Epub ahead of print]
    Bridging single-molecule and genome-wide studies of cellular mRNA translation.
    Adam Koch, Kotaro Tomuro, Taisei Wakigawa, Tatsuya Morisaki, Shintaro J Iwasaki, Timothy J Stasevich.
      The translation of mRNA is a tightly regulated, energy-intensive process that drives cellular diversity. Understanding its control requires tools that can capture behavior across scales. Over the past two decades, two complementary techniques have emerged that have transformed our understanding of mRNA translation within cells: ribosome profiling (Ribo-Seq) and live, single-molecule imaging. Ribo-Seq provides genome-wide, codon-level maps of ribosome positions, revealing pause sites, novel open reading frames, and global translation efficiencies. In contrast, live, single-molecule imaging visualizes translation on individual mRNAs in living cells, uncovering heterogeneous initiation, elongation, pausing, and spatial organization in real time. Together, these methods offer complementary strengths - molecular breadth versus temporal and spatial precision - but are rarely applied in tandem. Here, we review their principles, key discoveries, and recent innovations that are bringing them closer together, including endogenous tagging, higher-throughput imaging, absolute calibration, and spatially resolved footprinting. Integrating these approaches promises a unified, multiscale view of translation that connects the dynamics of individual ribosomes to genome-wide patterns of protein synthesis.
    DOI:  https://doi.org/10.1261/rna.080824.125
  8. Genes Dev. 2026 Jan 14.
    tRNA synthetase activity is required for stress granule and P-body assembly.
    Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon.
      Translation elongation defects activate the integrated stress response (ISR), but whether and how ribosome stalls are cleared to enable mRNA release for ribonucleoprotein (RNP) granule assembly remain unclear. We show that blocking tRNA aminoacylation generates persistent uncollided ribosome stalls that inhibit stress granule and P-body assembly despite robust ISR activation. Collided ribosomes are rapidly cleared by ZNF598-dependent ribosome-associated quality control within 4 h, while uncollided stalls resist clearance and persist for >16 h. Puromycin releases persistent stalls and restores RNP granule formation. The block in stress granule assembly is generalizable across tRNA synthetase inhibitors and amino acid deprivation. Therefore, stress granules represent signal integrators reporting translation elongation status when initiation is suppressed. Our findings reveal that translation quality control pathways selectively clear collided ribosomes, establish that translation elongation stress uncouples RNP granule assembly from the ISR, and suggest that tolerating uncollided stalls may be adaptive for cotranslational processes essential for cellular function.
    Keywords:  P-bodies; halofuginone; integrated stress response; ribosome collisions; ribosome-associated quality control; stress granules; tRNA synthetase; translation elongation
    DOI:  https://doi.org/10.1101/gad.353535.125
  9. bioRxiv. 2026 Jan 09. pii: 2026.01.09.698670. [Epub ahead of print]
    Mechanistic insights into E. coli recovery from growth arrest.
    Ahmed Hassan, Yuko Nakano, Howard Gamper, Isao Masuda, Matyas Pinkas, Sathya Nagarajan, Jonathan Dworkin, Gregor Blaha, Ya-Ming Hou, Gabriel Demo.
      Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli Δ rimM strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this arrested state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a significantly longer delay in recovery than other 30S maturation factors, including RbfA - the presumed primary factor in 30S maturation. Cryo-EM analysis of Δ rimM ribosomes revealed a delayed recruitment of ribosomal proteins to the 30S head domain and increased occupancy of the initiation factors IF1 and IF3, as well as recruitment of the silencing factor RsfS to the 50S subunit. These coordinated changes provide a safeguarding mechanism to block the assembly of premature 70S ribosomes. Notably, while the delayed 30S assembly in Δ rimM reduces the activity of global protein synthesis during the recovery phase, bacteria attempt to compensate for this deficiency by producing higher levels of the ribosomal machinery, indicating a programmatic change in energy allocation to generate the ribosome machinery. These findings highlight the importance of the RimM-assisted assembly of the ribosomal head domain for bacterial recovery from growth arrest.
    DOI:  https://doi.org/10.64898/2026.01.09.698670
  10. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1531. [Epub ahead of print]54(2):
    TlyA is a 23S and 16S 2'-O-methylcytidine methyltransferase important for ribosome assembly in Bacillus subtilis.
    Jennie L Hibma, Lia M Munson, Joshua D Jones, Taylor M Nye, Kristin S Koutmou, Lyle A Simmons.
      Ribosomal RNA (rRNA) methylation is conserved across biology, yet the effect of rRNA methylation on ribosome function is poorly understood. In this work, we identify a biological function for the rRNA 2'-O-methylcytidine methyltransferase TlyA, conserved between Bacillus subtilis and Mycobacterium tuberculosis (Mtb). The tlyA deletion in B. subtilis confers a cold sensitive phenotype and resistance to aminoglycoside and cyclic polypeptide antibiotics. We show that ∆tlyA cells have ribosome assembly defects characterized by accumulation of the 50S subunit. Using a genetic approach, we tested the importance of potential catalytic residues and S-adenosyl-l-methionine (SAM) cofactor binding sites identified based on sequence alignments with other rRNA methyltransferases. We show that B. subtilis TlyA uses the common rRNA methyltransferase catalytic triad KDK and SAM binding motif GxSxG. This differs from TlyA from Mtb, which requires an additional tetrapeptide linker. Together our work demonstrates that B. subtilis tlyA is critical for ribosome assembly and we identify key residues for TlyA function in vivo. Since Escherichia coli lacks TlyA or a functional equivalent, our work highlights key differences in ribosome maturation between B. subtilis, Mtb, and more divergent Gram-negative bacteria providing new insight into rRNA maturation and antibiotic resistance mechanisms.
    DOI:  https://doi.org/10.1093/nar/gkaf1531
  11. Eur Respir Rev. 2026 Jan;pii: 250049. [Epub ahead of print]35(179):
    The ribosomal landscape in influenza A virus infection: from molecular mechanisms to clinical relevance.
    Johannes Pott, Vitalii Kryvenko, István Vadász.
      Influenza A virus (IAV) infections continue to represent a significant global health concern, both in terms of severe individual cases of acute respiratory distress syndrome (ARDS) and the potential for the emergence of pandemics. Despite decades of research, therapeutic options remain limited and the pathogenesis of severe disease is not yet fully understood. One critical yet underappreciated aspect is how IAV reprogrammes the ribosomal landscape of the host to facilitate viral replication and evade immune responses. Ribosomes take centre stage during infection, as both the immune response and viral propagation depend on the protein synthesis machinery. Recent studies have shown that the ribosome is not a static structure but can undergo dynamic changes in composition and function (ribosomal heterogeneity), which may influence the balance between viral propagation and host defence. Additionally, cancer research has remarkably demonstrated the feasibility of targeting the ribosome therapeutically. In this review, we summarise emerging evidence on how IAV hijacks the ribosomal landscape, including ribosomal biogenesis, ribosomal proteins, translation factors and associated signalling pathways, and how these changes may shape the course of infection, immune response and lung injury. Drawing parallels with cancer biology, we explore whether components of this reprogrammed landscape could serve as therapeutic targets in severe IAV infection and ARDS. By connecting molecular mechanisms with clinical relevance, we aim to highlight a novel perspective on host-virus interaction that could open avenues for future treatment strategies.
    DOI:  https://doi.org/10.1183/16000617.0049-2025
  12. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1412. [Epub ahead of print]54(2):
    PolyA tail segmentation improves the stability of the template DNA and increases the translatability of in vitro transcribed mRNA.
    Tomasz Spiewla, Karol Czubak, Zofia Pilch, Marek R Baranowski, Pawel S Krawczyk, Kamila Affek, Wiktor Antczak, Marta Szulc-Gasiorowska, Sebastian Chmielinski, Seweryn Mroczek, Michal Brouze, Dominika Nowis, Jakub Golab, Andrzej Dziembowski, Jacek Jemielity, Joanna Kowalska.
      PolyA tail regulates messenger RNA (mRNA) localization, stability, and translation. PolyA length affects the durability and translational activity of both endogenously and exogenously delivered mRNAs. However, long polyA stretches can undergo recombination during amplification in bacterial plasmids, impairing the production of in vitro transcribed mRNA with long polyAs. PolyA tail segmentation with heteronucleotide spacers has recently emerged as a solution. Here, we developed segmented polyA patterns that stabilize the sequence during DNA amplification and enhance mRNA translation. We designed 15 novel genetically modified polyA variants, differing in the length, placement, and frequency of spacers, and the overall length (from ~120 to 200 nucleotides). We evaluated their stability in DNA plasmids and homogeneity, translational activity, and durability in cell culture of the resulting mRNAs, comparing them to A90 tail and other known solutions, including those from existing mRNA vaccines. Selected sequences were validated in vivo. Surprisingly, we found that even frequent heteronucleotide insertions produce functional polyA tails. The most notable enhancements in protein production were observed for a segmented tail exceeding 200 nt in length [A30(CA15)11; up to six-fold compared to mRNA with A90 tails]. Our findings extend the scope of possible polyA modification strategies, offering new possibilities for advancing mRNA therapeutics.
    DOI:  https://doi.org/10.1093/nar/gkaf1412
  13. bioRxiv. 2026 Jan 09. pii: 2026.01.09.698267. [Epub ahead of print]
    RNA Polymerase III subunit Polr3a is required for craniofacial cartilage and bone development.
    Bailey T Lubash, Roxana Gutierrez, Kade Fink, Colette A Hopkins, Jessica C Nelson, Kristin E N Watt.
      Transcription by RNA Polymerase III (Pol III) is essential for ribosome biogenesis and translation in all cells, but pathogenic variants in genes encoding subunits of Pol III lead to tissue-specific phenotypes including craniofacial differences. To understand the function of Pol III in craniofacial development, we examined polr3a mutant zebrafish. These mutants display hypoplasia of the neural crest cell-derived craniofacial cartilage and bone but, surprisingly, no significant changes were observed in neural crest cell proliferation or survival during embryogenesis. At larval stages, increased cell death was observed throughout the head, including in the craniofacial cartilage. These changes coincide with reduced transcription of transfer RNAs and reduced ribosome biogenesis in polr3a mutant zebrafish. To determine tissue-specific transcriptional changes, we performed single-cell RNA-sequencing. Analysis revealed both global and cartilage-specific changes, including upregulation of tp53 . However, Tp53 inhibition alone was not sufficient to rescue craniofacial cartilage and bone, indicating that additional factors are important to support cartilage and bone growth in polr3a mutants. Altogether, our study provides new mechanistic insights into the functions of Pol III in craniofacial development.
    DOI:  https://doi.org/10.64898/2026.01.09.698267
  14. J Comput Aided Mol Des. 2026 Jan 10. 40(1): 43
    Inhibitor screening identifies Entecavir as a promising candidate targeting human eIF4E to block cap-dependent translation in cancer: an integrated in silico and in vitro study.
    Kishore Nagasubramanian, Preethi Vincent, Krishna Kant Gupta, Sam Aldrin Chandran.
