bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–03–01
58 papers selected by
Cédric Chaveroux, CNRS
  1. The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation.
  2. HDAC5 -encoded Microprotein NISM Mediates Nucleolar Formation and Ribosomal RNA Synthesis.
  3. Context-dependent translation inhibition as a cancer therapeutic modality.
  4. Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants.
  5. "More" Artificial mRNAs: Beyond the Art of Nature.
  6. Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.
  7. Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity.
  8. α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.
  9. Translational buffering tunes gene expression in mice and humans.
  10. Coordinated translation initiation determines -1 programmed ribosomal frameshifting efficiency of chromosomal genes to impact on cell fitness.
  11. ATLAS: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions.
  12. Colorectal Cancer Puzzle: m6A Modification and Its Intricate Relationship With Drug Resistance.
  13. m6A Demethylation in Chloroplasts Enhances Stress Tolerance by Modulating the Stability of Photosynthesis-Associated mRNAs in Arabidopsis.
  14. Investigating Potential 5' UTR G-Quadruplexes Within NRF2 mRNA.
  15. Engineering of tRNAPro1E2 anticodon stem enhances multiple/consecutive ribosomal incorporation of N-methyl-l-α-amino acids and d-α-amino acids.
  16. DDX10 RNA Helicase: Structure, Function, and Oncogenic Roles Across Solid and Hematologic Tumors.
  17. Coding Transcript-Derived Small Interfering RNAs: Their Biogenesis and Molecular Function in Arabidopsis.
  18. BOLL-Containing Aggregates Mediate the Translational Regulation During Human Oogenesis.
  19. Inhibition of the integrated stress response rescues a histidyl-tRNA synthetase variant associated with Charcot-Marie-Tooth disease.
  20. The Inevitable Relationship Between Viruses and RNA Modifications Revealed Through Adenovirus Research.
  21. Dynamic landscape of transcription initiation by yeast RNA polymerase I.
  22. Utilizing bulk and single-cell RNA sequencing to identify potential biomarkers linked to angiogenesis and integrated stress response in chondrosarcoma.
  23. TDP-43 pathology is linked to motor neuron loss but is independent of stress granules in vivo.
  24. Evolution of Translation Initiation Factor 2 Extensions Links Initiation to Bacterial Stress Response.
  25. Molecular Mechanisms of RNA Polymerase I Transcription in Health and Disease: An Overview.
  26. m6A RNA Methylation Is Increased in Tumour Invasive Regions and Influences Invasive Capability and Chemotherapeutic Sensitivity in Adult Glioblastoma.
  27. A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing.
  28. ASFV MGF110-7L Inhibits eIF4G1 Expression via Endoplasmic Reticulum Stress to Block Host Translation.
  29. N6-methyladenosine methylation in acute lung injury: Mechanisms and research progress.
  30. Mechanobiology of the Nucleolus.
  31. Adenosine-to-Inosine (A-to-I) RNA Editing by ADAR1 to Control RNA Sensing in Cardiovascular Disease.
  32. [im6Am-DC: a model for predicting RNA sequence N6,2'-O-dimethyladenosine modification by integrating DenseNet and attention mechanism].
  33. RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.
  34. PXL: a Nucleic Acid-Binding Module of Promyelocytic Leukemia Protein.
  35. Ribosome-associated proteins in fungal ribosome homeostasis: Conceptual opportunities for peptide-based modulation.
  36. Identification of Inhibitors for eIF5A2-Dependent Translation Elongation by Monitoring the Translational Efficiency of Polyproline Motif in Mitochondrial Fission Regulator 1.
  37. Integrated Stress Response Signatures Drive Monocyte Dysfunction in GBA1- and LRRK2-Linked Parkinson's Disease.
  38. Polysomal profiling coupled to allele-specific proteomics reveals an EIF4H tranSNP allele possessing higher mRNA translation potential.
  39. In Cereibacter sphaeroides, expression of flagellin FlaA is posttranscriptionally controlled by the 5' untranslated region of its mRNA and the regulatory proteins FlaF, FlbT and FlbR.
  40. The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae.
  41. The Intersection of m6A Methylation and Immune Response in PCOS: A Bioinformatics Perspective.
  42. The Liver Fluke Opisthorchis felineus Exosomal tRNA-Derived Small RNAs as Potential Mediators of Host Manipulation.
  43. Co-translational control of protein stability and quality in plants.
  44. Dot Blot Assay for Detecting Global N6-Methyladenosine RNA Modification Levels.
  45. Integrative transcriptomic analysis identifies long noncoding RNA dysregulation and circadian disruption in reward and executive circuits of opioid use disorder.
  46. Degradation of alpha-synuclein/SNCA mRNA by RNautophagy.
  47. The Versatile Role of RNA N6-Methyladenosine (m6A) in Plant Resistance to Biotic Stress.
  48. Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling.
  49. U2AF2 controls alternative splicing in speckle-proximal regions in an RS domain-dependent manner.
  50. Metabolic RNA Labeling-Enabled Time-Resolved Single-Cell RNA Sequencing.
  51. Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria.
  52. Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate.
  53. NMD-mediated control of Tor influences adaptation to nutrient and temperature conditions in Cryptococcus neoformans.
  54. Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis.
  55. CELF1 is a non-canonical eIF4E binding protein that promotes translation of epithelial-mesenchymal transition effector mRNAs.
  56. Site-Directed Modification of mRNA with Functionalized Platinum(IV)-Ammines.
  57. Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons.
  58. m6A RNA modification and its emerging roles in diseases: recent advances and therapeutic implications.
  1. bioRxiv. 2026 Feb 12. pii: 2026.02.11.705401. [Epub ahead of print]
    The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation.
    Wen Xiao, Tanja Hann, Zion Perry, Vijaya Pandey, Jeffrey Cheng, James Wohlschlegel, Anna Marie Pyle, Douglas L Black.
      In most cells, Malat1 long noncoding RNA localizes to the nucleus where it affects splicing and chromatin function. In neurons Malat1 is exported to the cytoplasm where it is translated to generate the M1 micropeptide. Here we characterize an internal ribosome entry site (IRES) required for Malat1 translation. Although preceded by a long Malat1 5' RNA segment this element induces translation at the M1 AUG. In vivo chemical probing and structural modeling identified a 135 nt RNA secondary structure consisting of three stem loops that is sufficient for IRES activity. Using this minimal element for affinity purification from cell extracts, the IRES RNA selectively binds ribosomal subunits and translation factors. Depletion of the binding proteins Rack1 and hnRNP A2/B1 inhibits downstream IRES-dependent translation without affecting translation of an upstream ORF. Our study identifies an unexpected functional unit hidden within a widely studied long noncoding RNA.
    DOI:  https://doi.org/10.64898/2026.02.11.705401
  2. bioRxiv. 2026 Feb 22. pii: 2026.02.21.707204. [Epub ahead of print]
    HDAC5 -encoded Microprotein NISM Mediates Nucleolar Formation and Ribosomal RNA Synthesis.
    Kevin Cao, Dat Ha, Jesse Hulahan, Lilianna Houston, Gregory Tong, Jiayi Weng, Natasha Huey, Hannah E DeMerit, Pedro Ortega, Rémi Buisson, Kingshuk Ghosh, Thomas F Martinez.
      Ribosome biogenesis is the process by which ribosomal RNA (rRNA) and ribosomal proteins are synthesized, processed, and assembled into functional ribosomes. This process begins in the nucleolus, a multiphase liquid condensate. Here, we discover an arginine-rich disordered nucleolar microprotein encoded within the HDAC5 5'-UTR that we termed Nucleolar Integrity and Stress Microprotein (NISM). NISM overexpression leads to impaired rDNA transcription, triggering nucleolar stress, p53 activation, and suppressed proliferation. NISM knockout causes disruption of nucleolar structure and also induces p53 activation. Mechanistically, NISM interacts with the DExH-box RNA helicase DHX9 and regulates its activities related to pre-rRNA synthesis. Computational analyses and polymer physics-based mathematical modeling revealed that NISM coordinates nucleolar formation and pre-rRNA synthesis by enhancing the liquid-liquid phase separation of DHX9. This study establishes NISM as a regulator of nucleolar biology and deepens our understanding of how disordered microproteins can facilitate the formation of membraneless organelles.
    DOI:  https://doi.org/10.64898/2026.02.21.707204
  3. Nat Commun. 2026 Feb 24. pii: 1963. [Epub ahead of print]17(1):
    Context-dependent translation inhibition as a cancer therapeutic modality.
    Paige D Diamond, Paul V Sauer, Mikael Holm, Canessa J Swanson-Swett, Lucas Ferguson, Natalie M Bratset, Grant W Wienker, Justin Seiwert Sim, Hailey K Adams, Lillian Kenner, Margot Meyers, David Gygi, Zef A Könst, Sogole Sami Bahmanyar, Lawrence G Hamann, Anthony P Schuller.
      Recent work has demonstrated that some bacterial antibiotics that inhibit protein synthesis by binding the peptidyl transferase center (PTC) of the ribosome act in a context-dependent manner, inhibiting translation elongation only at specific amino acids. However, this phenomenon has yet to be documented for compounds that inhibit the PTC of the human ribosome. Here, we use structure-based design to guide the synthesis of such PTC-binding, context-dependent inhibitors of the human ribosome, termed interdictors. In the PTC, these compounds preferentially interact with nascent protein residues that exhibit complementary physiochemical properties to the moieties of the small molecule, causing structural rearrangements in both the nascent polypeptide chain and ribosomal RNA. Further, the compounds differentially impact ribosome surveillance pathways, including the ribotoxic stress response. Finally, we confirm their anti-tumor activity after oral dosing in a mouse xenograft model of triple-negative breast cancer. Together, our data establish targeting oncogenic dependency factors through context-dependent inhibition of translation as a potential small molecule therapeutic modality for historically difficult to address cancers.
    DOI:  https://doi.org/10.1038/s41467-026-69891-2
  4. bioRxiv. 2026 Feb 18. pii: 2026.02.17.706363. [Epub ahead of print]
    Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants.
    Robert T Steinbock, Orlando B Scudero, Joseph M Dybas, Amber R N Abbott, Katarzyna Kulej, Richard Lauman, Holly Chan, Eva L Agostino, Namrata Kumar, Skyler Briggs, Nicholas A Parenti, Yize Li, James M Burke, Susan R Weiss, Alexander M Price, Matthew D Weitzman.
      Recognition of dsRNA triggers antiviral defense mediated by PKR and OAS3/RNase L pathways through translational arrest and RNA decay. This is accompanied by assembly of distinct cytoplasmic ribonucleoprotein (RNP) condensates termed stress granules (SGs) and RNase L-dependent bodies (RLBs). Here we show that adenovirus infection differentially modulates dsRNA sensors and RNP granule assembly. Infection with splicing-defective ΔE4 mutant leads to dsRNA accumulation and activation of both PKR and OAS3/RNase L, promoting formation of RLB-like granules. In contrast, mutants lacking virus-associated (VA) RNAs trigger PKR activation and assembly of SGs despite absence of detectable dsRNA. Proteomic analysis revealed distinct protein compositions of canonical SGs and RLBs, which were reflected in virus-induced granules. While ΔVA-induced granules were PKR-dependent, ΔE4 mutants induced RLB-like granules independently of PKR and RNase L. In these cells, granule assembly coincided with translational arrest independent of eIF2α phosphorylation, indicating additional pathways linking nuclear dsRNA sensing to translational control and RNP granule assembly during viral infection. These findings provide novel insights into how distinct dsRNA sensors modulate translation and RNP condensates in response to stress.
    DOI:  https://doi.org/10.64898/2026.02.17.706363
  5. Adv Sci (Weinh). 2026 Feb 26. e21523
    "More" Artificial mRNAs: Beyond the Art of Nature.
    Yuanzhe Cui, Minami Fukui, Hirohisa Ohno, Hirohide Saito.
      Messenger RNA (mRNA) has emerged as a versatile platform for gene expression and therapeutic innovation. Early engineering efforts focused on optimizing canonical mRNA components-the 5' cap, untranslated regions, coding sequence, and poly(A) tail-to enhance stability, translational efficiency, and safety. These refinements culminated in the success of mRNA vaccines and consequently enabled diverse biomedical applications ranging from gene and cell therapy to genome editing. More recently, research has expanded beyond the structural constraints of natural mRNAs, giving rise to non-canonical architectures, such as circular, branched, self-amplifying, and lantern-shaped RNAs. These designs confer novel properties, including resistance to degradation, autonomous replication, and programmable control of translation. Progress in chemical modification, ribozyme engineering, and RNA nanotechnology has further accelerated the diversification of synthetic mRNA. Together with advances in synthesis, purification, and delivery technologies, these innovations are transforming mRNA from a transient messenger into a designable molecular system. This review revisits the evolution of mRNA engineering-from natural optimization to creative structural redesign-and outlines emerging concepts that illustrate how synthetic mRNA is expanding the possibilities of gene expression control.