      Eukaryotic translation initiation factor 4E (eIF4E) plays a critical role in cap-dependent translation by binding the 7-methylguanosine (m⁷G) cap at the 5' end of mRNAs, thereby regulating the synthesis of proteins essential for cell growth, survival, and proliferation. Under homeostatic conditions, eIF4E selectively translates a subset of mRNAs; however, in cancer, aberrant signaling leads to persistent activation of eIF4E, promoting tumor progression, metastasis, and resistance to therapy. Despite its clinical relevance, very few studies have explored direct targeting of eIF4E's cap-binding function using small molecules as a therapeutic strategy. In the present study, we adopted a multi-layered in silico and experimental pipeline to identify small-molecule inhibitors that can effectively disrupt human eIF4E activity. A library of over 400,000 compounds from the ZINC database was virtually screened using the Glide docking protocol in Schrödinger-Maestro. Compounds were shortlisted based on binding affinity and drug-likeness properties. Among the top hits, ZINC145267992, a nucleoside-like molecule, showed promising interaction with the cap-binding pocket of eIF4E. To overcome potential druggability limitations and improve clinical relevance, Entecavir (ETV), a clinically approved antiviral drug for hepatitis B and a structural analogue of ZINC145267992, was identified as a candidate for drug repurposing. Molecular dynamics simulations confirmed the stable interaction of ETV with eIF4E. Our findings not only reinforce the feasibility of targeting eIF4E in cancer but also demonstrate that repurposing FDA-approved drugs like Entecavir could offer a practical and efficient route to therapeutic intervention. This integrative approach opens new avenues for eIF4E-targeted strategies in oncology, aiming to selectively impair oncogenic translation.
    Keywords:  Anti-cancer activity; Entecavir; In vitro assay; Molecular docking and simulations; eIF4E inhibitors
    DOI:  https://doi.org/10.1007/s10822-025-00759-1
  15. Nucleic Acids Res. 2026 Jan 05. pii: gkaf1421. [Epub ahead of print]54(1):
    Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4.
    Xiaojie Han, Seisuke Yamashita, Kozo Tomita.
      Lin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferases 4 and 7 (TUT4/7) represses let-7 expression by blocking Dicer processing, thereby regulating cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM). Here, we report the cryogenic electron microscopy structure of human TUT4 complexed with Lin28A and oligo-uridylated pre-let-7, representing the elongation stage of oligo-uridylylation. Structural and biochemical analyses suggest that, after recruitment of pre-let-7 to the LIM through interactions between its terminal stem-loop and Lin28A, the CM associates with the LIM through protein-protein interactions. The double-stranded stem region of pre-let-7 is surrounded by the CM and LIM, the upper portion of the duplex unwinds, and the 3' end of pre-let-7 is positioned in the CM catalytic site for the initiation of oligo-uridylylation. At the oligo-uridylylation stage, the CM finger domain clamps the double-stranded region of pre-let-7, thereby further stabilizing the pre-let-7:TUT4 complex, enabling processive elongation of the uridine tail by the CM. Thus, the LIM functions as a stable anchor, working together with Lin28A to ensure efficient and processive oligo-uridylylation of pre-let-7.
    DOI:  https://doi.org/10.1093/nar/gkaf1421
  16. Nat Protoc. 2026 Jan 15.
    iTP-seq: a scalable profiling workflow to characterize bacterial translation landscapes in vitro.
    Mélanie Gillard, Thibaud T Renault, C Axel Innis.
      Uneven translation rates resulting from mRNA context, tRNA abundance, nascent amino acid sequence or various external factors play a key role in controlling the expression level and folding of the proteome. Inverse toeprinting coupled to next-generation sequencing (iTP-seq) is a scalable in vitro method for characterizing bacterial translation landscapes, complementary to ribosome profiling (Ribo-seq), a widely used method for determining transcriptome-wide protein synthesis rates in vivo. In iTP-seq, ribosome-protected mRNA fragments known as inverse toeprints are generated by using RNase R, a highly processive 3' to 5' RNA exonuclease. Deep sequencing of these fragments reveals the position of the leading ribosome on each mRNA with codon resolution, as well as the full upstream coding regions translated by these ribosomes. Consequently, the method requires no a priori knowledge of the translated sequences, enabling work with fully customizable transcript libraries rather than previously sequenced genomes. As a standardized framework for inverse toeprint generation, amplification and sequencing, iTP-seq can be used in combination with different types of libraries, in vitro translation conditions and data-analysis pipelines tailored to address a range of biological questions. Here, we present a robust protocol for iTP-seq and show how it can be integrated into a broader workflow to enable the study of context-dependent translation inhibitors, such as antibiotics. The time required to complete this workflow is ~10 d, and the workflow can be carried out by an experienced molecular biologist, with data analysis also requiring a working knowledge of command-line tools and Python scripts.
    DOI:  https://doi.org/10.1038/s41596-025-01294-x
  17. bioRxiv. 2026 Jan 07. pii: 2026.01.06.698062. [Epub ahead of print]
    Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.
    Abby R Thurm, Tanya H Nguyen, Jesus Damian Torres Campos, Matthew Mansfield, Lacramioara Bintu, Lauren D Hagler.
      RNA structures that form inside living cells influence processes ranging from translation to RNA decay, many of which are controlled by RNA-binding proteins (RBPs). Because RBP specificity depends on both local RNA structure and sequence motifs, traditional pulldown-based methods often obscure the structural context of bound RNAs. Here, a quantitative framework based on dimethyl sulfate mutational profiling and sequencing (DMS-MaPseq) is introduced that jointly measures RNA structure and protein binding at single-nucleotide resolution in human cells, enabling estimation of effective RNA-protein affinities and fractional occupancy directly in cells. Application of this approach to a 1,600-member library of MS2 hairpin mutants reveals that RNA folding is the strongest determinant of MS2 coat protein (MCP) recognition, and that stable MS2 structures must form for MCP to bind its target sequence. MCP also shows strong preference for its consensus loop sequence while displaying minimal dependence on stem length beyond ten base pairs or on stem GC content. Incorporation of an inducible degron fused to MCP allows precise tuning of intracellular protein concentrations analogous to those of many endogenous RBPs and show that DMS reactivity changes can be used to infer binding specificities across a subsaturating regime. A quantitative occupancy framework further shows that inferred fraction-bound values accurately predict how efficiently MCP fused to a downregulatory-domain drives RNA degradation. Together, these results establish a generalizable approach for measuring RBP-RNA affinities with structural resolution in living cells, dissecting how sequence and structure contribute to RBP recognition, and quantitatively linking occupancy to functional output.
    DOI:  https://doi.org/10.64898/2026.01.06.698062
  18. NAR Genom Bioinform. 2026 Mar;8(1): lqaf197
    Structural analysis of uridine modifications in solved RNA structures.
    Sebastian J Arteaga, Brent M Znosko.
      Naturally occurring uridine modifications in RNA play critical roles in modulating RNA stability, translation, and immune responses. While detection methods have advanced, a comprehensive structural analysis across experimentally determined RNA 3D structures remains limited. In this study, we systematically examined six uridine modifications-pseudouridine (PSU), 5-methyluridine (5MU), 3-methyluridine (UR3), O2'-methyluridine (OMU), 4-thiouridine (4SU), and 5,6-dihydrouridine (H2U)-using data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank. After curation, we identified 2982 PSU, 736 5MU, 232 UR3, 429 OMU, 314 4SU, and 171 H2U residues across RNA-containing structures. These modifications were primarily found in ribosomal and transfer RNAs, often localized within hairpin secondary structures. Sugar pucker analysis revealed modification-specific preferences for C3'-endo and C2'-endo conformations. To assess structural impacts, we generated sequence-representative structures and compared modified versus unmodified forms using all-atom root-mean-square deviation analysis. Most modifications showed high similarity to their unmodified counterparts (RMSD [Formula: see text] 1.0 Å), though deviations were notable for certain PSU-, 5MU-, and 4SU-containing motifs. Despite overall similarity, interaction differences were observed between modified and canonical uridines. This work provides a detailed structural overview of uridine modifications, offering insights into their conformational behavior and implications for RNA function. These findings may inform future efforts in RNA-targeted therapeutics and structural biology.
    DOI:  https://doi.org/10.1093/nargab/lqaf197
  19. G3 (Bethesda). 2026 Jan 14. pii: jkaf313. [Epub ahead of print]
    Noc1 downregulation induces nucleolar stress and upregulates p53 isoforms, with a robust increase of the truncated p53E isoform in Drosophila wing discs.
    Andrea Vutera Cuda, Shivani Bajaj, Valeria Manara, Paola Bellosta.
      Disruption of ribosome biogenesis triggers nucleolar stress, a conserved cellular response that activates p53. We previously demonstrated that depletion of Nucleolar Complex Protein 1 (Noc1) in Drosophila wing imaginal discs impairs rRNA maturation and ribosome assembly, resulting in elevated p53 levels and apoptosis, hallmarks of nucleolar stress. The Drosophila p53 gene produces four mRNA isoforms, yet their individual contributions to nucleolar stress responses remain poorly understood. Using newly designed isoform-specific qPCR primers, we found that although all p53 isoforms exhibit moderate transcriptional changes following Noc1 reduction, the truncated isoform p53E is robustly and preferentially upregulated. Notably, p53E lacks the N-terminal transactivation domain and has been reported to negatively regulate p53-induced apoptosis in specific tissues. Furthermore, our analyses indicate that γ-H2AV accumulation arises from caspase-dependent apoptosis rather than primary genomic lesions, suggesting the activation of a p53-dependent stress pathway distinct from canonical genotoxic pathways. Together, these findings suggest that p53E may be part of a novel mechanism activated during nucleolar stress, providing insight into how cells adapt to defects in ribosome biogenesis.
    Keywords:   Drosophila imaginal discs; Noc1; apoptosis; isoform primer design; mutant screen; nucleolar stress; p53 isoforms; primer specificity; γ-H2AV
    DOI:  https://doi.org/10.1093/g3journal/jkaf313
  20. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1512. [Epub ahead of print]54(2):
    Tho1 and MOS11 promote nucleic acid double-strand unwinding by facilitating DEAD-box helicase oligomerization.
    Fabienne Becker, Matthias Bastian Miosga, Minhaz Mannan, Vera Bettenworth, Wieland Steinchen, Katja Sträßer, Peter Friedhoff.
      DEAD-box helicases are essential for gene expression and RNA metabolism. However, the mechanisms regulating their activity remain largely elusive. The DEAD-box helicase DDX39B/UAP56 forms a 2:1 complex with the C-terminal domain (CTD) of RNA-binding protein Tho1, but the functional relevance of this interaction is still elusive. Here, we show that the Tho1-CTD stimulates the helicase activity of Sub2, the yeast homologue of DDX39B/UAP56, by acting as a rigid scaffold that promotes Sub2 oligomerization on RNA. The Tho1-CTD has two conserved α-helical motifs, each interacting with one Sub2, and we demonstrate that both motifs are essential for the stimulation. This scaffolding mechanism is shared across species, as the Tho1 ortholog MOS11 from Arabidopsis thaliana stimulates A. thaliana UAP56. Interestingly, MOS11 has five of the conserved α-helical motifs, which are connected by flexible linkers. We show that the number and spatial separation of these motifs are critical for stimulation and that MOS11 stimulates unwinding on a broader range of substrates than the Tho1-CTD. The cofactor-mediated helicase oligomerization is reminiscent of the self-oligomerization observed for other DEAD-box helicases. Furthermore, our data illustrate how cofactor architecture affects substrate specificity and provide a comprehensive mechanistic framework for cofactor-mediated helicase activation.
    DOI:  https://doi.org/10.1093/nar/gkaf1512
  21. bioRxiv. 2026 Jan 09. pii: 2026.01.08.698407. [Epub ahead of print]
    LOTUS-domain proteins activate Vasa to drive germ granule assembly.
    Ian F Price, Chin Wang, Wen Tang.
      Germline development relies on perinuclear membraneless germ granules, yet the mechanisms underlying their assembly remain incompletely understood. Here we uncover a conserved and central role for LOTUS-domain proteins in driving germ granule assembly. In C. elegans , the LOTUS-domain protein EGGD-1/MIP-1 at sub-stoichiometric levels recruits Vasa protein GLH-1 to the nuclear periphery. Acting as a catalyst, EGGD-1 impacts the ATPase cycles of GLH-1 by preferentially binding to its open conformation, enhancing its RNA binding activities, and facilitating its transition to the closed conformation. GLH-1 in the closed state enriches mRNAs at the nuclear periphery, which enables the accumulation of RNA-binding proteins including PGL-1 and PGL-3. Using human cells, we demonstrate the LOTUS-domain protein TDRD5 similarly recruits DDX4, the human Vasa homolog, and stimulates the formation of intermitochondrial cement. Collectively, these findings reveal evolutionarily conserved stimulatory effect of LOTUS-domain protein in Vasa activity and provide a unified model for germ granule assembly across species.
    DOI:  https://doi.org/10.64898/2026.01.08.698407
  22. Genetics. 2026 Jan 13. pii: iyag007. [Epub ahead of print]
    The Ubiquitin-Proteasome Pathway Mediates Selective Degradation of Unloaded Argonaute Proteins in C. elegans.
    Jenny M Zhao, Dieu An H Nguyen, Diego Cervantes, Brandon Vong, Carolyn M Phillips.
      Argonaute proteins are essential effectors of small RNA-mediated gene regulation, yet the extent to which their stability depends on small RNA loading remains poorly understood. In Caenorhabditis elegans, we systematically disrupted the small RNA binding capacity of multiple Argonaute proteins to assess their stability in the absence of small RNA partners. We found that while most Argonautes remain stable when unable to bind small RNAs, a subset, including PRG-1, HRDE-1, and PPW-2, exhibited markedly reduced protein levels. Focusing on the PIWI-clade Argonaute PRG-1, we show that its destabilization occurs post-translationally and is independent of mRNA expression or translational efficiency. Instead, unbound PRG-1 is targeted for degradation by the ubiquitin-proteasome system. Additionally, the failure to load piRNAs disrupts PRG-1 localization to perinuclear germ granules. We further identify the E3 ubiquitin ligase EEL-1 as a factor contributing to the degradation of unloaded PRG-1. These findings uncover a critical role for small RNA loading in maintaining the stability and localization of a subset of Argonaute proteins, and reveal a quality control mechanism that selectively eliminates unbound PRG-1 to preserve germline regulatory fidelity.
    DOI:  https://doi.org/10.1093/genetics/iyag007
  23. bioRxiv. 2026 Jan 05. pii: 2026.01.05.697706. [Epub ahead of print]
    CNOT10 is involved in TTP-mediated AU-rich element containing mRNA metabolism, independent of mRNA decay regulation.
    Yukitomo Arao, Jason G Williams, Wi Lai.
      Tristetraprolin (TTP)/ ZFP36 is an RNA binding protein that is involved in the turnover regulation of target adenylate-uridylate-rich RNA element (ARE) containing mRNAs. AREs are present in the 3'-untranslated region of transcripts expressed from many immediate-early genes, including cytokines and chemokines. It has been demonstrated that TTP-mediated post-transcriptional mRNA decay regulation is crucial for modulating physiological control, particularly in response to inflammatory stimulation. TTP is associated with the CCR4-NOT deadenylation complex through the TTP C-terminus to promote mRNA decay. However, it is not fully understood whether there are additional sites within TTP that contribute to its function through interacting with other factors. We analyzed the functionality of the unique tryptophan residues located in the TTP N-terminus using a cell-based assay system that consists of a tetracycline-responsive CMV promoter-driven, intron-inserted luciferase (LUC). This system enabled us to analyze TTP activity during both the early phase and the steady-state phase of gene expression, as well as in the post-transcriptional mRNA decay following the treatment of tetracycline analogs. Meanwhile, we identified putative TTP associates using a proximity labeling method. We found that tryptophan residues in the TTP N-terminus together with CNOT10, a component of the CCR4-NOT complex, were involved specifically in the reduction of the ARE-containing LUC mRNA level during the early phase of gene expression. However, they were not involved in the decay of LUC mRNA in the steady-state phase. We propose a novel post-transcriptional TTP functionality in the reduction of ARE-containing mRNA level, which differs from the well-characterized mRNA decay activity.
    DOI:  https://doi.org/10.64898/2026.01.05.697706
  24. Apoptosis. 2026 Jan 10. 31(1): 8
    m6A modification and its clinical applications in gynaecological cancer.
    Chavi Ahlawat, Priya Yadav, Nikita Balhara, Sandeep Goyal, Ravindresh Chhabra, Ritu Yadav.
      N6-methyladenosine (m6A) RNA modification plays a pivotal role in gynaecological cancers by regulating tumor initiation, progression, and therapeutic resistance. m6A RNA modification include writers (METTL3/14, RBM15, ZC3H13, WTAP), which catalyze methylation; erasers (ALKBH5, FTO), which remove methyl groups; and readers (YTHDC1, YTHDF1/2/3, IGF2BP1/2/3, HNRNPC/G, HNRNPA2BP1), which interpret m6A marks to regulate the RNA fate. These regulators alter basic RNA metabolism, such as splicing, mRNA stability, translation, and degradation. In gynaecological cancers, both oncogenic and tumor suppressive signaling pathways are also altered by these regulators. Due to their diagnostic, prognostic and predictive value, m6A regulators have emerged as promising biomarkers in gynaecological cancers in recent years. This review highlights the role of m6A regulators and critically evaluates their biomarker and clinical potential in gynaecological cancers.
    Keywords:  CC; EC; Erasers; OC; RNA modification; Readers; Therapy; cirRNA; lncRNA; m6A writers
    DOI:  https://doi.org/10.1007/s10495-025-02204-y
  25. bioRxiv. 2026 Jan 07. pii: 2026.01.07.698160. [Epub ahead of print]
    A long non-coding RNA, afu-254 , is required for the oxidative stress response, cell wall stress response, azole susceptibility and virulence in Aspergillus fumigatus.
    Ritu Devkota, Nava Poudyal, Jazmin Reyes Servin, Julianna Lenz, Kelly M Shepardson, Sourabh Dhingra.
      Long non-coding RNAs play an important role in stress response in all forms of life; however, a tight regulation of lncRNAs is required for normal function. Abnormal expression of lncRNA is associated with uncontrolled cell growth in many forms of cancer. Recent studies have highlighted the role of lncRNAs in Aspergillus fumigatus in azole stress response and virulence. Here, using a transcriptome dataset of A. fumigatus response to stress, we identified afu-254 as an 854bp lncRNA that plays a role in modulating oxidative stress, fungal ARC response, cell wall stress, macrophage phagocytosis and killing ex vivo , and virulence in an invertebrate model of Aspergillus infection. Importantly, afu-254 does not produce cross-azole susceptible response and plays a role in fungal azole response against posaconazole and itraconazole but not voriconazole. Furthermore, we showed that stochiometric levels of afu-254 are important for its function, and ectopic overexpression of afu-254 in the WT strain leads to an antimorph. This phenotype is due to a higher ordered structure that is denatured with heat, indicating the presence of a non-functional structure. In conclusion, we characterized a novel lncRNA, afu-254 , that is important for stress response and virulence in the pathogenic fungus A. fumigatus .
    Importance: Failure of azole treatment for invasive Aspergillus infection by both drug-resistant and drug-sensitive isolates is an area of concern and global importance. Fungal stress response is multifaceted, and long non-coding RNAs have emerged as important players in mediating it, including regulating responses to azole antifungals. Here, we have identified a long non-coding RNA, afu-254 , that plays a role in modulating fungal response to oxidative stress, cell wall stress, azole stress, immune cell stress and is indispensable for virulence in an invertebrate model of invasive Aspergillus infection.
    DOI:  https://doi.org/10.64898/2026.01.07.698160
  26. Nucleic Acids Res. 2026 Jan 14. pii: gkag017. [Epub ahead of print]54(2):
    Strategic variations in sarbecovirus and merbecovirus Nsp1 linker regions for translation inhibition.
    Ruixi Yan, Mingbo Wu, Xiangyu Ge, Qianqian Jin, Moyu Wang, Haolong Zhou, Yan Li, Yue Wang, Shuai Yuan.
      Nonstructural protein 1 (Nsp1) is a key virulence factor of coronaviruses, and its stable binding to the 40S ribosomal mRNA entry channel facilitates multiple functions, including suppression of host immune responses and degradation of host mRNA. To understand the structural basis of the conserved protein across viral lineages, we determined the cryo-EM structures of Nsp1-40S complexes of four coronaviruses from wild animals. Our results show that all Nsp1 proteins engage the mRNA entry channel via their C-terminal domain (CTD), but do not fully restrict the rotational mobility of the 40S head, which retains ∼5° of movement and repositions the Nsp1 linker region. Comparative analysis revealed distinct patterns in the linker regions connecting the N- and CTDs. Sarbecovirus Nsp1 contains a longer linker, whereas the merbecovirus Nsp1 adopts a shorter linker that navigates structural constraints more readily. Functionally, we find that linker length correlates with translation inhibition efficiency, suggesting a structural tuning mechanism. Additionally, variations in linker and helix 1 of the CTD among different lineages may serve as molecular markers for viral classification. Together, our results provide a comparative structural framework for understanding how coronavirus Nsp1 proteins modulate host translation and reflect evolutionary adaptations in ribosome engagement.
    DOI:  https://doi.org/10.1093/nar/gkag017
  27. Nat Rev Immunol. 2026 Jan 15.
    RNA-binding proteins and ribonucleoproteins as determinants of immunity.
    Martin Turner, Georg Petkau.
      Infection triggers one of the most dramatic systemic responses in the body, and the coordinated activation and function of immune cells requires a dynamic regulation of transcriptomes and proteomes. This is achieved by RNA-binding proteins, which, together with RNA, form ribonucleoproteins. These proteins expand the information content of the genome and determine the lifespan, localization and function of RNA. Moreover, they control when, where and how much protein is produced. They can also mediate cell-autonomous immunity to foreign RNA and to misfolded self-RNAs and ensure the fidelity of the transcriptome by acting as RNA modifiers and chaperones to prevent RNA misfolding. These activities are integrated with gene expression programmes that are induced by the pathogen-sensing mechanisms of immune cells, which together activate, and later resolve, immune responses. Here, we review the activities of RNA-binding proteins in immune cells and discuss how perturbations of their function can result in immunodeficiency, autoimmunity and chronic inflammation.