    Keywords:  RNA engineering; RNA therapeutics; branched RNA; circular RNA; microRNA‐responsive switch; self‐amplifying RNA; synthetic mRNA
    DOI:  https://doi.org/10.1002/advs.202521523
  6. JBMR Plus. 2026 Mar;10(3): ziag018
    Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.
    Alzbeta Chabronova, Guus G H van den Akker, Tim J M Welting, Mandy J Peffers.
      Musculoskeletal (MSK) tissues are highly dynamic systems that rely on tightly regulated protein synthesis to maintain homeostasis and structural integrity, adapt to physiological stimuli, and respond to injury. The deregulation of protein synthesis is implicated in a wide range of MSK pathologies. At the core of protein synthesis are ribosomes, complex molecular nanomachines that translate mRNAs and generate proteins. Once considered uniform entities passively exerting their function, ribosomes are now recognized to be heterogeneous in their composition and capable of specialized functions. These emerging concepts of ribosome heterogeneity and specialization are increasingly recognized as key regulators of physiological and pathological cellular processes across fields. Although the MSK field has yet to fully embrace and integrate ribosome-centered research, accumulating evidence suggests that ribosome heterogeneity and specialization might have profound implications for MSK (patho)biology. In this review, we summarize the emerging data across MSK tissues (bone, skeletal muscle, articular cartilage, tendons, and ligaments), highlighting the roles of ribosomes in supporting development, maintaining homeostasis, and facilitating cellular and tissue functions and adaptations, but also driving pathological changes and disease progression. Furthermore, we also outline recent key technological and methodological advances that are critical for uncovering the full scope, significance, and dynamic regulation of ribosome heterogeneity and specialization in MSK (patho)biology. As the field moves forward, ribosome-centered research holds great promise in revealing new mechanisms underlying MSK biology and identifying novel therapeutic targets.
    Keywords:  2′-O-methylation; protein synthesis; pseudouridylation; ribosomal RNA; ribosomal proteins; ribosome heterogeneity; ribosome specialization; ribosome-associated proteins; snoRNAs; translation regulation
    DOI:  https://doi.org/10.1093/jbmrpl/ziag018
  7. RNA. 2026 Feb 26. pii: rna.080699.125. [Epub ahead of print]
    Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity.
    Agnes Karasik, Grant D Jones, Nicholas R Guydosh.
      RNase L is an endonuclease that responds to infections by cleaving most host- and pathogen-derived single-stranded RNAs. This widespread RNA cleavage can lead to death of the infected cell via the ribotoxic stress response (RSR). An ongoing challenge is to understand how RNase L's endonuclease activity triggers cell death to benefit the host. To address this question, we used nanopore-based long-read sequencing to show that 3' mRNA fragments in the cell were not fully degraded after RNase L activation and that these fragments were translated by ribosomes. We further asked whether ribosomes on mRNA fragments stall when they reach 3' ends created by RNase L. We used ribosome profiling to capture footprints protected by these ribosomes, which can be identified by their short length (15-18 nt). We found that RNase L activation increased the number of stalled ribosomes at RNase L cleavage sites. Loss of the ribosome rescue factor PELO increased the number of short footprints derived from stalled ribosomes and augmented the RSR. Our work therefore establishes a role for fragmented mRNA in causing ribosome stalling that promotes innate immunity via the RSR.
    Keywords:  PELO; endonuclease; mRNA fragments; nanopore; ribosome profiling
    DOI:  https://doi.org/10.1261/rna.080699.125
  8. Genes Dev. 2026 Feb 23.
    α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.
    Kirti Mittal, Lamisa Ataei, Miguel Ramalho-Santos.
      While most newly synthesized RNA is exported to the cytoplasm, a portion of noncoding RNA is retained in the nucleus and remains highly associated with chromatin. The strong binding of this RNA fraction to insoluble chromatin impairs its recovery in standard transcriptomic studies. Therefore, the landscape and potential functions of chromatin-associated RNAs are poorly understood. Recent studies indicate that chromatin-associated transcripts can have regulatory roles, particularly during mammalian development. Here we compare the dynamics of cytoplasmic versus chromatin-bound transcriptomes of naive and primed human embryonic stem cells (hESCs) as well as fibroblasts. We found a remarkable enrichment for RNA transcribed from α-satellite repeat (ALR) in the chromatin fraction of naive hESCs compared with primed hESCs. The colocalization and interaction of ALR RNA with polypyrimidine tract binding protein 1 (PTBP1) and CUG-binding protein (CUGBP) indicate that ALR RNA foci mark the perinucleolar compartment (PNC), a nuclear subcompartment previously thought to be exclusive to cancer cells. Knockdown of ALR RNA leads to dispersion of PTBP1/CUGBP foci, upregulation of ribosomal RNA, and global hypertranscription in naive hESCs. In contrast, loss of PTBP1 does not disturb ALR RNA localization, indicating that ALR is upstream in the hierarchy of organization of the PNC in hESCs. These results reveal a role for ALR RNA in nuclear compartmentalization and tuning rRNA synthesis in naive hESCs. Moreover, this study opens new avenues to dissect the function of ALR RNA and the PNC in cancer contexts.
    Keywords:  PTBP1; chromatin-associated RNA; human embryonic stem cells; nucleolus; perinucleolar compartment; ribosomal RNA; α-satellite RNA
    DOI:  https://doi.org/10.1101/gad.353162.125
  9. Genome Biol. 2026 Feb 26.
    Translational buffering tunes gene expression in mice and humans.
    Shilpa Rao, Aden Y Le, Logan Persyn, Can Cenik.
       BACKGROUND: Translational buffering refers to the regulation of ribosome occupancy to offset the effects of transcriptional variation. While previous studies have primarily investigated translational buffering in yeast under genetic variation or environmental stress, it remains unclear how widespread this is across mammalian genes in various cellular contexts.
    RESULTS: We performed a uniform analysis of 1,515 matched ribosome profiling and RNA-seq datasets from humans and mice. This resource enabled us to assess translational buffering through comparative analysis of variation in ribosome occupancy and RNA expression, and by examining the relationship between mRNA abundance and translation efficiency. We found that translational buffering is partly conserved between humans and mice; homologous genes showed moderate cross-species correlation in mRNA-translation efficiency relationships and strong enrichment of shared buffered genes, particularly those encoding ribosomal, RNA-binding, and proteasomal proteins. Although identified buffered genes associate with specific sequence features, these alone are insufficient to predict translational buffering, highlighting the importance of cellular context. Genes exhibiting translational buffering show lower variation in protein abundance in cancer cell lines and tissues. We also observed that translationally buffered genes are more likely to be haploinsufficient and triplosensitive, suggesting a demand for stringent dosage limits.
    CONCLUSIONS: We hypothesize two models of translational buffering, namely the "differential accessibility model" and the "translation initiation rate model", suggesting that different transcripts align with one or the other. Our study explores the translational buffering potential of genes across diverse conditions, elucidates their distinctive features, and provides insights into the mechanisms driving this effect.
    Keywords:  Ribosome occupancy; Translation efficiency; Translational buffering; mRNA variation
    DOI:  https://doi.org/10.1186/s13059-026-04010-4
  10. FEBS J. 2026 Feb 22.
    Coordinated translation initiation determines -1 programmed ribosomal frameshifting efficiency of chromosomal genes to impact on cell fitness.
    Sih-Yun Tai, Masayuki Hashimoto, Yi-Fang Zhuang, Hao-Wen Liang, Hsin-Pei Huang, The-Phuong Nguyen, Meng-Han Tu, Shih-Cheng Chen, Whei-Fen Wu, René C L Olsthoorn, Chien-Hung Yu.
      The conserved -1 programmed ribosomal frameshifting (-1PRF), essential for eubacteria and RNA viruses, is thought to be exclusively regulated during translation elongation. One of the two required -1PRF cis-acting elements is a frameshifting stimulatory element (FSE), which pauses the elongating ribosome to stimulate -1PRF and is consecutively deformed. Consequently, the remaining hypothesis involves the coordination between translation initiation and FSE reformation, which facilitates the -1PRF events in trailing ribosomes. Here, we create a system that allows a tunable translation initiation rate based on the MS2 bacteriophage coat protein translation initiation hairpin to assess this conjecture. We discovered a conserved negative correlation between translation initiation rate and -1PRF efficiency in eubacteria and mammalian cells. Mechanistic exploration using Escherichia coli (E. coli) shows that a higher initiation rate reduces the frequencies of FSE reformation, resulting in lower -1PRF efficiency. The role of translation initiation-mediated -1PRF was examined in an E. coli cellular copA/copA(Z) -1PRF event. The results showed that a higher translation initiation rate leads to lower -1PRF efficiency, sensitizing E. coli to copper stress. Together, these results suggest that translation initiation is an additional mechanism to regulate -1PRF to coordinate optimal protein synthesis for cell fitness, further providing the basis to investigate the interplay between translation initiation and elongation.
    Keywords:  RNA structure; copper stress; recoding; ribosomal frameshifting; translation initiation
    DOI:  https://doi.org/10.1111/febs.70462
  11. bioRxiv. 2026 Feb 19. pii: 2026.02.17.706471. [Epub ahead of print]
    ATLAS: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions.
    Jingyi Li, Jian Wang, Srinivasan Ekambaram, Nikolay V Dokholyan.
      The structures of RNA exhibit recurrent patterns, which are defined as motifs. Motifs are crucial for the biological functions of RNA molecules. The 3D RNA motif library includes 3D RNA structures, providing a resource for motif-based RNA 3D structure prediction and design. We built the Advanced Template Library for Assembly and Structure (ATLAS) that features graph representations of RNA structures, atomic 3D structures from the Protein Data Bank (PDB), and an isomorphism graph searching algorithm. ATLAS includes nucleotide-level graph representations of RNA motifs and corresponding PDB IDs from the PDB and 3D atomic structures retrieved from the PDB. We provide the web service to search for and download RNA motifs and user-defined structures, supporting non-WC interactions. Graph representations include two types of graphs: motifs with non-Watson-Crick (non-WC) and without non-WC. Compared to existing motif libraries, ATLAS includes graph representations with non-Watson-Crick interactions and pseudoknots and integrates the latest RNA structures from the PDB. We also develop a measure of similarity between RNAs based on shared motifs. We proposed a physics-inspired, time-dependent mechanistic model for RNA evolution, whose steady-state solution fits the global distribution of RNA structural similarity.
    DOI:  https://doi.org/10.64898/2026.02.17.706471
  12. Front Biosci (Landmark Ed). 2026 Feb 13. 31(2): 45750
    Colorectal Cancer Puzzle: m6A Modification and Its Intricate Relationship With Drug Resistance.
    Mengxiang Yang, Zhihui Dai, Yuejun Han, Yijing Shen, Jianping Wang.
      Colorectal cancer (CRC) is a globally prevalent malignancy with rising incidence and mortality rates over the past decades. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotes, and plays a pivotal role in post-transcriptional regulation. m6A is dynamically modulated by three core components, namely methyltransferases (writers), demethylases (erasers), and binding proteins (readers), which together govern the transcription, processing, translation, decay, and stability of mRNA. There has been accumulating evidence for the association of dysregulated m6A modification with CRC pathogenesis, metastasis, and therapeutic resistance. This review summarizes the biogenesis of m6A modification and its regulatory mechanisms, and discusses the dysregulation of m6A-related factors in CRC and the functional impacts. Most importantly, the review highlights the key roles of m6A modification in mediating CRC resistance to chemotherapy, targeted therapy, and immunotherapy. These insights may facilitate the development of novel therapeutic strategies for CRC.
    Keywords:  N6-methyladenosine; RNA demethylases; RNA methyltransferases; colorectal neoplasms; drug resistance
    DOI:  https://doi.org/10.31083/FBL45750
  13. Plant Cell Environ. 2026 Feb 26.
    m6A Demethylation in Chloroplasts Enhances Stress Tolerance by Modulating the Stability of Photosynthesis-Associated mRNAs in Arabidopsis.
    Rongpeng Han, Jianzhong Hu, Yasira Shoaib, Tao Xu, Hunseung Kang.