    DOI:  https://doi.org/10.1038/s41577-025-01254-2
  28. Biochimie. 2026 Jan 13. pii: S0300-9084(26)00005-2. [Epub ahead of print]
    Recent advances in protein synthesis inhibitors.
    Alisa P Chernyshova, Petr V Sergiev, Dmitrii A Lukianov, Vera A Alferova.
      Antimicrobial resistance threatens the long-standing efficacy of antibiotics and underscores the need to expand, refine, and diversify antimicrobial therapies. Translation is a uniquely druggable process: its machinery is essential, conserved in bacteria, and sufficiently divergent from the eukaryotic counterpart to enable selectivity. This review synthesizes recent progress on inhibitors of initiation, elongation, termination, and recycling. High-resolution structural and biophysical studies have resolved longstanding ambiguities, reassigned ribosomal binding sites, uncovered stage-specific activities in scaffolds previously thought to act elsewhere, and revealed multistage, context-dependent mechanisms. Beyond the canonical stages, quality-control pathways that offer orthogonal points of intervention were observed. Collectively, these advances support structure-guided, context-aware, and hybrid/combination strategies for antibiotic design and therapeutic development.
    Keywords:  antibiotics; protein synthesis inhibitors; ribosome; translation
    DOI:  https://doi.org/10.1016/j.biochi.2026.01.005
  29. Neurology. 2026 Feb 10. 106(3): e214618
    What Are the Roles of Mitochondrial Stress Responses and Mitohormesis in Neurodegenerative Disorders?
    Eduardo Benarroch.
      Mitochondrial dysfunction is a key pathogenic component of neurodegenerative disorders. Mitochondrial stress, created by accumulation of misfolded proteins, reactive oxygen species, and other mechanisms, triggers signals that promote changes in protein translation and gene transcription aimed at protecting and restoring mitochondrial function and maintaining cellular homeostasis. These quality control responses are the integrated stress response and the mitochondrial unfolded protein response. When triggered by mild mitochondrial stress, these adaptive responses promote mitohormesis, which enhances cell survival and lifespan. The exchange of information between mitochondria allows mitochondrial stress in specific tissues to initiate beneficial adaptations affecting mitochondrial populations in remote tissues and organs. Experimental and human observational studies indicate that approaches to trigger mitohormesis, such as physical exercise, have beneficial effects in neurodegenerative disorders.
    DOI:  https://doi.org/10.1212/WNL.0000000000214618
  30. RNA. 2026 Jan 14. pii: rna.080898.125. [Epub ahead of print]
    Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
    Ashley Chin, Jonathan Bergeman, Laudine Communal, Seda Barutcu, Jonathan Boulais, Gene Yeo, Anne-Marie Mes-Masson, Eric Lecuyer.
      Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. In this study, we report that several mRNAs encoding evolutionarily conserved epithelial polarity regulatory proteins, including Zo-1, Afdn and Scrib, are localized to cell junction regions in Drosophila epithelial tissues and human epithelial cells. Targeting of these mRNAs coincides with robust junctional distribution of their encoded proteins, and these transcripts are translated in proximity to cell junction regions. Through systematic immuno-labeling, we identify a collection of RNA binding proteins with cell junction distribution patterns, several of which associate with junctional transcripts and are functionally required for proper targeting of ZO-1 and SCRIB proteins. Loss-of-function of two candidate factors, MAGOH and PCBP3, differentially impacts junctional mRNA, with MAGOH knock-down reducing Zo-1 and Scrib transcript targeting and localized translation, while PCBP3 knock-down only perturbs local translation. Depletion of Drosophila MAGO in vivo in follicular epithelial cells also disrupts the distribution of junctional transcripts and proteins. Finally, through tissue microarray analysis of ovarian cancer tumor specimens, we find that the expression of MAGOH and ZO-1 is positively correlated and that both proteins are potential biomarkers of good prognosis. We conclude that localized mRNA regulation at cell junction regions is important for modulating epithelial cell integrity.
    Keywords:  Cell Junction Regions; Epithelial Cell Integrity; Localized Translation; RNA Binding Proteins; mRNA Localization
    DOI:  https://doi.org/10.1261/rna.080898.125
  31. J Gen Virol. 2026 Jan;107(1):
    Nucleolar targeting of lyssavirus P-protein is isoform- and phylogroup-specific.
    Gregory W Moseley, Yilin Zhang, Cassandra T David, Stephen M Rawlinson.
      The nucleolus is a multifunctional hub and a common target of viral proteins, yet its role in infections by cytoplasmically replicating RNA viruses remains poorly defined. In rabies virus (RABV), the phosphoprotein (P-protein) isoform P3 localizes to nucleoli and inhibits rRNA biogenesis, whereas P1 lacks nucleolar targeting, even when forced into the nucleus. Here, we show that nucleolar targeting is an isoform- and phylogroup-specific property of lyssavirus P-proteins. Isoforms P3-P5 accumulate in nucleoli, whereas P1 and P2 are excluded. Comparative analyses revealed that P3 nucleolar targeting is conserved in phylogroup I but absent in phylogroup II lyssaviruses. Co-immunoprecipitation assays identified conserved interactions with nucleolin and nucleophosmin (NPM1) but divergent binding to Treacle and nucleolar and coiled-body phosphoprotein 1 (NOLC1). These findings define nucleolar targeting as a gain-of-function of truncated P isoforms, demonstrate its conservation across phylogroup I lyssaviruses and suggest broader engagement with membraneless compartments, highlighting potential therapeutic vulnerabilities.
    Keywords:  RNA virus; nuclear trafficking; nucleolus; phosphoprotein; rabies
    DOI:  https://doi.org/10.1099/jgv.0.002214
  32. Curr Gene Ther. 2026 Jan 08.
    Targeted TP53 and KRAS Modulation Via AuNP-Mediated RNA Delivery Suppresses Cancer Progression.
    Muhammed Dündar, Dilek Çam Derin, İrem Nur Menevşe, Enes Gültekin, Ahmet Koç.
       BACKGROUND: Small RNAs play a pivotal role in gene regulation, mediating RNAinduced transcriptional activation and post-transcriptional gene silencing. Their high specificity and versatility make them indispensable tools for investigating gene function, elucidating disease mechanisms, and developing targeted therapeutic strategies.
    METHODS: We developed an AuNP-based RNA delivery system to enhance stability and uptake of therapeutic RNAs targeting TP53 and KRAS pathways. AuNPs were synthesized via citrate reduction and conjugated with siRNA.923 (KRAS-targeting siRNA) and dsP53-285 (p53-stimulating saRNA). A549 and HCT116 cells were transfected with conjugates. Gene expression was analyzed by RT-qPCR and Western blotting. Functional assays, including flow cytometry for cell cycle and apoptosis, MTT and colony formation assays for proliferation, and transwell assays for migration and invasion, were conducted.
    RESULTS: Individual transfection of AuNP-conjugated siRNA.923 effectively downregulated KRAS expression, whereas AuNP-dsP53-285 upregulated TP53 expression in both A549 and HCT116 cell lines. Co-transfection with AuNP-siRNA.923/dsP53-285 resulted in a significantly greater increase in TP53 mRNA and protein levels, without affecting KRAS mRNA or protein levels, in both cell lines compared with individual transfections. Functionally, the AuNP-based dual small RNA delivery system induced cell cycle arrest at the G0/G1 phase, significantly enhanced apoptosis, and markedly reduced cell proliferation, colony formation, migration, and invasion relative to individual RNA transfections.
    CONCLUSION: These findings demonstrate that AuNP-mediated co-delivery of siRNA and saRNA effectively modulates the KRAS-p53 signaling axis and enhances therapeutic potential in KRASmutant, TP53-wild-type cancers. Further studies, including in vivo investigations, are warranted to evaluate the translational feasibility and clinical relevance of this combinatorial approach.
    Keywords:  KRAS-p53 signaling; RNAs.; Small RNA therapy; cancer therapeutics; gene regulation and silencing; gold nanoparticle (AuNP) delivery
    DOI:  https://doi.org/10.2174/0115665232425141251028050552
  33. Bull Math Biol. 2026 Jan 14. 88(2): 16
    Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.
    Alexis M Hill, Kelly To, Claus O Wilke.
      Synonymous codon usage can influence protein expression, since codons with high numbers of corresponding tRNAs are naturally translated more rapidly than codons with fewer corresponding tRNAs. Although translation efficiency ultimately depends on the concentration of aminoacylated (charged) tRNAs, many theoretical models of translation have ignored tRNA dynamics and treated charged tRNAs as fixed resources. This simplification potentially limits these models from making accurate predictions in situations where charged tRNAs become limiting. Here, we derive a mathematical model of translation with explicit tRNA dynamics and tRNA re-charging, based on a stochastic simulation of this system that was previously applied to investigate codon usage in the context of gene overexpression. We use the mathematical model to systematically explore the relationship between codon usage and the protein expression rate, and find that in the regime where tRNA charging is a limiting reaction, it is always optimal to match codon frequencies to the tRNA pool. Conversely, when tRNA charging is not limiting, using 100% of the preferred codon is optimal for protein production. We also use the tRNA dynamics model to augment a whole-cell simulation of bacteriophage T7. Using this model, we demonstrate that the high expression rate of the T7 major capsid gene causes rare charged tRNAs to become entirely depleted, which explains the sensitivity of the major capsid gene to codon deoptimization.
    Keywords:  Codon usage bias; Gene recoding; Translation efficiency; tRNA Dynamics
    DOI:  https://doi.org/10.1007/s11538-025-01587-y
  34. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1536. [Epub ahead of print]54(2):
    Template nicking suppresses promoter-independent antisense transcription in IVT via R-loop-mediated strand displacement.
    Goeun Lee, Junhyung Ryu, Jinmin Jang, Wooseong Noh, Dong-Eun Kim.
      In vitro transcription (IVT) using T7 RNA polymerase is a cornerstone technology for synthetic messenger RNA (mRNA) production. However, a persistent challenge is the formation of immunogenic double-stranded RNA (dsRNA) byproducts, primarily arising from promoter-independent antisense transcription at free DNA ends. Here, we introduce the nicked low dsRNA template (NiLoT) strategy, a template engineering approach in which a single-strand nick is placed in the non-template DNA strand to promote R-loop formation and suppress antisense RNA synthesis. NiLoT significantly reduces dsRNA contamination without compromising RNA yield and enhances translational output while minimizing innate immune activation in human cells. This broadly applicable method improves IVT mRNA quality and supports more efficient and scalable RNA production.
    DOI:  https://doi.org/10.1093/nar/gkaf1536
  35. Apoptosis. 2026 Jan 10. 31(1): 10
    METTL3 safeguard cancer cells from programmed cell death during detachment from their surrounding extracellular matrix.
    Mahmood Hassan Dalhat, Ahmed Yaqinuddin, Yousef M Hawsawi, Mohammad Imran Khan.
      Extracellular matrix (ECM) detachment is crucial for metastasis in cancer cells. During tumorigenesis, a programmed cell death occurs to clear off the ECM detached cancer cells in the circulatory system; this phenomenon is referred to as anoikis. Metastatic cancer cells can evade anoikis by regulating mechanisms such as cell adhesion, cell growth, oxidative stress, cancer stemness, hypoxia and metabolic reprogramming. Studies have shown that RNA modifications regulate multiple cancer mechanisms; however, the role of RNA modifications in anoikis resistant is not established yet. Therefore, in this study, we assessed the role of N6-methyladenosine (m6A) modification of mRNAs in anoikis resistant conditions. First, we cultured cancer cells in low adhesive plates for six (6) days followed by quantitative real-time PCR (qRT-PCR) of major m6A regulators and quantification of the global m6A levels in detached versus attached cancer cells. We also assessed cell proliferation in detached cancer cells using STM2457, a potent and specific METTL3 inhibitor. Our results showed a significant (p < 0.05) increase in METTL3 expression and activity in anoikis resistant cancer cells. Furthermore, we observed an elevation in global m6A levels on mRNAs. Treatment of anoikis resistant cancer cells with STM2457 caused reduction in spheroid size, induction of apoptosis, and cell cycle arrest which were correlated with a decrease in global m6A levels. Conclusively, our findings reveal that METTL3-dependent m6A methylation sustains the survival and proliferation of anoikis-resistant cancer cells, highlighting an epitranscriptomic mechanism underlying metastatic fitness.
    Keywords:  Anoikis; Extracellular matrix; METTL3; RNA modification; Stemness
    DOI:  https://doi.org/10.1007/s10495-025-02203-z
  36. Nature. 2026 Jan 14.
    N1-Methylpseudouridine directly modulates translation dynamics.
    Batsheva Rozman, Karin Broennimann, K Shanmugha Rajan, Aharon Nachshon, Chiranjeet Saha, Tamar Arazi, Vishnu Mohan, Tamar Geiger, Clayton J Wollner, Justin M Richner, Eric Westhof, Ada Yonath, Anat Bashan, Noam Stern-Ginossar.
      The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology1. A critical feature of this approach is the incorporation of the modified nucleoside N1-methylpseudouridine (m1Ψ), which enhances antigen expression while reducing immunogenicity2-5. However, a comprehensive understanding of how m1Ψ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that m1Ψ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that m1Ψ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that m1Ψ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the m1Ψ-dependent enhancement of protein output is modulated by codon composition, and that m1Ψ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that m1Ψ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts.
    DOI:  https://doi.org/10.1038/s41586-025-09945-5
  37. ACS Synth Biol. 2026 Jan 17.
    Multilayer Host Engineering of Saccharomyces cerevisiae to Enhance Cricket Paralysis Virus (CrPV) Internal Ribosome Entry Site Mediated Translation.
    Zeyu Cao, Xiaotong Zou, Koichi Ito, Kei Endo.
      Internal ribosome entry sites (IRESs) provide compact RNA elements for noncanonical translation and hold promise as building blocks for RNA-based regulation in synthetic biology. However, the cricket paralysis virus (CrPV) IRES shows very low activity in Saccharomyces cerevisiae, limiting its broader utility despite extensive structural and biochemical studies. Here we report a yeast engineering strategy that enhances CrPV IRES-mediated translation by combining host modifications at three mechanistically distinct levels: translation initiation, tRNA modification, and mRNA stability. A reporter-based screen revealed host factors that influence IRES activity and uncovered a trade-off between IRES stimulation and maintenance of cap-dependent translation required for growth. Stepwise integration of nonsense-mediated decay deficiency, a tad3 temperature-sensitive allele, and wild-type eIF4E overexpression yielded a strain with up to an order-of-magnitude increase in reporter output compared with that of the parental strain. These results establish a proof-of-principle framework for host engineering of noncanonical translation.
    Keywords:  Cricket paralysis virus IRES; Translational control; Yeast engineering; mRNA stability; tRNA modification
    DOI:  https://doi.org/10.1021/acssynbio.5c00744
  38. bioRxiv. 2026 Jan 05. pii: 2026.01.05.697729. [Epub ahead of print]
    The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation.
    Jakob Farnung, Elena Slobodyanyuk, Peter Y Wang, Lianne W Blodgett, Daniel H Lin, Susanne von Gronau, Brenda A Schulman, David P Bartel.
      MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including mRNAs from most human genes 1-3 . Within each complex, the miRNA pairs to target mRNAs to specify their repression, and AGO provides effector function while also protecting the miRNA from cellular nucleases 2-5 . Although much has been learned about this mode of posttranscriptional gene regulation, less is known about how the miRNAs themselves are regulated. In one such regulatory pathway, unusual miRNA targets called "trigger" RNAs reverse the canonical regulatory logic and instead down-regulate microRNAs 6-21 . This target- d irected m iRNA d egradation (TDMD) is thought to require a c ullin- R ING E3 ligase (CRL) because it depends on the cullin protein CUL3 and other ubiquitylation components, including the BC-box protein ZSWIM8 (ref. 22,23). ZSWIM8 is required for murine perinatal viability and for destabilization of most short-lived miRNAs, but is otherwise poorly understood 23-25 . Here, we demonstrate that a human AGO-miRNA- trigger complex selectively binds ZSWIM8 for CUL3-mediated polyubiquitylation of the AGO protein within this complex. Cryogenic electron-microscopy (cryo-EM) analyses show how ZSWIM8 recognizes the distinct AGO2 and miRNA-trigger conformations shaped by pairing of the miRNA to the trigger. For example, this pairing extracts the miRNA from a binding pocket within AGO2, allowing the pocket to be captured by ZSWIM8, and it directs the trigger RNA along a distinct trajectory to be also recognized by ZSWIM8. These results biochemically establish AGO binding and polyubiquitylation as the key regulatory step of TDMD, define a unique CRL class, and reveal generalizable RNA-RNA, RNA-protein, and protein-protein interactions that specify the ubiquitin-mediated degradation of AGO with exquisite selectivity. The substrate features recognized by the E3 ubiquitin ligase do not conform to a conventional degron 26-28 , but rather establish a two-RNA-factor authentication mechanism specifying a protein ubiquitylation substrate.
    DOI:  https://doi.org/10.64898/2026.01.05.697729
  39. J Biochem Mol Toxicol. 2026 Jan;40(1): e70643
    WTAP Interferes With Ferroptosis by Regulating the m6A Modification of SF3B1 to Mediate the Malignant Progression of Endometrial Cancer.
    Xia Wang, Xiaoli Wu, Lingling Xu, Lu Yan, Xumei Wang, Jiarui Qin.
      Endometrial cancer (EC) poses a great threat to women's health worldwide. Splicing factor 3B, subunit 1 (SF3B1) and the methyltransferase Wilms tumor 1-associated protein (WTAP) have been confirmed to be involved in the progression of EC, but the relationship between them and whether they jointly regulate EC is still unclear. The mRNA and protein levels of SF3B1 and WTAP were analyzed by qRT-PCR and western blot. Then, cell proliferation, apoptosis, migration, and invasion behaviors were assessed by EdU, flow cytometry, wound healing, and Transwell assays. Bioinformatics tools were applied to predict the binding sites of WTAP on SF3B1 mRNA and the correlation between WTAP and SF3B1. The binding of the two and the m6A methylation level of SF3B1 were verified by RIP and MeRIP. Finally, the effect of WTAP/SF3B1 on EC tumors in vivo was determined by a xenograft tumor model. SF3B1 was highly expressed in EC and its knockdown inhibited the proliferation, expedited apoptosis, repressed migration and invasion, and promoted ferroptosis of EC cells. Besides, WTAP bound to SF3B1-bound mRNA and induced its m6A methylation modification. Overexpression of WTAP accelerated the malignant progression of EC cells and restrained ferroptosis. Interestingly, overexpression of SF3B1 completely abolished the tumor suppressive effect induced by WTAP knockdown. WTAP stimulated tumor growth in vivo and suppressed ferroptosis by stabilizing SF3B1 expression. In conclusion, WTAP effectively suppressed ferroptosis in EC cells by modulating SF3B1 via m6A methylation, thereby aggravating EC.
    Keywords:  EC; SF3B1; WTAP; m6A methylation modification
    DOI:  https://doi.org/10.1002/jbt.70643
  40. Int J Biol Sci. 2026 ;22(2): 920-950
    RNA Methylation in Cancer Metabolism: from Mechanisms to Therapeutic Opportunities.
    Zeyu Wu, Yuncan Xing, Shiwen Mei, Tixian Xiao, Fangze Wei, Qian Liu.
      One of the most important changes in the transformation of normal cells into tumor cells is metabolism. In order to satisfy the more active proliferation, migration and metastasis of cancer cells, abnormal changes occur in various pathways and molecules involved in metabolism, which eventually lead to metabolic reprogramming of tumor cells. This process involves the uptake of nutrients and changes in major metabolic forms. As an important part of post-transcriptional epigenetics, RNA methylation modifications can regulate RNA processing and metabolism, while dynamically and reversibly influencing the expression of specific molecules, thereby ultimately affecting diverse biological processes and cellular phenotypes. In this review, various types of RNA methylation modifications involved in cancer are summarized. Subsequently, we systematically elucidate the mechanism of RNA modification for metabolic reprogramming in cancer, including glucose, lipid, amino acid and mitochondrial metabolism. Most importantly, we discuss in depth the clinical significance of RNA modification in metabolic targeted therapy and immunotherapy from mechanism to therapeutic application.
    Keywords:  RNA methylation; cancer; clinical application; metabolism
    DOI:  https://doi.org/10.7150/ijbs.124177
  41. RNA. 2026 Jan 14. pii: rna.080830.125. [Epub ahead of print]
    Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.
    Zhuoyi Song, Eric L Van Nostrand.
      RNA binding proteins (RBPs) play essential roles in post-transcriptional gene regulation by interacting with a wide range of RNA targets. In addition to regulating RNA processing via individual RBP-RNA interactions, there is a growing appreciation of the regulatory impact of protein-associated RNA-RNA interactions that include both well-studied examples of small regulatory RNAs (e.g. microRNAs, snRNAs, snoRNAs, piRNAs) guiding ribonucleoprotein complexes to their targets as well as structured RNA elements defining the interaction landscape for an RBP. To elucidate the full scope of RBP-RNA interactions, CLIP ( crosslinking and immunoprecipitation)-based methods have emerged as powerful tools. Even with the wide application of CLIP and variant approaches, these methods are still under significant ongoing advancement to better accommodate diverse biological systems and experimental demands and improve scalability. In particular, recent years have seen an emergent focus on improved techniques to globally profile protein-associated RNA-RNA interactions. In this review, we provide a summary of recent improvements in traditional CLIP methods that improve the mapping of RBP-RNA interactions, with particular focus on those that specifically enable the profiling of protein-associated RNA-RNA interactions. We discuss the unique challenges involved in mapping protein-associated RNA-RNA interactions and highlight different ways current approaches address these challenges in order to offer a practical framework for researchers seeking to investigate RBP-associated RNA interactions.
    Keywords:  CLASH; CLIP; RNA interactions; RRI; chimeric CLIP
    DOI:  https://doi.org/10.1261/rna.080830.125
  42. Biochem Pharmacol. 2026 Jan 13. pii: S0006-2952(26)00037-7. [Epub ahead of print] 117706
    Valine availability controls oncogenic cell-cycle progression through translation of D-type cyclins.