      N6-methyladenosine (m6A) is the most prevalent epitranscriptomic modification found in eukaryotic mRNA. The levels of m6A are determined by the coordinated actions of methyltransferases ('writers') and demethylases ('erasers') that introduce and remove m6A marks, respectively. Recent studies have demonstrated that chloroplast mRNAs are highly rich in m6A; however, the significance of m6A methylation in chloroplasts remains unknown. As no mRNA m6A writers and erasers have been identified in chloroplasts, in this study, we artificially imported ALKBH10B, a well-characterised mRNA m6A eraser localised in the nucleus and cytoplasm in Arabidopsis (Arabidopsis thaliana), into chloroplasts to uncover the potential impact of m6A modification in chloroplasts on photosynthesis and abiotic stress response. We found that the chloroplast-targeted ALKBH10B successfully removes m6A marks from numerous mRNAs in chloroplasts. Notably, the ALKBH10B-mediated demethylation f m6A marks in chloroplast mRNAs enhanced salt and drought tolerance in Arabidopsis by modulating the stability of m6A-modified photosynthesis-associated mRNAs. Overall, our findings reveal that ALKBH10B-mediated m6A demethylation in chloroplast mRNAs enhances photosynthesis and stress tolerance, highlighting that modulation of RNA methylation in chloroplasts can be a potential means for breeding stress-tolerant plants.
    Keywords:  abiotic stress ALKBH10B; chloroplast; m6A demethylase; m6A methylation; photosynthesis
    DOI:  https://doi.org/10.1111/pce.70464
  14. Curr Issues Mol Biol. 2026 Feb 02. pii: 171. [Epub ahead of print]48(2):
    Investigating Potential 5' UTR G-Quadruplexes Within NRF2 mRNA.
    Hatice Esenkaya, Joe Bryant.
      Post-transcriptional regulation of gene expression is influenced by RNA-binding proteins (RBPs) and small non-coding RNAs that bind to conserved mRNA sequences to modulate mRNA processing. These regulatory molecules affect the structural conformation of mRNAs, creating formations like G-quadruplexes (G4s), which alter translation initiation and regulatory-factor site accessibility. Recent studies have highlighted Nuclear factor erythroid 2-related factor 2 (NRF2) as a key regulator of cellular redox homeostasis and cellular response to oxidative stress. An intriguing feature of NRF2 is the structural formation of its 5' untranslated region (UTR), which may promote or inhibit translation initiation depending on the cellular context. In this study with minigenes, we provide in vitro evidence of RNA G4s in the NRF2 mRNA's 5' UTR under basal (no stress) conditions. Achieved via electrophoretic mobility shift assay and fluorescence spectra in the presence of Pyridostatin. Understanding how structural motifs within NRF2 5' UTRs influence mRNA function provides insights into a common molecular mechanism underlying diseases where NRF2 is dysregulated, like cancers, cardiovascular disease, and neurodegeneration, and highlights potential therapeutic avenues through regulation of NRF2.
    Keywords:  5′ untranslated regions; G-quadruplexes; Nuclear factor erythroid 2–related factor; Pyridostatin; RNA-binding proteins; cancer
    DOI:  https://doi.org/10.3390/cimb48020171
  15. Nucleic Acids Res. 2026 Feb 24. pii: gkag137. [Epub ahead of print]54(5):
    Engineering of tRNAPro1E2 anticodon stem enhances multiple/consecutive ribosomal incorporation of N-methyl-l-α-amino acids and d-α-amino acids.
    Ryoichi Hirashima, Takayuki Katoh, Hiroaki Suga.
      Transfer RNA (tRNA) structures influence the incorporation efficiency of amino acids, particularly when nonproteinogenic amino acids (npAAs), such as N-methyl-l-α-amino acids (MeAAs) and d-α-amino acids (d-AAs), are charged. Such npAAs are generally far poorer substrates than the 20 canonical α-amino acids for translation. However, we have shown that their incorporation efficiencies could be improved by using a chimeric tRNA, termed tRNAPro1E2, bearing optimal T-stem and D-arm. Here we report that the engineering anticodon stem of tRNAPro1E2 further enhances multiple/consecutive elongation of MeAAs and d-AAs. By screening 149 types of anticodon stem mutants, we found eleven tRNAPro1E2 variants capable of enhancing the incorporation of N-methyl-l-leucine (MeLeu) or d-phenylalanine (d-Phe) at six codons by up to 4.5- and 4.4-fold, respectively. Interestingly, 7 out of the 11 variants showed different mobilities compared to the parental tRNAsPro1E2 in native polyacrylamide gel electrophoresis analysis, indicating that their unique conformations contributed to promoting peptidyl transfer reaction. These tRNAs exhibited increased incorporation efficiencies of not only MeLeu and d-Phe but also diverse MeAAs and d-AAs. Ribosomal synthesis of a model macrocyclic peptide containing three consecutive MeAAs and three d-AAs was also demonstrated with high quality, indicating their usefulness for the peptide library construction containing multiple exotic amino acids.
    DOI:  https://doi.org/10.1093/nar/gkag137
  16. Genes (Basel). 2026 Jan 27. pii: 138. [Epub ahead of print]17(2):
    DDX10 RNA Helicase: Structure, Function, and Oncogenic Roles Across Solid and Hematologic Tumors.
    Giorgia Isinelli, Genny Scacci, Arianna Capocchia, Carla Emiliani, Cristina Mecucci, Roberta La Starza, Danika Di Giacomo.
      DEAD-box (DDX) RNA helicases are essential regulators of RNA metabolism and gene expression. Among them, DDX10 remains poorly characterized despite growing evidence supporting its involvement in human diseases. This review provides a comprehensive analysis of DDX10, from its structural and functional features to its emerging roles in solid tumors and hematologic malignancies. We discuss how DDX10, through its conserved domains, contributes to pre-rRNA processing, ribosome biogenesis, and cell proliferation, and explore potential links between DDX10 and processes such as liquid-liquid phase separation (LLPS) and epigenetic regulation, which may underlie its roles in cancer cell plasticity and stress response. We argue that the dysregulation of these fundamental cellular processes positions DDX10 as a focal point where aberrant RNA metabolism and altered molecular condensates converge to disrupt transcriptional homeostasis and drive oncogenic transformation. Aberrant DDX10 expression is a recurrent feature across multiple cancers, where it promotes tumor progression, therapy resistance, and poor prognosis. Moreover, DDX10 participates in oncogenic fusion events, most notably the NUP98::DDX10 fusion identified in a subset of acute myeloid leukemias, which drives leukemogenesis by disrupting transcriptional regulation and cellular differentiation. Given its tumor-associated expression and diverse biological functions, DDX10 is increasingly recognized as a potential diagnostic biomarker and a promising target for therapeutic strategies. By consolidating current knowledge under this unifying framework, this review highlights the multifaceted roles of DDX10 in cancer biology, advocating further research into its molecular functions and translational potential.
    Keywords:  DDX10; DEAD-box RNA helicase; NUP98::DDX10 fusion; acute myeloid leukemia (AML); epigenetic regulation; liquid–liquid phase separation (LLPS); oncogenic transformation; ribosome biogenesis; solid tumors; tumor biomarker
    DOI:  https://doi.org/10.3390/genes17020138
  17. Int J Mol Sci. 2026 Feb 10. pii: 1701. [Epub ahead of print]27(4):
    Coding Transcript-Derived Small Interfering RNAs: Their Biogenesis and Molecular Function in Arabidopsis.
    Xintong Xu, Nier Chen, Xinwen Qing, Xiaoli Peng, Xiangze Chen, Beixin Mo, Yongbing Ren.
      Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system is impaired, the aberrant mRNA fragments were converted to double stranded forms by RNA-directed RNA polymerase 6 (RDR6) with the assistance of Suppressor of Gene Silencing 3 (SGS3) and subsequently processed by DICER-LIKE proteins into 21-nt and 22-nt ct-siRNAs. The accumulation of ct-siRNAs and the resulting suppression of their cognate genes are usually associated with altered plant growth and stress response. In this review, we summarize our current understanding of the ct-siRNAs, particularly their biogenesis under different RNA metabolic defective conditions. Comparative analysis of these genetic contexts indicates that ct-siRNAs act through translation inhibition and/or mRNA cleavage, with regulatory outcomes influenced by siRNA length and genetic background. We further summarize the biological consequence of ct-siRNA accumulation, which are frequently associated with impaired plant growth and stress adaptation. Finally, we discuss current controversies on ct-siRNAs research and highlight key unsolved questions for future investigation. Collectively, this review highlights ct-siRNAs as a link between impaired RNA metabolisms and post-transcriptional gene silencing, with context-dependent effects on plant growth and stress responses.
    Keywords:  DCL2; DCL4; EIN5/XRN4; RDR6; RQC; SGS3; SKI2; ct-siRNAs
    DOI:  https://doi.org/10.3390/ijms27041701
  18. Cell Prolif. 2026 Feb 25. e70181
    BOLL-Containing Aggregates Mediate the Translational Regulation During Human Oogenesis.
    Ying Li, Lingya Mao, Boyuan Liang, Longxin Xie, Wenpei Xiang, Kehkooi Kee.
      Human oocyte meiosis utilises a specialised translational control strategy to coordinate meiotic progression, mediated through dynamic regulation of mRNA stores. While germ cell-specific RNA-binding proteins (RBPs) are known to orchestrate this post-transcriptional programme, the mechanistic basis of RBP-mediated cell fate specification remains elusive. Here, we demonstrate that BOLL, a Deleted in Azoospermia (DAZ) family protein, forms protein aggregates during meiotic prophase to drive translational reprogramming in human oogenesis. We determined that BOLL enhances the translation efficiency of cell cycle regulators, as demonstrated by integrative translatome-transcriptome analysis combined with RNA immunoprecipitation sequencing. We also revealed the functional interaction network of BOLL with core translation machinery components through its conserved DAZ-containing domain. Crucially, we identified SDS-resistant protein aggregates as a structural signature of BOLL in human oocyte-like cells, demonstrated by semi-denaturing electrophoretic analysis. Using human foetal ovarian tissues and an hESC-derived oogenesis model, we delineate a paradigm wherein BOLL-containing aggregates exert spatiotemporal control over cell cycle genes during meiosis prophase. These findings reveal that protein aggregates of gametogenesis-specific RBPs constitute an evolutionarily conserved mechanism in mammalian reproductive regulation.
    Keywords:  human BOLL protein; oogenesis; protein aggregate; translational regulation
    DOI:  https://doi.org/10.1111/cpr.70181
  19. NAR Mol Med. 2026 Jan;3(1): ugag013
    Inhibition of the integrated stress response rescues a histidyl-tRNA synthetase variant associated with Charcot-Marie-Tooth disease.
    Maria Mahmood, Sarah D P Wilhelm, Marisa I Mendes, Desiree E Smith, Rosan Kenana, Kyle Hoffman, Angelica A Moresco, Victoria Mok Siu, Ilka U Heinemann.
      Cytoplasmic histidyl-tRNA synthetase (HARS1) is an essential protein in translation, ligating histidine to its cognate tRNAHis. HARS1 is one of several aminoacyl-transfer RNA (tRNA) synthetases associated with Charcot-Marie-Tooth disease, an axonal peripheral neuropathy. Advances in genetic testing identify many variants of uncertain significance. We characterize a novel heterozygous allele in HARS1, c.1200G > T (p.Leu400Phe) with a familial inheritance pattern of peripheral neuropathy. Using a humanized yeast model and biochemical assays, we determined that HARS-L400F causes HARS aggregation, reduced thermal stability, and a temperature-dependent reduction of aminoacylation activity. In humanized yeast, L400F leads to a pronounced growth defect, especially at elevated temperatures. Contrary to previously described pathogenic HARS alleles, cognate amino acid or tRNA substrate supplementation does not ameliorate the growth defect. We show that, in a humanized yeast model, HARS L400F leads to the activation of the integrated stress response (ISR) and upregulated chaperone expression. The yeast growth phenotype can be rescued by inhibition of the ISR using a specific inhibitor of general control non-depressible 2 (GCN2) kinase, opening a novel therapeutic avenue for pathogenic HARS1 alleles that do not respond to substrate supplementation.
    DOI:  https://doi.org/10.1093/narmme/ugag013
  20. Viruses. 2026 Feb 14. pii: 243. [Epub ahead of print]18(2):
    The Inevitable Relationship Between Viruses and RNA Modifications Revealed Through Adenovirus Research.