    Tomoaki Yamauchi, Runa Fukuzaki, Yumi Takahata, Yumi Okano, Kouki Suzuki, Akito Tsuruta, Shigehiro Ohdo, Satoru Koyanagi.
      Although rapid proliferation of cancer cells imposes a heightened demand for specific amino acids, the mechanistic links between amino acid availability and cell-cycle regulation remain poorly defined. Valine, a branched-chain amino acid, is traditionally recognized for its role in protein synthesis and energy metabolism, but its direct influence on malignant cell growth has not been established. Here, we identify intracellular valine as a critical regulator of oncogenic cell-cycle progression. Across murine hepatocarcinoma, breast cancer, renal cancer, colorectal adenocarcinoma, valine deprivation triggered G0/G1 phase arrest and potently suppressed their proliferation. Mechanistically, valine depletion upregulated eukaryotic translation initiation factor 4E binding protein 1 (4E-BP1), which repressed cyclin D1 and D2 translation by sequestering eukaryotic translation initiation factor 4E (eIF4E). Concurrently, valine deprivation induced Sestrin2 expression and inhibited mammalian target of rapamycin (mTOR) activity, converging to attenuate mRNA translation. These findings uncover a previously unrecognized role of valine as a direct molecular controller of the cancer cell cycle, acting through translational repression of D-type cyclins. Targeting exogenous valine supply, in combination with cell-cycle-directed therapies, may offer a promising strategy to suppress the growth of malignant tumors.
    Keywords:  Cancer; Cell cycle; Translation; Valine
    DOI:  https://doi.org/10.1016/j.bcp.2026.117706
  43. J Biochem. 2026 Jan 13. pii: mvag004. [Epub ahead of print]
    Translating the green code: Ribo-Seq for photosynthetic eukaryotes in focus.
    Naohiro Kawamoto, Shintaro Iwasaki.
      Because they are continually exposed to fluctuating environments, photosynthetic organisms, including land plants and algae, must adapt to a wide range of environmental conditions. For this purpose, translational control plays a pivotal role. The advent of ribosome profiling, or Ribo-Seq, has helped overcome the technical barriers faced by earlier methods, enabling comprehensive and quantitative analysis of protein synthesis. This review highlights recent advances in green lineage Ribo-Seq, covering technical innovations, diverse applications, and analytical insights. These findings emphasize the power and versatility of this technique in exploring translational regulation in photosynthetic species.
    DOI:  https://doi.org/10.1093/jb/mvag004
  44. Nucleic Acids Res. 2026 Jan 14. pii: gkag001. [Epub ahead of print]54(2):
    Single-molecule experiments reveal NusG displaces transcription initiation factor σ70 from mature elongation complexes.
    Pratip Mukherjee, Sk Alim, Sneha Shahu, Saradindu Mondal, Krishnananda Chattopadhyay, Mahipal Ganji, Abhishek Mazumder.
      The Escherichia coli transcription initiation factor σ70 was long believed to dissociate from RNA polymerase after promoter escape, following synthesis of short ~9-11 nt RNAs. However, recent evidence indicates σ70 is retained in elongation complexes (ECs), where it enhances pausing-implying that stochastic or factor-mediated displacement is required for processive elongation. Using fluorescence correlation spectroscopy, we quantified σ70 retention in the presence of elongation factors NusG and NusA, demonstrating that NusG-but not NusA-actively promotes σ70 dissociation. Single-molecule TIRF further revealed that NusG-mediated σ70 dissociation becomes favourable as ECs progress, with lower energy barriers for displacement in later elongation stages. These findings suggest a broader mechanistic paradigm in which elongation factors actively displace initiation factors to regulate transcription-a process that may be conserved across all domains of life.
    DOI:  https://doi.org/10.1093/nar/gkag001
  45. bioRxiv. 2026 Jan 10. pii: 2026.01.09.698617. [Epub ahead of print]
    Mapping of CELF1-RNA interactions reveals post-transcriptional control of lens development.
    Justine Viet, Matthieu Duot, Agnès Méreau, Yann Audic, Iwan Jan, David Reboutier, Catherine Le Goff-Gaillard, Sarah Y Coomson, Salil A Lachke, Carole Gautier-Courteille, Luc Paillard.
      Precise post-transcriptional regulation of gene expression is essential for vertebrate lens development. Disruption of the gene encoding the RNA-binding protein CELF1 leads to early-onset cataract in mice. Here, using iCLIP-seq in lenses, we mapped transcriptome-wide CELF1 binding sites, revealing interactions with the 3'UTRs of key transcripts involved in lens development and pathology like Gja8 , Jag1 , Maf , Pax6 , or Prox1 . Integrated analysis with transcriptomic data and luciferase reporter assays demonstrated that binding of CELF1 protein represses its target mRNAs by destabilizing transcripts and/or inhibiting their translation. Indeed, the cataract-linked genes Maf and Gja8 are upregulated in Celf1 cKO lenses. In Xenopus laevis , overexpression of maf resulted in abnormal lens structure and eye morphology, confirming the developmental relevance of CELF1-mediated repression. Our findings uncover a post-transcriptional network in which CELF1 controls lens morphogenesis by limiting the expression of critical genes at the mRNA level to achive their proper dosage.
    DOI:  https://doi.org/10.64898/2026.01.09.698617
  46. Nucleic Acids Res. 2026 Jan 05. pii: gkaf1452. [Epub ahead of print]54(1):
    Foliar-applied double-stranded RNA is mobile, transfers to plant pathogens, and triggers RNAi.
    Christopher A Brosnan, Stephen J Fletcher, Anne Sawyer, Felipe F de Felippes, Bernard J Carroll, Peter M Waterhouse, Neena Mitter, Donald M Gardiner.
      Foliar application of double-stranded RNA (dsRNA) as RNA interference (RNAi)-based biopesticides represents a sustainable alternative to chemical-based crop protection strategies. A key feature of RNAi in plants is its ability to act non-cell autonomously, a process that plays a critical role in plant development and protection against pathogens. Whether RNAi induced by foliar dsRNA application acts non-cell autonomously remains debated, with the mechanisms and implications of this movement largely unexplored. We show that upon foliar application, dsRNA enters the leaf vasculature and moves to vegetative, reproductive, and belowground tissues in multiple plant species. Unprocessed mobile dsRNA was detected in the apoplast, being maintained in new growth, indicating apoplastic rather than symplastic transport. Mobile dsRNA could transfer to infecting fungi, where it was processed and loaded by the fungal RNAi machinery to elicit gene silencing. Using a novel biochemical purification technique and small RNA sequencing, we detected functional small interfering RNA species derived from foliar-applied dsRNA that elicit effective silencing in both the applied and distal tissue types. Our mechanistic dissection of the uptake and movement of dsRNA provides crucial insights into the mode of action of RNAi biopesticides and stands to add significant benefit to this emerging field of plant protection.
    DOI:  https://doi.org/10.1093/nar/gkaf1452
  47. Mol Biol Rep. 2026 Jan 10. 53(1): 271
    Short-term hypoxia and nutrient deprivation stress induced shifts in p53 isoform expression in HepG2 tumourspheres.
    Li Qing Keoh, Muhammad Danish Ahmad Tarmizi, Sakunie Sawai, Lixian Oh, Thamil Selvee Ramasamy.
       BACKGROUND: The hypoxic, nutrient-deprived tumour microenvironment (TME), a hallmark of solid tumours, imposes cellular stress that can also paradoxically promote survival and resistance. While TP53 is the most frequently mutated gene in cancer, approximately 60% of hepatocellular carcinoma (HCC) cases retain wild-type TP53 (WTp53), suggesting its isoforms as potential tumorigenic modulators that override canonical tumour-suppressive functions. Therefore, this study aims to delineate p53 isoform profiles in response to short-term hypoxia and nutrient deprivation, recapitulating key stressors in the tumour biology.
    METHOD: We hereby established a 7-day HepG2 tumoursphere model by seeding 15,000 cells/well, which transitioned from normoxia (4 days) to a hypoxic (1% O2), low-serum (1% FBS) (HLS) condition (3 days). Expression of p53 isoforms and downstream targets was assessed.
    RESULTS: The formation of HepG2 tumoursphere at different seeding densities determined the diameter, viability and proliferation profiles, with 15,000 cells/well producing optimal, viable tumourspheres with the highest yield. HLS conditions significantly reduced tumoursphere size, proliferation capacity and viability. Strikingly, multiplex long-amplicon ddPCR revealed substantial upregulation of FLp53α/Δ40p53α, Δ40p53α and Δ133p53α/Δ160p53α mRNA transcripts. While FLp53α/Δ40p53α remained dominant, Δ40p53α and Δ133p53α/Δ160p53α progressively increased, altering the balance among the isoforms. This shift correlated with enhanced expression of the pro-proliferative and survival markers (PCNA and BCL2) and reduced expression of the pro-apoptotic marker (BAX) and cell cycle inhibitor (CDKN1A), suggesting a potential functional role of these isoforms in promoting tumour cell adaptation under stress.
    CONCLUSION: This study highlights stress-induced p53 isoform modulation as a potential survival mechanism in WTp53 HCC in response to TME stress, which warrants further exploration of isoform-specific p53 functions in understanding heterogeneity, resistance and cancer recurrence.
    Keywords:  HepG2 tumourspheres; Hepatocellular carcinoma; Hypoxia; Nutrient deprivation; p53 isoform
    DOI:  https://doi.org/10.1007/s11033-025-11415-0
  48. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1495. [Epub ahead of print]54(2):
    Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.
    Elise K Kammerdiener, Sarah K Garcia, Margaret K Bales, Dawn M Klingeman, Adam M Guss, Richard J Giannone, Robert L Hettich, Carrie A Eckert, William G Alexander.
      Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.
    DOI:  https://doi.org/10.1093/nar/gkaf1495
  49. Cell Mol Biol Lett. 2026 Jan 16.
    TGFβ pathway represses hepatic ribosome biogenesis and protein synthesis by regulating p70S6K-S6RP proteins.
    Athanasios Stavropoulos, Vassiliki Stamatopoulou, Eleftherios Pavlos, Maria Manioudaki, Stratigoula Sakellariou, Constantinos Stathopoulos, Maria Xilouri.
       BACKGROUND: Transforming growth factor-beta (TGFβ)-superfamily signaling has been implicated in the regulation of hepatocyte growth and regeneration after acute or chronic liver injury. However, the precise mechanisms underlying TGFβ signaling in the distinct hepatic cell types during the progression of liver fibrosis remain largely unknown. We aim to identify the downstream molecular mechanisms of TGFβ-signaling modulation on hepatocytes.
    METHODS: To modulate TGFβ-superfamily signaling in vivo, Smad3 or Smad7 were adenovirally overexpressed in mouse liver. Parallelly, hepatosphere cultures were treated with recombinant TGFβ1 and subjected to transcriptomic analysis. These data were compared with transcriptomes from Smad7-overexpressing livers. To broaden the analysis, publicly available RNA-seq datasets from TGFβ-treated hepatic stellate cells and hepatocellular carcinoma lines were meta-analyzed. Finally, human liver tissues from cirrhotic and healthy individuals were examined for fibrosis and ribosome biogenesis markers to validate murine findings.
    RESULTS: Acute hepatic overexpression of Smad3 induced a transient fibrotic phenotype in the mouse liver. In hepatosphere cultures, TGFβ1 treatment suppressed key components of ribosomal assembly, whereas Smad7 overexpression exerted the opposite effect in the mouse liver, thus highlighting ribosome biogenesis as a major cellular process negatively regulated by the TGFβ superfamily. Inhibition of TGFβ signaling via Smad7 increased hepatic protein content (a critical parameter for restoring hepatic homeostasis upon liver damage), activated the nucleolus, and prompted the production of ribosomal pre-mRNAs without affecting p53 levels. Mechanistically, SMAD7-mediated inactivation of TGFβ signaling triggered selectively the p70S6K-S6RP regulatory axis, independently of cellular myelocytomatosis oncogene (c-MYC), mechanistic target of rapamycin (mTOR), and mitogen-activated protein kinase (MAPK) pathways. Importantly, analysis of hepatic tissue from cirrhotic patients and controls unveiled a negative association between TGFβ signaling and ribosome biogenesis in fibrotic livers. Complementary meta-analysis of RNA-seq data demonstrated that TGFβ regulates ribosome biogenesis in a cell type-specific manner, suppressing it in hepatocytes while enhancing it in hepatic stellate cells, consistent with their distinct functional states and transcriptional landscapes.
    CONCLUSIONS: Collectively, our data reveal a SMAD-dependent regulatory role of TGFβ-superfamily signaling on hepatocytes that is tightly connected with hepatic growth to ensure proper energy homeostasis and metabolism. This is a critical regeneration parameter, which is closely related to the restoration of hepatic mass, especially following liver injury and fibrosis.
    Keywords:  Cell signaling; Cirrhosis; Liver growth; Regeneration; Ribosome; Smads; Translation
    DOI:  https://doi.org/10.1186/s11658-025-00853-0
  50. Plant Methods. 2026 Jan 13.
    Introduction of the Ribo-BiFC method to plants using a split mVenus approach.
    Karel Raabe, Alena Náprstková, Janto Pieters, Elnura Torutaeva, Veronika Jirásková, Zahra Kahrizi, Palash Chandra Mondol, Christos Michailidis, David Honys.
       BACKGROUND: Translation is a fundamental process for every living organism. In plants, the rate of translation is tightly modulated during development and in responses to environmental cues. However, it is challenging to measure the actual translation state of the tissues in vivo.
    RESULTS: Here, we report the introduction of an in vivo translation marker based on bimolecular fluorescence complementation, the Ribo-BiFC. We combined a method originally developed for the fruitflies with an improved low background split-mVenus BiFC system previously described in plants. We labelled small subunit ribosomal proteins (RPS) and large subunit ribosomal proteins (RPL) of Arabidopsis thaliana with fragments of the mVenus fluorescent protein (FP). We tested the Ribo-BiFC method using transiently expressed recombinant ribosomal proteins in epidermal cells of Nicotiana benthamiana. The BiFC-tagged ribosomal proteins complemented the mVenus molecule and were detected by fluorescence microscopy, potentially visualizing the close proximity of translating assembled 80S ribosomal subunits. Although the resulting signal is less intense than that of known interactors, its detection points to the functionality of the system.
    CONCLUSIONS: This Ribo-BiFC approach has further potential for use in stable transgenic lines in enabling the visualisation of translational rate in plant tissues and changing translation dynamics during plant development, under abiotic stress or in different genetic backgrounds.
    Keywords:  Bimolecular fluorescence complementation; Ribosome; Translation; Translation rate
    DOI:  https://doi.org/10.1186/s13007-025-01494-2
  51. bioRxiv. 2026 Jan 07. pii: 2026.01.07.698137. [Epub ahead of print]
    Regulation of trehalose biosynthesis and thermotolerance by the Cryptococcus neoformans HECT E3 ubiquitin ligase Rsp5.
    Alejandro L Antonia, Lukas M du Plooy, Siobhan R Duffy, Jeffrey Kuhn, Erik J Soderblom, J Andrew Alspaugh.
      Microorganisms including fungi adapt to profound changes in their local environment during human infections. After exposure to high temperature and other stress conditions, the opportunistic fungal pathogen Cryptococcus neoformans enacts changes in metabolism, cell wall structure, and transmembrane transport that allow it to survive and proliferate in a mammalian host. This stress response program is regulated by the HECT E3-ubiquitin ligase Rsp5 which is required for growth at high salinity, pH and temperature. However, the complete set of Rsp5 substrates that direct these molecular changes remains incompletely understood. Here we demonstrate that C. neoformans Rsp5 confers increased tolerance to temperature and salt stress in part through regulation of the trehalose biosynthesis pathway. Two enzymes in the trehalose biosynthesis pathway, Tps1 and Tps2, are differentially ubiquitinated by Rsp5 after exposure to stress conditions. We directly measured trehalose production after exposure to high temperature and found that a C. neoformans strain lacking Rsp5 is unable to induce trehalose production. Quantitative proteomic analysis of the C. neoformans response to high salinity identified Rsp5-dependent and independent adaptations to osmotic stress, and that Rsp5-dependent ubiquitination does not alter the abundance of Tps1 or Tps2. These results demonstrate that regulation of trehalose biosynthesis is one of the cellular mechanisms by which Rsp5-dependent ubiquitination in C. neoformans facilitates survival in response to stressors encountered in the human infection environment.
    Importance: Cryptococcus neoformans is an opportunistic fungal pathogen that kills over 180,000 people every year with few effective treatment options. As a yeast that normally lives in the environment, C. neoformans has to survive large changes in its physical environment, including elevated body temperature, when it causes human infections. Here we show how C. neoformans uses a protein modification to regulate production of a fungal-specific metabolic pathway important for survival at human body temperature. Unraveling how environmental fungi tolerate and survive temperature and other stressors will help to understand how they cause disease and identify new and better ways to treat these deadly infections.
    DOI:  https://doi.org/10.64898/2026.01.07.698137
  52. Aging Med (Milton). 2025 Dec;8(6): 612-623
    Mechanism of RNA Oxidation and Its Inhibitor Involved in Ang II-Induced Cardiomyocyte Hypertrophy.
    Tong Liu, Jin Bian.
       Objectives: To explore the mechanism of RNA oxidation and its inhibitor MTHI involved in cardiomyocyte hypertrophy.
    Methods: The hypertrophic H9c2 cardiomyocytes were stimulated with different concentrations and times of Ang II (Ang II) to construct a model of hypertensive heart failure in vitro. Transfection of H9c2 cells with the MTH1 overexpression plasmid was performed. The mRNA expression of ANP, BNP, and β-MHC in each experimental group was detected by PCR. The expression of 8-oxoG in H9c2 cells was determined by immunofluorescence and enzyme-linked immunosorbent assay (ELISA). The activation of the ERK-MAPK pathway and the amount of MTH1 protein were detected by WB semi-quantitative method.
    Results: Notably, RNA oxidation is a critical event in cellular senescence, and its accumulation is strongly linked to the aging process and the development of age-related diseases. In our model of cardiomyocyte hypertrophy, the oxidative damage of RNA was aggravated, and the expression of MTH1 was increased. At the same time, the sequence of ERK-MAPK pathway proteins was activated. It can be seen that the oxidative damage of RNA is related to the process of cardiomyocyte hypertrophy. After transfection of the MTH1 overexpression plasmid into the cardiomyocyte hypertrophy model, we found that the amount of 8-oxoG decreased, and the activation of ERK-MAPK signaling pathway proteins decreased, and H9c2 cell hypertrophy decreased. Therefore, we concluded that 8-oxoG may aggravate the hypertrophy of the cardiomyocyte hypertrophy model by activating the ERK-MAPK pathway.
    Conclusion: The oxidative damage of RNA is involved in the process of cardiomyocyte hypertrophy. The mechanism may be that 8-oxoG, a product of RNA oxidation, activates the downstream ERK-MAPK signaling pathway. These findings provide new perspectives for further exploration into the role of RNA oxidation in the pathogenesis of age-related diseases, particularly heart failure.
    Keywords:  8‐oxoG; ERK–MAPK; RNA oxidation; cardiomyocyte hypertrophy
    DOI:  https://doi.org/10.1002/agm2.70057
  53. Comput Biol Chem. 2026 Jan 08. pii: S1476-9271(26)00003-4. [Epub ahead of print]122 108878
    Structural basis of long non-coding RNA PVT1 interactions with select mRNAs universal in pan-cancer system: A computational study.
    Euphinia Tiberius Kharsyiemiong, Bhupal Haribhakta Raghunandan, Seema Mishra.
      PVT1 lncRNA can regulate multi-gene expression through diverse mechanisms, one of which is through binding interactions with mRNAs. Our previous study highlighted its regulatory role in pan-cancer systems through predicted interactions with select mRNAs that are significantly differentially expressed across 15 cancer types. The structural basis of these interactions are yet to be propounded. Here, in order to identify and compare secondary structural features that may mediate PVT1 binding to select cancer-relevant mRNAs, and to determine evidence of evolutionary conservation, if any, we adopted the secondary structure folding information to identify key intermolecular interactions mediating the binding of PVT1 to specific regions, 5'UTR, coding region, and 3'UTR, of these select mRNAs, which may influence the translation process. Forming stable secondary structures, using both Watson-Crick and non-Watson-Crick base pairs, the flexibility of PVT1 lncRNA in interacting with these varied molecules at specific locations is deduced at the secondary structure level. To demonstrate the possible presence of conserved structural elements in PVT1 secondary structure generated based on 7SL non-coding RNA seed sequences, covariation analysis identified 10 significantly co-varying base pairs, suggesting structural conservation. The location of the start point of these lncRNA-mRNA interactions is majorly in the open loop regions. A-U nucleotides in the loops are observed to be higher in number than G-C nucleotides in PVT1 secondary structure. This may initiate multiple base-pairing interactions with other macromolecules more readily, owing to a lesser strength of the hydrogen bonding interactions between A-U base pairs. In the case of these mRNAs, comparatively speaking, there is a variability in the number of purines in the loop regions in their respective secondary structures. Since GC content correlates with the stability of mRNA secondary structures, our analysis shows that even though there is a variable sequence length, some of these mRNAs may demonstrate a higher stability of their specific secondary structures based on a higher GC content. Further, in order to potentially correlate with high protein expression, the distal segment of CDS and the 3'UTR regions of mRNAs require the presence of increased secondary structure. In our analysis, we found the same underlying pattern in a few of our select mRNA molecules. Exploration of the sequence and structural details of these lncRNA-mRNA interactions led us to an insight on a probable mechanism of a single PVT1 molecule being able to bind multiple mRNAs simultaneously or sequentially, in a spatio-temporal manner. Our research also seeks to further elucidate the contribution of bases and intermolecular interactions in the formation of these complexes.
    Keywords:  Covariation; PVT1; Pan-cancer; Secondary structures; Structural basis; mRNA
    DOI:  https://doi.org/10.1016/j.compbiolchem.2026.108878
  54. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1508. [Epub ahead of print]54(2):
    Metal ions govern coronavirus endoribonuclease activity.