    Shuichi Hashimoto, Fumiaki Uchiumi, Hideaki Furuya, Radhakrishnan Padmanabhan.
      Over the past two decades, it has become clear that gene expression in eukaryotic cells is regulated by diverse RNA molecules. In this process, new RNAs have been discovered, and the roles of their modified molecules have been progressively elucidated. In this review, we first describe how RNA and its modifications function in virus-infected cells. We use adenovirus and several other viruses as models during the early stages of infection, which we believe determines the fate of infected cells. Next, we reviewed the process of identifying the early mRNA transcription initiation sites in adenovirus-infected cells. The results showed that the transcription initiation sites for the E1 and E4 mRNAs-known as adenovirus oncogenes-are highly complex. The same level of complexity in transcription initiation sites has been suggested for oncogenes in several other DNA tumor viruses, including SV40, polyomavirus, and papillomavirus. It is now understood that the transcription of the early adenovirus mRNA involves alternative splicing, rather than constitutive splicing, as we previously demonstrated. Furthermore, recent research indicates that the abnormal alternative splicing of intracellular mRNA may induce cellular carcinogenesis. Finally, we discuss whether alternative splicing plays a role in the carcinogenic effects of DNA tumor viruses, such as adenovirus. Additionally, we discuss that alternative splicing plays a crucial role in adenovirus replication.
    Keywords:  RNA modification; adenovirus; alternative splicing; methylation; transcription initiation site; viral multiplication; viral oncogenes
    DOI:  https://doi.org/10.3390/v18020243
  21. Nucleic Acids Res. 2026 Feb 24. pii: gkag153. [Epub ahead of print]54(5):
    Dynamic landscape of transcription initiation by yeast RNA polymerase I.
    Olena Parilova, Piia Bartos, Anssi M Malinen.
      RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA, a key step in ribosome biogenesis. Elevated Pol I activity supports rapid cell growth-a hallmark of cancer-making Pol I a therapeutic target. The initial step in synthesis involves assembly of the Pol I transcription initiation complex on the gene promoter; however, its quantitative and dynamic parameters remain poorly defined. Here, we integrate biochemical, biophysical, and molecular dynamics approaches to dissect promoter and transcription start site (TSS) recognition by the Saccharomyces cerevisiae Pol I machinery. We show that core factor (CF) identifies the promoter through a two-step mechanism: a rapid encounter is followed by a slower conformational transition that establishes stabilizing interactions. In contrast, CF binds nonpromoter DNA in a single step without such transitions, forming nonspecific complexes that dissociate quickly. Correct promoter binding allows CF to recruit and position Pol I near the TSS, inducing DNA bending, helix distortion, and melting as the preinitiation complex converts into an active state. These functional and dynamic parameters contribute to a quantitative framework for elucidating the molecular mechanisms of Pol I regulation and inhibition.
    DOI:  https://doi.org/10.1093/nar/gkag153
  22. Sci Rep. 2026 Feb 21.
    Utilizing bulk and single-cell RNA sequencing to identify potential biomarkers linked to angiogenesis and integrated stress response in chondrosarcoma.
    Shihong Li, Jian Zhao, Qingqing Qin, Hai Huang, Dong Liu, Yang Liu, Dongyu Peng, Huimin Yu, Haohan Jing, Yucheng Wu, Feng Li, Zuzhi Meng, Dongfa Liao, Wei Wang, Cairu Wang.
      Chondrosarcoma (CS) is the second most common bone sarcoma with a cartilage matrix. Angiogenesis and integrated stress response (ISR) exert a vital influence on the development of CS. This research aimed to conduct a comprehensive analysis to pinpoint angiogenesis and ISR-related potential biomarkers in CS and to elucidate their potential molecular mechanisms. CS data were from GEO. Potential biomarkers were identified and confirmed using differential expression analysis, WGCNA, and expression assessment. Moreover, enrichment analysis was employed to examine relevant pathways. Molecular regulatory network, compound prediction, and molecular docking analyses further explored the key regulatory roles of potential biomarkers in CS. GSE184118 was used to determine key cells and perform pseudo-time and cell communication analyses. Finally, RT-qPCR was used to confirm potential biomarker expression levels. Overall, three potential biomarkers (HSPA8, LMNA and SERPINH1) were determined, and their expression trends were consistent across the GSE30835 and GSE22855 datasets. Potential biomarkers were significantly enriched in the pathways like "medicus variant mutation caused aberrant HTT to 26S proteasome mediated protein degradation" in CS. Moreover, 9 transcription factors (TFs) (like STAT1), 69 key microRNAs (miRNAs) (like hsa-miR-361-3p), and 78 long non-coding RNAs (lncRNAs) (like NEAT1) were found to have relationships with potential biomarkers, and potential biomarkers had stable binding affinity with adenosine diphosphate (ADP) and lonafarnib. Moreover, pseudo-time analysis demonstrated a notable correlation between potential biomarkers' expression and differentiation status of key cells (stromal cells (excluding leucocytes)), and cell communication revealed the strong interactions between stromal cells and chondroid clusters 1. Importantly, RT-qPCR confirmed higher expression of HSPA8, LMNA and SERPINH1 in CS patients. The findings suggested that HSPA8, LMNA and SERPINH1 might offer novel insights for the development of targeted therapies for CS associated with angiogenesis and ISR.
    Keywords:  Angiogenesis; Chondrosarcoma; Integrated stress response; Potential biomarkers; Single-cell RNA sequencing
    DOI:  https://doi.org/10.1038/s41598-026-40800-3
  23. bioRxiv. 2026 Feb 13. pii: 2026.02.11.705439. [Epub ahead of print]
    TDP-43 pathology is linked to motor neuron loss but is independent of stress granules in vivo.
    Alicia Dubinski, Ala Ferdi, Mariam Choughari, Holly Spence, Arpita Adhikary, Carolane Fauchon, Melissa Touati, Myriam Gagné, Martha Liu, Sarah Peyrard, Jenna Gregory, Christine Vande Velde.
      Nuclear depletion and cytoplasmic aggregation of TDP-43 are pathological hallmarks of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease, and the recently defined limbic-predominant age-related TDP-43 encephalopathy (LATE). Chronic activation of the integrated stress response (ISR) and persistence of stress granules, phase-separated assemblies proposed to function as a protective mechanism, have been hypothesized to initiate the formation of pathological TDP-43 inclusions observed in post-mortem neurons. However, recent clinical trials targeting the ISR and stress granule dissolution failed to demonstrate clinical benefit despite robust target engagement, calling this model into question. Here, we employ a recurrent hyperthermia paradigm to directly examine the relationship between stress granules and TDP-43 pathology in vivo . We find that RNA-binding proteins classically associated with stress granules persist as phase-separated cytoplasmic structures in spinal motor neurons of both non-transgenic and mutant TDP-43 mice. Importantly, these structures are reversible and spatially distinct from TDP-43 puncta. Moreover, in a mutant TDP-43 mouse model with an impaired acute stress granule response, stress exposure induces TDP-43 nuclear export and cytoplasmic accumulation. Recurrent stress in these mice leads to a selective loss of spinal α-motor neurons. Together, our findings demonstrate that TDP-43 nuclear clearance and cytoplasmic demixing occur independently of stress granules in vivo , challenging prevailing models of TDP-43 pathogenesis and highlighting important implications for therapeutic strategies targeting the ISR.
    DOI:  https://doi.org/10.64898/2026.02.11.705439
  24. bioRxiv. 2026 Feb 09. pii: 2026.02.08.704698. [Epub ahead of print]
    Evolution of Translation Initiation Factor 2 Extensions Links Initiation to Bacterial Stress Response.
    Evrim Fer, Rajdeep Banerjee, Katsumi Hagino, Kaitlyn M McGrath, Betül Kaçar.
      Terminal extensions are recurrent features in protein evolution, often linked to environmental adaptation and novel regulatory or interaction functions. Here, we combine comparative genomics, structural modeling, and functional assays to elucidate the evolutionary diversification and functional significance of one of the key proteins of all cells, translation initiation factor 2 (IF2) terminal extensions across the tree of life. Specifically, we reconstruct the first comprehensive evolutionary map of IF2 across life, analyzing ∼800 homologs and classify seven distinct structural architectures of IF2 based on extension regions. These extensions are enriched for intrinsically disordered and phase-separation-promoting residues, suggesting roles beyond the conserved catalytic core. Further, functional characterization of IF2 with varying N-terminal lengths show that loss of the N-terminal extension slows bacterial growth specifically under temperature and pH stress. Appending C-terminal extensions from different organisms to the Escherichia coli IF2 demonstrates a conserved role for these extensions in adaptation to temperature and anaerobiosis. Our findings establish the functional significance of IF2 terminal extensions, linking their evolutionary diversification to stress-dependent regulation of translation.
    DOI:  https://doi.org/10.64898/2026.02.08.704698
  25. Mol Cell Biol. 2026 Feb 23. 1-22
    Molecular Mechanisms of RNA Polymerase I Transcription in Health and Disease: An Overview.
    Bridget M Walker, Jonathan Y Chung, Haleigh G Pascual, Jyoti D Adala, Bruce A Knutson.
      RNA polymerase I (Pol I) is a specialized eukaryotic enzyme responsible for transcribing ribosomal DNA into precursor rRNA, a process that initiates ribosome biogenesis and supports cellular growth, metabolism, and proliferation. Recent structural and mechanistic studies have revealed unique features of Pol I architecture that enable high transcriptional output and tight regulatory control. Pol I activity is dynamically regulated by signaling pathways, epigenetic mechanisms, and chromatin structure, integrating environmental and metabolic cues to fine-tune ribosome production. Dysregulation of Pol I transcription is associated with a wide spectrum of human diseases: hyperactivation is a hallmark of cancer, whereas loss-of-function mutations cause ribosomopathies, leukodystrophies, and neurodegenerative disorders through nucleolar stress. Targeted therapies, including small-molecule inhibitors and emerging peptide-based approaches, are expanding clinical strategies to modulate Pol I activity. Beyond its canonical role, Pol I contributes to genome stability, immune regulation, and host-pathogen interactions, broadening its therapeutic relevance. This review integrates structural, mechanistic, and disease perspectives on Pol I, highlighting how fundamental discoveries are informing the next generation of targeted interventions across oncology, neurodegeneration, developmental disorders, infection, and aging.
    Keywords:  RNA polymerase I; cancer; ribosomopathy; therapeutic targets
    DOI:  https://doi.org/10.1080/10985549.2026.2628826
  26. Int J Mol Sci. 2026 Feb 18. pii: 1967. [Epub ahead of print]27(4):
    m6A RNA Methylation Is Increased in Tumour Invasive Regions and Influences Invasive Capability and Chemotherapeutic Sensitivity in Adult Glioblastoma.
    Masar Radhi, Jonathan Rowlinson, Lauryn Walker, Simon Deacon, Helen Miranda Knight, Stuart Smith.
      Adult glioblastoma multiforme (GBM) is the most common primary malignant brain tumour caused by multiple molecular factors. N6-methyl-adenosine (m6A) is an abundant RNA modification that governs cellular RNA metabolism. We hypothesise that changes in m6A-modified RNA and regulatory machinery such as the writer proteins, Methyltransferase 3 (METTL3) and WT1-associating protein (WTAP), the demethyltransferase protein, and Alpha-ketoglutarate dependent dioxygenase (FTO), are driving factors of GBM development and treatment resistance. Here, we investigated m6A-RNA spatial and quantitative abundance and expression of m6A effector proteins directly in GBM tissue and patient-derived low-passage primary adult GBM and low-grade glioma (LGG) cells, and explored the consequences of m6A-RNA disruption on GBM invasive capabilities, self-renewal and responsiveness to temozolomide (TMZ). We observed that METTL3, WTAP and FTO transcript and protein expression were significantly increased in cells derived from invasive regions of GBM tumours, and elevated WTAP and FTO expression significantly correlated with poor GBM patient survival. We further found that the abundance of m6A-modified RNA in GBM tumours was significant higher in rim and invasive tissue, as well as significantly higher in patient-derived cells from GBM tumour invasive regions. Functional depletion of these effector proteins significantly altered m6A levels on and the expression of the pluripotency stem cell marker SOX2 while also impairing self-renewal and cell invasion behaviour and increasing sensitivity to TMZ. The targeting of RNA modification regulatory mechanisms reveals novel therapeutic strategies aimed at improving clinical outcomes for GBM patients.
    Keywords:  N6-methyl-adenosine; glioblastoma multiforme; invasive capability and chemotherapeutic sensitivity
    DOI:  https://doi.org/10.3390/ijms27041967
  27. bioRxiv. 2026 Feb 22. pii: 2026.02.22.707292. [Epub ahead of print]
    A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing.
    Diorge P Souza, Mira B May, Jackson Carrion, Vikram Alva, Alex Bisson, Joseph H Davis.
      Ribosome hibernation helps cells survive stress by reversibly silencing translation and limiting degradation of ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation remains poorly understood. Using cryoEM to analyze lysates from a model archaeon, we identified AHA (AMPKγ-HPF from Archaea), a broadly conserved ribosome-associated protein factor composed of two distinct modules. Structural analyses showed that AHA's C-terminal domain binds the small subunit, while its N-terminal region recognizes the large subunit, occluding the mRNA channel and the A- and P-tRNA binding sites and thereby enforcing translational silencing. Consistent with this proposed function, ΔAHA cells displayed reduced viability, depletion of ribosomal proteins during stationary phase, and impaired recovery upon return to growth. Phylogenetic analyses revealed that AHA's C-terminal domain shares homology with the bacterial Hibernation Promoting Factor (HPF), indicating an origin in the last universal common ancestor (LUCA) and thereby identifying HPF as a universal hibernation module. Strikingly, we observed two AMP molecues bound to AHA's N-terminal CBS-tetrad, which we found was structurally and evolutionary related to the eukaryotic energy sensor AMPKγ, thus linking energy sensing between archaea and eukaryotes. Together, these findings uncover a widespread archaeal ribosome hibernation factor and establish a direct evolutionary link between prokaryotic translational silencing and eukaryotic energy sensing.
    DOI:  https://doi.org/10.64898/2026.02.22.707292
  28. Viruses. 2026 Feb 12. pii: 229. [Epub ahead of print]18(2):
    ASFV MGF110-7L Inhibits eIF4G1 Expression via Endoplasmic Reticulum Stress to Block Host Translation.
    Xinyu Gao, Suduo Jiang, Liyan Zhang, Zhenqiu Gao, Lijie Xiao, Hongwei Cao.
      African swine fever virus (ASFV) is a highly contagious and lethal double-stranded DNA virus that relies on host cellular translation machinery for replication and immune evasion. The multigene family 110 (MGF110) contains several members with incompletely defined functions. Here, the role of MGF110-7L in host translation regulation was investigated in HEK-293T and PK15 cells. Ribopuromycylation assays demonstrated that MGF110-7L expression resulted in potent, dose- and time-dependent inhibition of nascent polypeptide synthesis. Western blotting revealed a selective reduction in eIF4G1 protein abundance, with no significant changes in eIF4G2, eIF4E, and eIF4A, while eIF4G1 mRNA levels remained unaffected, indicating post-transcriptional regulation. Overexpression of eIF4G1 partially rescued translation suppression. MGF110-7L also decreased eIF4B phosphorylation and activated the PERK/eIF2α pathway, consistent with the induction of endoplasmic reticulum (ER) stress. ER stress promoted stress granule (SG) formation and enhanced eIF4G1 association with the SG marker G3BP1. The inhibitor assays demonstrated that the suppression of eIF2α phosphorylation by ISRIB restored the abundance of eIF4G1 protein. In addition, the downregulation of eIF4G1 was reversed by the inhibition of autophagy using bafilomycin A1, indicating an SG-linked autophagy-lysosome degradation pathway. Co-immunoprecipitation assays confirmed increased eIF4G1-G3BP1 interaction, but no direct binding between MGF110-7L and eIF4G1. This work provides the first experimental evidence that an ASFV protein, MGF110-7L, suppresses cap-dependent translation through SG-mediated autophagic degradation of eIF4G1, thereby revealing a previously unrecognized mechanism of ASFV translational control. These findings not only extend current understanding of ASFV-host interactions but also suggest potential molecular targets for antiviral strategies and rational vaccine design.
    Keywords:  African swine fever virus; endoplasmic reticulum stress; eukaryotic initiation factors 4G1; host translation hijacking; the multigene family 110-7L
    DOI:  https://doi.org/10.3390/v18020229
  29. J Intensive Med. 2026 Feb;6(1): 28-33
    N6-methyladenosine methylation in acute lung injury: Mechanisms and research progress.
    Yating Hu, Yijie Wang, Xiyue Liu, Xiaoli Xue, Binbin Li, Fangwei Li.
      N6-methyladenosine (m6A) methylation is the most prevalent and abundant internal post-transcriptional RNA modification in eukaryotic cells, playing an important regulatory role in various biological processes. The biological functions of m6A modification are dynamically and reversibly mediated by methyltransferases (writers), demethylases (erasers), and m6A binding proteins (readers). Acute lung injury (ALI) is a common critical condition characterized by diffuse edema within the pulmonary interstitium and alveoli, and is associated with high morbidity and mortality. Recent studies have identified that aberrant expression of m6A regulators is closely associated with ALI development. This review highlights the progress in research on m6A writers, erasers, and readers in ALI, focusing on their molecular regulatory mechanisms. Elucidating the molecular mechanisms of m6A and its associated proteins in ALI may reveal new therapeutic strategies and targets.
    Keywords:  Acute lung injury; Acute respiratory distress syndrome; RNA Methylations; Sepsis; m6A RNA Methylation
    DOI:  https://doi.org/10.1016/j.jointm.2025.07.001
  30. Biol Cell. 2026 Feb;118(2): e70052
    Mechanobiology of the Nucleolus.
    Yuthika Shetty, Monika Elzbieta Dolega.
      Ribosome biogenesis is an essential and energy-demanding process required to maintain cellular proteostasis. The nucleolus, which orchestrates this vital process, assembles as a nuclear condensate and exhibits remarkable plasticity in its structure, function, and protein composition. This dynamic membraneless organization of the nucleolus contributes to its involvement in diverse signaling pathways, influencing cell cycle regulation, proliferation, apoptosis, differentiation, and cellular stress response. Here, we focus on how mechanical cues influence nucleolar biology. Although classical mechanotransduction is mediated by membrane-anchored signaling proteins and the cytoskeleton that propagate forces within the cell, how mechanical cues influence the organization and function of dynamically assembled, membraneless condensates remains an open question. In this review, we explore how mechanical stimuli impact the nucleolus, the most prominent nuclear condensate. We examine how extrinsic forces alter nuclear structure, thereby affecting nucleolar organization, and function. Finally, we highlight emerging evidence that positions the nucleolus as a key mediator of nuclear mechano-adaptation, linking extracellular matrix (ECM) cues, migration, confinement, and external mechanical stress to nucleolar assembly and ribosome biogenesis.
    DOI:  https://doi.org/10.1111/boc.70052
  31. Arterioscler Thromb Vasc Biol. 2026 Feb 26.
    Adenosine-to-Inosine (A-to-I) RNA Editing by ADAR1 to Control RNA Sensing in Cardiovascular Disease.
    Chad S Weldy, Jin Billy Li, Thomas Quertermous.
      Across biology, organisms have retained a mechanism to diversify the RNA transcriptome through RNA editing. Mediated by ADAR (adenosine deaminase acting on RNA) enzymes, Adenosines in double-stranded RNA (dsRNA) structures can be edited to Inosines (adenosine-to-inosine edit). Although this can change the amino acid sequence if it occurs in a coding sequence of mRNA, the majority of RNA editing in mammalian cells is found in noncoding repetitive elements. These repetitive elements have a predisposition to form long dsRNA structures that can mimic a dsRNA virus. Since the initial discoveries of RNA editing over 30 years ago, investigators have now identified ADAR1 to play a crucial role in suppressing innate immune activation and type I interferon signaling. Through adenosine-to-inosine editing, these dsRNA change their conformational structures and evade activation of the innate immune dsRNA sensor, MDA5. In human disease, although rare loss-of-function variants of ADAR1 have been associated with severe autoimmune disease, there has also been a rapid advance in our understanding of this molecular pathway in common complex diseases. We now understand that common genetic variants can impact RNA editing frequencies, and variants that decrease RNA editing are associated with an increase in risk of numerous autoinflammatory disorders as well as coronary artery disease. This rapid advance in our understanding of the genetic determinants of RNA editing and coronary artery disease has been mirrored by new discoveries in molecular biology, where deficient RNA editing within the vascular wall and smooth muscle cell now highlights endogenous RNA sensing by MDA5 as a causal mechanism of coronary artery disease and other vascular disorders. Here, in this review, we provide a focused look at major advances in RNA editing and cardiovascular disease and put these discoveries into historical context with a goal to map the next steps to advance these molecular pathways to new therapeutic discovery.
    Keywords:  RNA editing; RNA, double-stranded; adenosine deaminase; cardiovascular diseases; coronary artery disease
    DOI:  https://doi.org/10.1161/ATVBAHA.125.323847
  32. Sheng Wu Gong Cheng Xue Bao. 2025 Dec 17. pii: 1000-3061(2026)02-0955-16. [Epub ahead of print]42(2): 955-970
    [im6Am-DC: a model for predicting RNA sequence N6,2'-O-dimethyladenosine modification by integrating DenseNet and attention mechanism].
    Xin Wei, Jian Tu, Jun Qi, Siqin Hu, Jianhua Jia.
      N6,2'-O-dimethyladenosine (m6Am), as a critical RNA epigenetic modification, has become a hot topic in current research due to its unique chemical structure and biological functions. m6Am not only regulates mRNA stability and half-life but also modulates its interactions with translation initiation factors and RNA-binding proteins, thereby playing a crucial role in post-transcriptional regulation. Recent medical research indicates that m6Am is closely associated with metabolic disorders such as obesity and type 2 diabetes mellitus, as well as multiple viral infections and tumor development. Therefore, predicting m6Am site holds significant importance for early diagnosis and precision treatment of diseases. Although the biological functions of m6Am modification are gradually attracting attention, related research is still limited by the limitations of detection technology and high costs. Computational biology methods provide new ideas for large-scale identification of m6Am sites. This paper proposes an imbalanced m6Am site prediction model-im6Am-DC. The model employs a DenseNet architecture to extract high-level local features and introduces a CA attention mechanism to highlight crucial feature information. Furthermore, to solve the data imbalance, the model utilizes the focal loss function. Experimental results showed that on the full transcript dataset, the im6Am-DC model achieved the sensitivity (Sn) of 0.523 7, specificity (Sp) of 0.988 4, accuracy (Acc) of 0.946 1, and Matthews correlation coefficient (MCC) of 0.629 8. On the mature RNA dataset, the model demonstrated equally strong performance across these metrics. Simultaneously, we employed the im6Am-DC model to predict across multiple distinct datasets, including unbalanced m6Am site datasets, balanced m6Am site datasets, and other types of RNA modification sites. This comprehensive, multidimensional approach enabled us to evaluate the performance and application potential of the model. The results demonstrate that the im6Am-DC model exhibits significant advantages in predicting unbalanced m6Am sites, providing effective technical support for studying the roles of m6Am modifications and exploring related disease mechanisms.
    Keywords:  DenseNet; N6,2'-O-dimethyladenosine; RNA epigenetic modification; attention mechanism; focal loss
    DOI:  https://doi.org/10.13345/j.cjb.250651
  33. Nucleic Acids Res. 2026 Feb 24. pii: gkag090. [Epub ahead of print]54(5):
    RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.
    Riccardo Mosca, Carlos J Gallardo-Dodd, Qun Li, Christian Sommerauer, Justas Šidiškis, Jonas Nørskov Søndergaard, Claudia Kutter.
      Over the past decade, thousands of putative human RNA-binding proteins (RBPs) have been identified, increasing the need for methods that define their RNA-binding capacities across diverse biological settings. Existing methods rely either on antibody-based in vivo capture (e.g. CLIP-seq), which depends on cross-linking efficiency and antibody availability, or on synthetic oligonucleotide-based assays (e.g. RNAcompete), which use artificial RNA substrates and cannot assess binding across the native transcriptome. To bridge this gap, we developed RNA affinity purification followed by sequencing (RAPseq), an in vitro method that profiles RBP-binding to native cellular RNA, enabling large-scale transcriptome-wide characterization of RNA-protein interactions without antibodies or synthetic probes. Using RAPseq, we characterized the RNA interactomes of 11 canonical RBPs and 26 non-canonical RBPs, and uncovered novel and specialized moonlighting RNA-binding activities. Applying RAPseq to vertebrate HUR proteins revealed recognition of a conserved RNA-binding motif but showed species-specific binding preferences. Profiling of five pathological IGF2BP family variants exhibited distinct gain- and loss-of-function binding patterns, with implications for cancer biology. Our combinatorial RBP-binding assay (co-RAPseq) uncovered cooperative RNA-binding by HUR and PTBP1, including de novo estimation of the optimal binding distance. Lastly, we introduce a modification-sensitive assay (mod-RAPseq) to distinguish between modification-dependent and -independent RNA-binding sites of YTHDF1 and YBX1. Overall, our simple, scalable, and versatile method enables exploration of complex RNA-protein interactions and the regulatory layers that shape post-transcriptional gene regulation.