    Xionglue Wang, Jing Li, Zhichao Liu, Longfei Wang, Bin Zhu.
      Coronavirus nonstructural protein 15 (nsp15) is an endoribonuclease that restricts viral double-stranded RNA (dsRNA) accumulation in the cytosol to evade host immunity. Given the co-localization of nsp15 and replicating viral RNA, the mechanism controlling nsp15 activity is essential, yet poorly understood. Although metal ions are widely used as cofactors for enzymes, their role in nsp15 remains elusive. Here, we show that Co2+ or Ni2+ potently activates, whereas Zn2+ inhibits nsp15 of multiple coronaviruses. In the presence of Co2+, cryo-electron microscopy structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp15/dsRNA complexes indicate higher dsRNA-binding affinity. Active-site mutation H249A weakens the effects of Co2+, Ni2+, and Zn2+ on SARS-CoV-2 nsp15. Furthermore, the Co2+- or Ni2+-dependent activation of nsp15 is inhibited upon Zn2+ addition, suggesting competitive regulation. Overall, our work identifies the activator and inhibitor ions of nsp15 and suggests a metal-dependent regulatory mechanism of nsp15 activity.
    DOI:  https://doi.org/10.1093/nar/gkaf1508
  55. Chem Biol Drug Des. 2026 Jan;107(1): e70242
    EIF2AK2 Globally Binds and Regulates the Expression and Alternative Splicing of T2D-Related Genes in INS1 Cell.
    Lili Ning, Tong Liu, Yuanyuan Lv, Yan Cheng, Maoguang Yang, Hanqing Cai.
      This study aimed to investigate the impact of the RNA-binding protein eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) gene, also known as PKR, on the condition of islet beta cells. In this study, EIF2AK2 was overexpressed in INS1 cells, and transcriptome data following EIF2AK2 overexpression were obtained using RNA-seq technology. Additionally, potential target genes that bind to EIF2AK2 were identified through iRIP-seq technology. The proteins interacting with EIF2AK2 were characterized using co-immunoprecipitation (CO-IP) combined with mass spectrometry to elucidate the molecular regulatory mechanisms of EIF2AK2 in INS1 cells. RNA-seq results indicated that in INS1 cells overexpressing EIF2AK2, 1171 genes were differentially expressed, and 2161 alternative splicing events were significantly altered. iRIP-seq data demonstrated that reads from the immunoprecipitated samples were significantly enriched in the intronic and coding sequence (CDS) regions. EIF2AK2 preferentially binds to the GCGGCGG motif in RNA. Comprehensive analysis suggests that EIF2AK2 may directly bind to and regulate the expression of Dusp8, Btg1, and Prkce, thereby affecting pancreatic islet cell functions. Furthermore, EIF2AK2 may influence islet cell function by modulating the alternative splicing of Zfr and Pias2. Additionally, combined with Co-IP mass spectrometry data, it was discovered that EIF2AK2 can interact with 649 proteins, including various differentially expressed RNA-binding proteins, transcription factors, and histones, which may be associated with diabetes. Our results indicate that EIF2AK2 may regulate the expression or alternative splicing of mRNA related to type 2 diabetes through direct or indirect binding. Additionally, it may influence the progression of type 2 diabetes by interacting with other proteins. We propose that EIF2AK2 plays a significant role in diabetic islet beta cells, and its aberrant regulatory pattern is closely associated with the onset and progression of type 2 diabetes.
    Keywords:  EIF2AK2; RNA binding proteins; islet β‐cell; protein–protein interaction; type 2 diabetes
    DOI:  https://doi.org/10.1111/cbdd.70242
  56. Phytother Res. 2026 Jan 11.
    A Novel Mechanism of Berberine Targeting EIF2AK2 Dimerization Attenuates Methylglyoxal-Induced Endothelial Senescence and Apoptosis.
    Jinxiang Chen, Yumeng Yang, Haiyang Li, Junjing Xiong, Liqun Wang, Chunxiang Zhang, Mao Luo.
      Vascular aging, a central feature of organismal aging, involves endothelial cell (EC) structural and functional alterations. Methylglyoxal (MGO), a key advanced glycation end product precursor, pathologically accumulates during aging. While MGO induces EC apoptosis via mitochondrial pathways and endothelial dysfunction, its role in cellular senescence remains unclear. The integrated stress response (ISR) sensor Eukaryotic Translation Initiation Factor 2 Alpha Kinase 2 (EIF2AK2), also known as PKR, has emerged beyond its well-established antiviral role as a critical regulator of cellular senescence. This study explores the novel mechanism of berberine (BBR) on targeting EIF2AK2 dimerization to attenuate MGO-induced EC senescence and apoptosis. In vitro, MGO-treated HUVECs assessed EIF2AK2 dimerization/phosphorylation and senescence (p16, p21) and apoptosis (cleaved caspase-3) markers. In vivo, three aging models (MGO-induced aortic injury, D-gal-induced accelerated aging, natural aging) evaluated MGO accumulation and EIF2AK2 pathway activation (phospho-EIF2AK2, ATF4), demonstrating BBR's efficacy via EIF2AK2 axis modulation. Here, we present the first evidence demonstrating that EIF2AK2 dimerization and subsequent activation significantly exacerbate EC senescence and apoptosis in both in vivo and in vitro models, characterized by upregulation of pro-apoptotic markers (Cleaved caspase-3, Bax) and senescence-associated proteins (P53, P21, P16), along with downregulation of the anti-apoptotic protein Bcl-2. EIF2AK2 has been identified as a key cellular target of the natural isoquinoline alkaloid BBR. Our findings further establish that BBR ameliorates MGO-induced vascular EC senescence and apoptosis through selective inhibition of EIF2AK2 dimerization and subsequent eIF2α phosphorylation. Notably, pharmacological suppression of EIF2AK2 with C16 synergistically enhances BBR's protective effects against MGO-induced EC senescence and apoptosis. Collectively, this study reveals a novel mechanistic pathway by which MGO drives EC senescence/apoptosis via EIF2AK2 dimerization/activation and validates BBR's therapeutic potential for vascular pathologies. EIF2AK2 emerges as a promising target for developing novel vascular protection strategies.
    Keywords:  EIF2AK2; MGO; berberine; senescence
    DOI:  https://doi.org/10.1002/ptr.70203
  57. Elife. 2026 Jan 12. pii: RP104808. [Epub ahead of print]14
    Dilated cardiomyopathy-associated RNA-binding motif protein 20 regulates long pre-mRNAs in neurons.
    Giulia Di Bartolomei, Raúl Ortiz, Dietmar Schreiner, Susanne Falkner, Esther E J M Creemers, Peter Scheiffele.
      Precise coordination of molecular programs and neuronal growth governs the formation, maintenance, and adaptation of neuronal circuits. RNA metabolism has emerged as a key regulatory node of neural development and nervous system pathologies. To uncover cell-type-specific RNA regulators, we systematically investigated expression of RNA recognition motif-containing proteins in the mouse neocortex. Surprisingly, we found RNA-binding motif protein 20 (RBM20), an alternative splicing regulator associated with dilated cardiomyopathy, to be expressed in cortical parvalbumin interneurons and mitral cells of the olfactory bulb. Genome-wide mapping of RBM20 target mRNAs revealed that neuronal RBM20 binds pre-mRNAs in distal intronic regions. Loss of neuronal RBM20 has only modest impact on alternative splice isoforms but results in a significant reduction in an array of mature mRNAs in the neuronal cytoplasm. This phenotype is particularly pronounced for genes with long introns that encode synaptic proteins. We hypothesize that RBM20 ensures fidelity of pre-mRNA splicing by suppressing nonproductive splicing events in long neuronal genes. This work highlights a common requirement for RBM20-dependent transcriptome regulation in cardiomyocytes and neurons and demonstrates that a major genetic risk factor of heart disease impacts neuronal gene expression.
    Keywords:  alternative splicing; autism; cardiomyopathy; cell biology; mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.104808
  58. Bone Res. 2026 Jan 12. 14(1): 5
    Biologics for bone regeneration: advances in cell, protein, gene, and mRNA therapies.
    Claudia Del Toro Runzer, Elizabeth R Balmayor, Martijn van Griensven.
      Bone fractures represent a significant global healthcare burden. Although fractures typically heal on their own, some fail to regenerate properly, leading to nonunion, a condition that causes prolonged disability, morbidity, and mortality. The challenge of treating nonunion fractures is further complicated in patients with underlying bone disorders where systemic and local factors impair bone healing. Traditional treatment approaches, including autografts, allografts, xenografts, and synthetic biomaterials, face limitations such as donor site pain, immune rejection, and insufficient mechanical strength, underscoring the need for alternative strategies. Biologic therapies have emerged as promising tools to enhance bone regeneration by leveraging the body's natural healing processes. This review explores the critical role of conventional and emerging biologics in fracture healing. We categorize biologic therapies into protein-based treatments, gene and transcript therapies, small molecules, peptides, and cell-based therapies, highlighting their mechanisms of action, advantages, and clinical relevance. Finally, we examine the potential applications of biologics in treating fractures associated with bone disorders such as osteoporosis, osteogenesis imperfecta, rickets, osteomalacia, Paget's disease, and bone tumors. By integrating biologic therapies with existing biomaterial-based strategies, these innovative approaches have the potential to transform clinical management and improve outcomes for patients with difficult-to-heal fractures.
    DOI:  https://doi.org/10.1038/s41413-025-00487-0
  59. Cell Death Dis. 2026 Jan 16. 17(1): 46
    Regulation of stress tolerance by CREB1 sustains multiple myeloma cell survival.
    Ruchi Kudalkar, Johnathan Altom, Joshua Galloway, Vincent Manning, Sara Taranto, Francesca Cottini.
      Multiple myeloma (MM) cells originate from antibody-producing plasma cells and endure chronic oxidative and proteotoxic stress due to the excessive production of immunoglobulins and free light chains. We previously demonstrated that CD56 (also known as neuronal cell adhesion molecule 1) promotes cAMP-responsive element binding (CREB1) activation in MM cells to drive survival, without fully elucidating its mechanism of action. In this study, we describe the global role of CREB1 in regulating tolerance to cellular stresses in MM. Here, we present data to demonstrate that CREB1 directly or indirectly influences key proteins involved in the clearance of oxidants, the unfolded protein response (UPR), and autophagy. In silico data from real patients with MM showed that patients with high CREB1 expression have greater activation of gene sets associated with endurance of stress. We confirmed by genomic and pharmacological modulation that CREB1 activates the mTOR pathway, halting autophagy, and directly binds to the promoter of NRF2 and PERK, modulating genes involved in oxidation and protein stress adaptation. Of particular importance was the identification of TXNIP among the regulated genes. Notably, the TXNIP gene belongs to the 1q21 cytoband, which is amplified in 30 percent of patients with MM, leading to poor outcomes. We showed for the first time that TXNIP inhibition is also toxic against MM cells, interfering with UPR and autophagy. Thus, our data highlights the essential roles of CREB1 and TXNIP in MM cell survival under chronic stress, providing new insights into MM pathophysiology and novel therapeutic strategies for patients with high-risk disease.
    DOI:  https://doi.org/10.1038/s41419-025-08246-z
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