    DOI:  https://doi.org/10.1093/nar/gkag090
  34. bioRxiv. 2026 Feb 20. pii: 2026.02.19.706916. [Epub ahead of print]
    PXL: a Nucleic Acid-Binding Module of Promyelocytic Leukemia Protein.
    Daniel Fairchild, Irina V Semenova, Dane Geddes-Buehre, Yunfeng Li, Renata Szczepaniak, Sandra K Weller, Bing Hao, Irina Bezsonova.
      The promyelocytic leukemia protein (PML) is a stress-response factor that assembles into PML nuclear bodies, dynamic subnuclear compartments involved in tumor suppression and antiviral defense. The most abundant isoform, PML-1, has been linked to transcriptional regulation, genome stability, and antiviral responses, yet the molecular basis of these functions remains unclear. Here, we report that PML-1 contains a unique nucleic acid- binding module, PXL, and determine its three-dimensional structure by X-ray crystallography. Further biochemical, mutational, and cellular analyses, including RNA-seq, demonstrate that this module selectively binds single-stranded G-rich RNA and DNA motifs and modulates the transcriptome. These findings reveal an unexpected molecular function of PML and provide a framework for understanding its roles in nuclear organization and gene regulation.
    DOI:  https://doi.org/10.64898/2026.02.19.706916
  35. J Microbiol. 2026 Feb 24.
    Ribosome-associated proteins in fungal ribosome homeostasis: Conceptual opportunities for peptide-based modulation.
    Yongjun Kim, Chang-Jun Ji, Seohyun Park, Junsuk Lee, Jiwoon Jung, Yejin Kim, Dabin Pyeon, Yoon-Mo Yang.
      Ribosomes are essential macromolecular machines that facilitate protein synthesis and have long been recognized as effective targets for antimicrobial agents. While structural differences between prokaryotic and eukaryotic ribosomes form the basis for selective antibiotics against bacteria, similar approaches for developing antifungal agents targeting ribosomes have remained limited due to the high sequence and structural conservation with human ribosomes. However, emerging insights into ribosome homeostasis, including ribosome biogenesis, turnover, and hibernation, have uncovered a set of ribosome-associated proteins whose function is critical yet display greater sequence divergence from their human counterparts. These observations suggest that these regulatory components may represent viable antifungal targets by disrupting fungal proteostasis. The present review aims to explore this developing concept by examining ribosome-associated factors and considering whether short ribosomal protein-derived peptides may eventually serve as druggable molecules for selectively modulating these pathways in fungal pathogens.
    Keywords:  antifungal peptide; ribosomal protein; ribosome homeostasis
    DOI:  https://doi.org/10.71150/jm.2511006
  36. Biol Pharm Bull. 2026 ;49(2): 355-363
    Identification of Inhibitors for eIF5A2-Dependent Translation Elongation by Monitoring the Translational Efficiency of Polyproline Motif in Mitochondrial Fission Regulator 1.
    Masato Suzuki, Masahiro Komeno, Ryosuke Yasumura, Ayuna Miwa, Misaki Enomoto, Hitoshi Kotani, Ken Matsumoto, Kazunori Akimoto, Chiaki Takahashi, Kazuei Igarashi, Kyohei Higashi.
      We previously reported that eukaryotic translation initiation factor 5A2 (eIF5A2), rather than eIF5A1, is important for the proliferation of HeLa S3 and MDA-MB-231 cells, despite the 84% amino acid sequence identity between eIF5A1 and eIF5A2. In addition, individual upregulated genes, including mitochondrial fission regulator 1 (MTFR1), which has a proline-rich motif, by eIF5A2 were different from those in eIF5A1. Thus, eIF5A2-dependent translational elongation is a promising target for cancer treatment with minimal side effects. In this study, we constructed a high-throughput screening system to identify eIF5A2-dependent translation elongation inhibitors by monitoring the translation efficiency of the MTFR1-luciferase fusion protein in HeLa S3 cells. Orlistat and andrographolide (AGP) were suggested as inhibitors of eIF5A2-dependent translation elongation among 1744 compounds from libraries. In addition to the findings related to AGP, the present study revealed that orlistat and the silencing of eIF5A2 suppressed the invasive activity of MDA-MB-231 cells. Downregulation of heparanase 1 expression, but not of matrix metalloproteinase-2 (MMP2) and MMP9, by eIF5A2 silencing was similar to that by treatment with orlistat and AGP, suggesting that orlistat and AGP were, at least in part, capable of attenuating eIF5A2-dependent translation elongation through the repression of eIF5A2 expression. Based on these observations, monitoring the translational efficiency of MTFR1 synthesis may be useful for identifying new eIF5A2 inhibitors.
    Keywords:  andrographolide; eukaryotic translation initiation factor 5A2; onco-ribosome; orlistat; translation elongation
    DOI:  https://doi.org/10.1248/bpb.b25-00720
  37. Res Sq. 2026 Feb 16. pii: rs.3.rs-8615050. [Epub ahead of print]
    Integrated Stress Response Signatures Drive Monocyte Dysfunction in GBA1- and LRRK2-Linked Parkinson's Disease.
    Daniele Mattei, Erica Brophy, Mikaela Rosen, Oriol Narcis Majos, Aloysius Domingo, Elena Meijia, Claudia De Sanctis, Beomjin Jang, Tarek Khashan, Mengxi Yang, Deborah Raymond, Casey Young, Jack Humphrey, Elisa Navarro, Amanda Allan, Katherine Leaver, Viktoriya Katsnelson, Alexander Chung, Benjamin Muller, Matthew Swan, Vicki L Shanker, Mariel Pullman, Adina Wise Adina Wise, Roberto Ortega, Kelly Astudillo, Steven Frucht, Susan Bressman, Giulietta Riboldi, Laurie J Ozelius, Rachel Saunders-Pullman, Towfique Raj.
      Monocytes are increasingly implicated in Parkinson's disease (PD) pathogenesis, with idiopathic cases showing mitochondrial and lysosomal dysfunction. However, the impact of PD-associated mutations on monocytes remains unclear. To address this, we investigated transcriptomic and functional disturbances in peripheral monocytes from patients with GBA1 - and LRRK2 -associated PD and idiopathic PD. Transcriptomic data revealed shared and mutation-specific signatures, including those related to immune dysregulation, and consistent defects in lysosomal, proteasomal and mitochondrial pathways. Network and pathway analyses further uncovered downregulation in protein translation and enrichment of integrated stress response (ISR) signatures, alongside aberrant expression of genes linked to ER stress, mitophagy and type-I interferon signaling. Protein levels of heat-shock proteins and ISR effectors were elevated at baseline and following α-synuclein exposure, consistent with impaired proteostasis. Live-cell assays demonstrated defects in lysosomal function, mitochondrial dynamics, and phagocytosis, most pronounced in GBA1 - and LRRK2 -associated PD but evident across all PD groups. Together, these findings define a PD-associated myeloid state of immunodegeneration , marked by impaired clearance, proteostasis failure, and mitochondrial dysfunction across genetic and idiopathic PD.
    DOI:  https://doi.org/10.21203/rs.3.rs-8615050/v1
  38. Mol Cell Proteomics. 2026 Feb 19. pii: S1535-9476(26)00031-9. [Epub ahead of print] 101535
    Polysomal profiling coupled to allele-specific proteomics reveals an EIF4H tranSNP allele possessing higher mRNA translation potential.
    Meriem Hadjer Hamadou, Laura Alunno, Daniele Peroni, Michael Pancher, Fabio Mazza, Tecla Venturelli, Romina Belli, Erik Dassi, Alessandro Romanel, Alberto Inga.
      To search for genetic sources of allele-specific mRNA translation, we leveraged heterozygous polymorphisms and variants present in the exome of HCT116 colorectal adenocarcinoma-derived cells, computing allelic fractions from both total and polysome-associated RNA from RNA-seq data. Allelic imbalance in polysomal RNA led us to nominate 52 coding variants associated with allele-specific mRNA translation, of which 16 are nonsynonymous. To validate instances of allele-specific translation, a proteomics workflow was developed that combines label-free shotgun analysis, high-pH reversed-phase peptide fractionation, and targeted parallel reaction monitoring (PRM) using isotope-labeled peptide standards. Using this approach, we provide proof-of-concept validation of the heterozygous G>A, R183H missense SNV rs1554710467 in the EIF4H gene. The variant is present in two EIF4H alternative spliced variants, which showed equivalent translation efficiency in HCT116 cells but differ in abundance. The alternative peptide containing H183 was significantly more abundant than the corresponding reference peptide containing R183, consistent with the overrepresentation of the alternative allele in polysomal RNA in HCT116 cells. A dual-fluorescence ribosome-stalling assay confirmed the enhanced translation potential of the variant allele. The two EIF4H allelic proteins exhibited similar stability and subpolysomal localization. This study demonstrates the feasibility of using allele-specific proteomics at the endogenous protein levels by exploiting heterozygous coding variants. Overall, our approach extends the toolbox available to investigate allele-specific differences in mRNA translation potential, a relatively underexplored layer of gene expression regulation that could reveal inter-individual differences in disease-relevant phenotypes.
    Keywords:  EIF4H; SNPs; allele-specific proteomics; allelic imbalance; mRNA translation
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101535
  39. Biochim Biophys Acta Gene Regul Mech. 2026 Feb 25. pii: S1874-9399(26)00013-1. [Epub ahead of print] 195147
    In Cereibacter sphaeroides, expression of flagellin FlaA is posttranscriptionally controlled by the 5' untranslated region of its mRNA and the regulatory proteins FlaF, FlbT and FlbR.
    Julia M Benítez, Benjamín Vega-Baray, Manuel González-Vera, Sebastián Poggio, Laura Camarena.
      In bacteria, flagellar filaments consist of thousands of flagellin subunits, making their assembly energetically costly. Flagellin synthesis is tightly regulated and in alpha-proteobacteria, this is achieved through a posttranscriptional mechanism mediated by the FlbT and FlaF proteins, although, their specific roles appear to vary among different species. In this study, we show that in Cereibacter sphaeroides in addition to FlaF and FlbT, a third regulatory protein, FlbR, posttranscriptionally regulate the FlaA flagellin synthesis. In the absence of any of these proteins, a severe reduction of FlaA is observed compared to the wild-type strain. This effect does not correlate with the expression of a reporter gene under the control of the flaA promoter but a marked decrease in flaA mRNA levels was observed. Because FlaA synthesis was restored by deleting the 5'-UTR of the flaA mRNA, we propose that this region is presumably the target of FlaF, FlbT and FlbR to control flaA mRNA stability. Furthermore, we show that FlbT by itself binds the flaA 5'-UTR. This posttranscriptional regulation is likely relevant during flagellar morphogenesis, given that preventing the assembly of early flagellar structures results in a reduction of FlaA, which is reversed upon deletion of the 5'-UTR. However, the negative role of the 5'-UTR was not reproduced when this region was placed upstream of a reporter gene, indicating that other regions of the flaA mRNA may also contribute to its regulation.
    Keywords:  5′ untranslated region (5′-UTR); Bacterial flagella; Posttranscriptional control; Translation control; mRNA stability
    DOI:  https://doi.org/10.1016/j.bbagrm.2026.195147
  40. bioRxiv. 2026 Feb 21. pii: 2026.02.20.707122. [Epub ahead of print]
    The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae.
    Brandon S Bruno, Evan M Platten, Lisa Houston, Christina E Brule, Elizabeth J Grayhack.
      Translation elongation and efficiency are modulated by the genetic code. In the yeast Saccharomyces cerevisiae, 17 inhibitory codon pairs, distinguished by requirements for wobble decoding and distinct codon order, result in reduced translation efficiency and slow translation. Nine of these inhibitory pairs are functionally important as they are disproportionately strongly conserved within the orthologous genes in Saccharomyces sensu stricto . For three pairs, including CGA-CGA, inhibition is triggered by ribosome collisions and known quality control responses, but the mechanisms by which other pairs cause inhibition is unknown. Here, we examined of the molecular basis of inhibition by the slowly translated, highly conserved Leu Pro CUC-CCG codon pair yielding four findings. First, inhibition is mediated by tRNA Leu(UAG) , which decodes CUC by a U●C wobble interaction and effectively competes with the nonessential W●C base pairing tRNA Leu(GAG) . Second, despite nearly universal conservation of U33 in tRNAs, the C33 alteration in tRNA Leu(GAG) does not significantly impair its function. Third, inhibition is likely due to ribosome collisions as many suppressors have mutations predicted to reduce ribosome concentration, including mutations in large ribosomal subunit proteins, RNA polymerase I, and ribosome assembly factors. Furthermore, local reduction in ribosome concentration suppresses inhibition. Fourth, we find a link between the metabolic state and CUC-CCG inhibition, as we find six suppressor mutations in SCH9 , a downstream effector of TORC1 that mediates ribosome production. As Sch9 is inactive during starvation, causing reduced ribosome concentration, one biological function of inhibitory pairs may be to mediate a change in relative expression during starvation conditions.
    DOI:  https://doi.org/10.64898/2026.02.20.707122
  41. Immun Inflamm Dis. 2026 Feb;14(2): e70376
    The Intersection of m6A Methylation and Immune Response in PCOS: A Bioinformatics Perspective.
    Wenting Xu, Lingli Shi, Aifang Lu, Lijuan Cui, Haiqing Qian, Jiahui Wang, Mengyu Tang, Lili Zhu, Lihong Wang.
       BACKGROUND: Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, the molecular underpinnings of which remain largely undefined. The most common methylation modification of RNA, N6-methyladenosine (m6A), plays an important role in various reproductive and endocrine disorders. This study investigates key m6A genes in PCOS and their association with immune cell infiltration using advanced bioinformatics methods.
    METHODS: We utilized gene expression data and clinical information from the Gene Expression Omnibus database data sets GSE137684, GSE80432, and GSE114419. The expression of m6A-related genes was analyzed across all samples. Using the GSVA and CIBERSORT packages in R, we developed a diagnostic model based on the m6A gene-protein interaction network, conducted enrichment analysis of hub genes, and assessed the correlation between these genes and immune cell infiltration.
    RESULTS: Analysis of data sets GSE137684 and GSE804322 identified variable expression patterns among three categories of m6A genes. A diagnostic model centered on m6A gene expression was established, highlighting five genes-WTAP, METTL14, ZC3H13, PCIF1, and RBM15-with significant effect coefficients. Unsupervised clustering of hub genes indicated that METTL14, HNRNPA2B1, YTHDF3, YTHDF2, YTHDC1, and YTHDC2 are potential discriminators in PCOS. The analysis of immune infiltration revealed a correlation between m6A regulators and immune cell levels, with METTL3 showing the most significant regulatory impact.
    CONCLUSION: N6-methyladenosine RNA methylation regulators are intricately linked with the development of PCOS and may influence immune cell infiltration in affected individuals. This study enhances our understanding of the molecular interactions in PCOS and suggests potential biomarkers for diagnosis and targets for therapeutic intervention.
    Keywords:  bioinformatics; immune infiltration; methylation; polycystic ovary syndrome
    DOI:  https://doi.org/10.1002/iid3.70376
  42. Biomolecules. 2026 Feb 04. pii: 244. [Epub ahead of print]16(2):
    The Liver Fluke Opisthorchis felineus Exosomal tRNA-Derived Small RNAs as Potential Mediators of Host Manipulation.
    Ekaterina Lishai, Maria Pakharukova.
      The role of extracellular vesicle non-coding RNAs in host-parasite interactions remains poorly understood, particularly for human liver flukes. Although tRNA-derived small RNAs (tsRNAs) are emerging as new regulatory molecules in parasite exosomes, they have not yet been characterized for the liver flukes. We performed small RNA sequencing to profile tsRNAs in the exosome-like vesicles derived from the liver fluke Opisthorchis felineus. Transcriptomic data from human cholangiocytes were analyzed to assess the enrichment of the predicted target genes among differentially expressed genes. We identified 247 functional tRNA genes in the O. felineus genome. Exosome-like vesicles were highly enriched for particular tsRNAs: derived from tRNA-Asp-GTC, tRNA-Ile-AAT, tRNA-Lys, tRNA-His, and tRNA-Tyr. This enrichment was independent of both genomic tRNA copy number and the amino acid composition of the trematode proteome. In silico prediction revealed that these tsRNAs target human genes involved in cell cycle, migration, and proliferation. Notably, these predicted target genes were significantly enriched among the differentially expressed genes in treated cholangiocytes. Our study provides the first evidence that O. felineus exosomes carry a specific repertoire of tsRNAs with the potential to regulate host gene networks. We propose that tsRNAs may contribute to host cell manipulation during O. felineus infection.
    Keywords:  RNA interference; exosome-like vesicles; non-coding RNA; opisthorchiasis; tRNA genes; transfer RNA
    DOI:  https://doi.org/10.3390/biom16020244
  43. J Exp Bot. 2026 Feb 24. pii: erag103. [Epub ahead of print]
    Co-translational control of protein stability and quality in plants.
    Daniel J Gibbs.
      Proteostasis relies on the coordinated control of protein synthesis, folding, modification and degradation, and an increasingly clear picture is emerging that many important decisions governing protein fate occur co-translationally. As nascent chains first appear at the ribosome exit tunnel, they encounter a suite of ribosome-associated enzymes that begin to shape whether proteins fold productively, acquire the correct N-terminal imprinting modifications, or require surveillance and removal. This review focuses on two major facets of co-translational control that determine protein and proteome stability, with particular attention to recent advances in plants. First, N-terminal (Nt-) methionine excision, Nt- acetylation and Nt-myristoylation are examined as early imprinting steps that define the chemical identity and regulatory trajectories of newly synthesized proteins, including how they influence targeting to N-degron pathways of proteolysis. Second, ribosome-associated quality control (RQC) pathways that sense ribosome stalling or collision are outlined, along with their roles in directing aberrant nascent chains towards ubiquitylation, extraction and degradation before they can accumulate and trigger proteotoxic stress. Together, these modification and surveillance mechanisms form an integrated decision-making network that establishes protein stability at the earliest stages of synthesis, contributing to proteostasis and impacting plant growth, development, and stress adaptation.
    Keywords:  Co-translational and ribosome-associated quality control; N-degron pathway; N-terminal acetylation (NTA); N-terminal methionine excision (NME); N-terminal myristoylation; protein degradation; ubiquitin proteasome system
    DOI:  https://doi.org/10.1093/jxb/erag103
  44. J Vis Exp. 2026 Feb 06.
    Dot Blot Assay for Detecting Global N6-Methyladenosine RNA Modification Levels.
    Suxia Guo, Junli Chang, Xiaobo Wang, Fulai Zhao, Peng Zhao, Binghan Yan, Chujie Zhou, Junjie Tong, Xinyu Zhang, Yuping Hong, Xingyuan Sun, Yanping Yang.
      N6-methyladenosine (m⁶A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA) and serves as a key regulator of post-transcriptional gene expression. Methods for investigating m⁶A can be applied at multiple levels of resolution, including global quantification, nucleotide-specific detection, and analysis of particular transcripts of interest. Among these, the dot blot assay provides a straightforward, rapid, and cost-effective approach for semi-quantitative evaluation of global m⁶A modification levels. In this assay, cells are first processed to extract total RNA, which is then diluted and denatured. The RNA samples are spotted onto a nylon membrane, probed with an anti-m⁶A antibody, and visualized by chemiluminescence, with signal intensity indicating the relative abundance of methylation. Finally, quantification and comparison of signal intensities are performed by measuring grayscale values with ImageJ. Compared with sequencing or mass spectrometry-based methods, dot blot requires minimal instrumentation and technical expertise, making it particularly suited for routine screening, preliminary functional studies, and comparative analyses. This protocol provides a detailed and reproducible workflow for implementing the m⁶A dot blot assay in both basic research and translational applications.
    DOI:  https://doi.org/10.3791/69860
  45. medRxiv. 2026 Feb 17. pii: 2026.02.14.26346327. [Epub ahead of print]
    Integrative transcriptomic analysis identifies long noncoding RNA dysregulation and circadian disruption in reward and executive circuits of opioid use disorder.
    Zixiu Li, Chen Fu, Peng Zhou, Ryan W Logan, Chan Zhou.
      Opioid use disorder (OUD) is characterized by compulsive drug seeking and impaired executive control arising from maladaptive plasticity within cortico-striatal circuits. While transcriptomic studies have identified coding gene alterations in the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC), the contribution of the noncoding genome remains poorly defined. Here, we performed integrative transcriptomic analysis of postmortem human NAc and DLPFC to systematically identify and characterize long noncoding RNAs (lncRNAs) in OUD. We identified 36,225 lncRNA loci expressed across reward and executive regions, approximately half of which were previously unannotated. OUD was associated with widespread lncRNA dysregulation in NAc and DLPFC, with lncRNA-centered co-expression modules enriched for neuroimmune signaling, phosphorylation-dependent synaptic pathways, and intracellular receptor cascades. Notably, OUD disrupted circadian rhythmicity of lncRNAs to a degree comparable to or exceeding mRNAs, implicating temporal reorganization of noncoding networks in addiction pathology. Integration with single-nucleus transcriptomic data revealed pronounced neuronal and glial cell type specificity among OUD-associated lncRNAs. Together, these findings demonstrate that lncRNAs represent a critical regulatory layer in reward and executive circuits and suggest that spatial, temporal, and cellular remodeling of the noncoding transcriptome contributes to circuit dysfunction in OUD.
    DOI:  https://doi.org/10.64898/2026.02.14.26346327
  46. Neurochem Int. 2026 Feb 24. pii: S0197-0186(26)00028-8. [Epub ahead of print] 106137
    Degradation of alpha-synuclein/SNCA mRNA by RNautophagy.
    Chihana Kabuta, Fumihiko Hakuno, Naoyuki Kataoka, Shin-Ichiro Takahashi, Tomohiro Kabuta.
      α-Synuclein is a neuronal protein and main component of Lewy bodies, the pathological hallmark of Lewy body diseases such as Parkinson's disease and dementia with Lewy bodies. While the accumulation of α-synuclein in neurons is implicated in the pathogenesis of these disorders, the mechanisms underlying α-synuclein mRNA degradation remain poorly understood. RNautophagy is a lysosomal RNA degradation pathway in which RNA is directly taken up into lysosomes and subsequently degraded. SIDT2, a lysosomal membrane protein, mediates the uptake of RNA. In this study, we investigated whether SIDT2-mediated RNautophagy degrades α-synuclein mRNA. Knockdown of SIDT2 led to reduced degradation of α-synuclein mRNA, whereas overexpression of wild-type SIDT2 enhanced its degradation, suggesting its role in α-synuclein mRNA turnover. In contrast, overexpression of the RNA uptake-deficient S564A mutant did not enhance degradation, indicating that RNA uptake activity is required for SIDT2-mediated degradation of α-synuclein mRNA. Using a series of deletion mutants, we identified a guanine (G)-rich sequence within the 5' untranslated region (5'-UTR) of α-synuclein mRNA as a key determinant of SIDT2-dependent degradation. Furthermore, insertion of the G-rich sequence into the 5'-UTR of GFP mRNA promoted SIDT2-dependent degradation of GFP mRNA and reduced GFP protein expression. Taken together, these results indicate that SIDT2-mediated RNautophagy contributes to the degradation of α-synuclein mRNA via the G-rich region within the 5'-UTR. Our findings may also provide insights into the pathogenesis of Lewy body diseases.
    Keywords:  Autophagy; Dementia with Lewy bodies; Guanine-rich region; Lysosomes; Neurodegenerative disorder; Parkinson’s disease
    DOI:  https://doi.org/10.1016/j.neuint.2026.106137
  47. Plant Cell Environ. 2026 Feb 22.
    The Versatile Role of RNA N6-Methyladenosine (m6A) in Plant Resistance to Biotic Stress.
    Meiqiu Xu, Feifan Zhang, Junjiang Chen, Meiqi Zhang, Olivier Songue Same, Lunji Wang, Guillaume Legrand Ngolong Ngea.
      Concerns about biotic stress in agriculture have recently increased with the emergence of persistent pathogens and pests. N6-methyladenosine (m6A) RNA is a conserved epitranscriptomic modification. Recent advances in plant biotechnology and m6A profiling have generated unprecedented knowledge. Our review emphasizes recent state-of-the-art reports regarding m6A modulation of plant responses to biotic stress. We found that m6A modification plays a "master rheostat" role in plant immunity, potentially integrating signaling, transcription, protein turnover, and global metabolic pathways to achieve vigorous, as well as balanced, responses to biotic stress. This review highlights the potential for m6A to dynamically modulate interactions between plant defense hormones and defense pathways. m6A modulates the stability and activity of transcription factors, regulates defense proteins, antimicrobial metabolite production, antiviral defense, systemic acquired resistance, and the ubiquitin-proteasome pathway. Our review examines contextual factors that coordinate the activity of m6A-associated proteins and modulate global m6A dynamics. Importantly, we have addressed m6A in the context of promising trade-offs between defense and growth, and in the role of m6A-associated proteins in liquid-liquid phase separation to control hormonal transcript levels and fine-tune the plant defense response. Overall, this review proposes a new horizon for developing more biotic-stress-resilient plants.
    Keywords:  N6‐methyladenosine RNA (m6A); agricultural biotechnology; brown planthopper (Nilaparvata lugens); m6A‐associated proteins; plant pathogen and pest; plant resistance; plant response to biotic stress; wheat yellow mosaic virus (WYMV) infection
    DOI:  https://doi.org/10.1111/pce.70449
  48. RNA. 2026 Feb 23. pii: rna.080913.125. [Epub ahead of print]
    Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling.
    Matthew Hackbart, Patrick Wang, Victoria Gnazzo, Carolina B Lopez.
      Detection of foreign RNAs is a crucial activation step for innate immunity pathways in response to viral infections. Retinoic acid-inducible gene I (RIG-I) is a cytoplasmic RNA sensor that triggers type I and III interferon (IFN) expression and activates the antiviral response in response to RNA virus infection. The activating ligand for RIG-I has been shown to be 5'-triphosphated, blunt-ended, double-stranded (ds)RNA, but questions remain on the impact of other RNA motifs on RIG-I activation. Here we show that immune-activating copy-back viral genomes (cbVGs) contain RNA stem loops away from the 5' end of the RNA that enhance RIG-I signaling and IFN expression. Importantly, the sequence of the terminal loops of the activating motifs impacts the strength of IFN expression. Additionally, we show that synthetic versions of these cbVG-derived stem loops trigger innate immune responses in mice demonstrating their potential as immunostimulants in vivo.
    DOI:  https://doi.org/10.1261/rna.080913.125
  49. Nucleic Acids Res. 2026 Feb 24. pii: gkag143. [Epub ahead of print]54(5):
    U2AF2 controls alternative splicing in speckle-proximal regions in an RS domain-dependent manner.
    Serhii Pankivskyi, Asaki Kobayashi, Jean de Matha Salone, Kimberley Gargoly, David Pastré, Alexandre Maucuer.
      Splicing factor U2AF2 is known to play a pivotal role for 3' splice site recognition at an early step of spliceosome assembly. Here, using proximity labeling and biochemical confirmations, we extend the repertoire of putative functional partners of U2AF2 mainly for splicing, chromatin modification, transcription, 3' end processing, and RNA methylation. Removal of the U2AF2 RS domain alters numerous interactions, including self-association, reduces its localization to nuclear speckles, and impacts splicing genome-wide in a manner that depends both on splicing signals and on intron length. Indeed, cassette exon flanked by short introns in genes or transcripts located close to speckles are the most affected by U2AF2 knockdown or RS domain removal. Finally, we show that phosphorylation sites within the U2AF2 RS domain are required for normal splicing, suggesting that its RS domain mediates U2AF2 regulation. Our in-depth bioinformatics analyses reinforce previous observations that alternatively spliced transcripts accumulate in the proximity of speckles. Our results suggest that although U2AF2 is clearly enriched in these regions, its local concentration remains limiting. Consequently, a global reduction in U2AF2 disproportionately affects splicing in the vicinity of nuclear speckles. This provides new insight into how spatial protein availability contributes to the regulation of alternative splicing.
    DOI:  https://doi.org/10.1093/nar/gkag143
  50. Acc Chem Res. 2026 Feb 27.
    Metabolic RNA Labeling-Enabled Time-Resolved Single-Cell RNA Sequencing.
    Kun Yin, Shichao Lin, Chaoyong Yang.
      ConspectusGene expression of cells is a highly heterogeneous and dynamic program that changes over time in various biological processes such as embryogenesis, disease progression, and response to stimuli. Understanding the molecular mechanisms of heterogeneous and dynamic gene expression is crucial for advancing our knowledge of health and disease. The recent development of single-cell RNA sequencing (scRNA-seq) technologies has offered a great opportunity to dissect cellular heterogeneity by profiling the transcriptomes of individual cells. However, scRNA-seq captures only static snapshots of gene expression and fails to temporally resolve the RNA dynamics. Therefore, the rapid changes in transcription, the coordinated regulation of RNA synthesis and degradation rates, and the cellular interactions driving cell fate decisions remain poorly understood. In the past few years, metabolic RNA labeling-based scRNA-seq has emerged as a cutting-edge chemical tool to tackle these challenges. Nucleoside analogs are applied to label newly transcribed RNAs and distinguish them from pre-existing RNAs. This time-resolved technology unbiasedly captures the true RNA dynamics for thousands of genes in each of the individual cells, providing unprecedented insight into the regulation of heterogeneous and dynamic gene expression in diverse biological processes.In this Account, we highlight the recent advances achieved by our group and other laboratories in metabolic RNA labeling-enabled time-resolved scRNA-seq. First, we summarize the recent development of time-resolved scRNA-seq by integrating metabolic RNA labeling (e.g., 4-thioridine labeling) with various scRNA-seq platforms. We highlight our size-exclusion and locally quasi-static hydrodynamics-based Well-TEMP-seq method, which greatly improves the performance of time-resolved scRNA-seq (higher throughput, higher cell barcoding efficiency, and RNA recovery rate) and lowers the cost. Next, we extend the labeling strategy from single nucleoside labeling to double nucleoside labeling and develop scDUAL-seq The sequential (pulse-pulse) labeling by two different nucleosides in scDUAL-seq addresses the limitation of single nucleoside labeling in the simultaneous monitoring of RNA synthesis and degradation processes and accurate measurement of RNA kinetics. The ability of scDUAL-seq to discriminate between different cell states also allows the unveiling of the interplay between RNA synthesis and degradation that controls distinct RNA regulatory strategy transitions during dynamic processes. Then, we discuss the further development of in vivo metabolic RNA labeling-based scRNA-seq by our laboratory (Dyna-vivo-seq) and others, which advances the time-resolved scRNA-seq studies from cultured cells to animal models. This innovation opens new avenues to reveal single-cell RNA dynamics in living organisms. Finally, we introduce our attempts to integrate time-resolved scRNA-seq with spatial transcriptomics, adding a spatial dimension to temporal RNA dynamics. This new paradigm allows the dissection of the spatiotemporal regulation of gene expression and cell fate decisions through cell-cell interactions in the tissue microenvironment, which holds great promise for biomedical applications.Our perspectives on the current limitations of the chemical tools for single-cell RNA dynamics profiling and the future directions for improvement are also provided. We anticipate that this Account will inspire chemists to develop advanced chemical tools to profile the heterogeneous and dynamic gene expression programs and offer transformative insights into the molecular landscape of RNA dynamics in health and disease.
    DOI:  https://doi.org/10.1021/acs.accounts.6c00010
  51. Microorganisms. 2026 Feb 05. pii: 377. [Epub ahead of print]14(2):
    Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria.
    Xuhua Xia.
      Bacterial species differ dramatically in their growth rates, reflecting distinct ecological strategies and physiological constraints. Because protein synthesis is a major determinant of cellular replication, I examined how genomic investment in the translation machinery varies across bacteria with widely different doubling times. Using 20 bacterial species spanning two major bacterial kingdoms (Bacillati and Pseudomonadati), I quantified ribosomal RNA (rrn) operon number, total tRNA gene number, and the allocation of tRNA genes among amino acids. Rapidly replicating Vibrio natriegens has 11 rrn operons and 129 tRNA genes in its genome, whereas slowly replicating Borrelia burgdorferi has only one rrn operon and 32 tRNA genes. I show that both the rrn operon number and the tRNA gene number decline sharply with increasing generation time, a pattern observed independently within each bacterial kingdom. Moreover, tRNA gene allocation is highly non-uniform: amino acids that are frequently used in proteins and encoded by large synonymous codon families are supported by disproportionately more tRNA genes. This relationship is well described by a simple model incorporating amino acid usage and codon family size, as illustrated in rapidly growing species such as Vibrio natriegens and Clostridium perfringens. In contrast, slow-growing bacteria maintain relatively minimalist translation systems. Together, these results demonstrate that bacterial genomes are systematically optimized for translation in a manner tightly coupled to growth strategy, revealing how natural selection tunes both the capacity and structure of the translation machinery.
    Keywords:  Borrelia burgdorferi; Clostridium perfringens; Mycobacterium tuberculosis; Vibrio natriegens; doubling time; rrn operons; tRNA; translation efficiency
    DOI:  https://doi.org/10.3390/microorganisms14020377
  52. Nucleic Acids Res. 2026 Feb 05. pii: gkag128. [Epub ahead of print]54(4):
    Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate.
    Rudradeep Mukherjee, Michael J Guertin.
      We present a simple model for analyzing and interpreting data from kinetic experiments that measure engaged RNA polymerase occupancy. The framework represents the densities of nascent transcripts within the pause region and the gene body as steady-state values determined by four key transcriptional processes: initiation, pause release, premature termination, and elongation. We validate the model's predictions using data from experiments that rapidly inhibit initiation and pause release. The model successfully classified factors based on the steps in early transcription that they regulate, confirming TBP and ZNF143 as initiation factors and heat shock factor and glucocorticoid receptor as pause release factors. We found that most paused polymerases terminate and paused polymerases are short-lived with half lives less than a minute. We make this model available as software to serve as a quantitative tool for determining the kinetic mechanisms of transcriptional regulation.
    DOI:  https://doi.org/10.1093/nar/gkag128
  53. bioRxiv. 2026 Feb 20. pii: 2026.02.19.706931. [Epub ahead of print]
    NMD-mediated control of Tor influences adaptation to nutrient and temperature conditions in Cryptococcus neoformans.
    Sean R Duffy, John C Panepinto.
      The yeast Cryptococcus neoformans is an opportunistic human pathogen capable of surviving within various environmental conditions. The repertoire of antifungal agents effective in treating cryptococcal infection is limited, necessitating the identification of alternative treatment strategies. Nonsense-mediated decay (NMD) is an RNA decay mechanism that serves as a post-transcriptional regulator of gene expression. While the absence of NMD in C. neoformans sensitizes cells to the antifungal fluconazole, the mechanism underlying this sensitivity and role of NMD in C. neoformans biology remained unexplored. Using phenotypic analysis and RNA-sequencing analysis, we identify basal dysregulation of thermal- and nutrient-adaptive genes and demonstrate temperature- and/or nutrient-dependent phenotypic suppression of upf1 Δ phenotypes, including fluconazole sensitivity and resistance to rapamycin. We determine rapamycin co-treatment also suppresses the upf1 Δ fluconazole sensitivity, implicating dysregulation of Tor signaling in phenotypic outcomes when NMD is absent. We then investigate Tor-sensitive signaling in the upf1 Δ mutant, finding inhibition of cell wall integrity (CWI) signaling and hyperactivation of the kinase Gcn2, both of which returned to wildtype-like levels by either rapamycin treatment, nutrient limitation, or constitutive thermal stress. These results indicated NMD is required for appropriate regulation of Tor signaling in unstressed conditions and suggested upf1 Δ phenotypes are driven in part by Tor hyperactivation. A phenotypic screen of mutants lacking Tor regulators revealed that deletion of the Tor-suppressing IML1 gene recapitulates upf1 Δ phenotypes and signaling defects, consistent with Tor hyperactivation. Taken together, our results suggest NMD participates in the regulation of Tor signaling in C. neoformans . Future work will investigate how specific targets of NMD impact Tor signaling and promote fluconazole sensitivity in C. neoformans .
    Importance: Pulmonary and central nervous system infections cause by Cryptococcus neoformans are responsible for about 112,000 deaths annually. Ten-week mortality remains high at 25% with use of frontline antifungals which imposes major health risks due to inherent toxicity. Thus, a need arises to identify novel avenues of treatment, including ways of boosting the efficacy of widely available antifungals such as fluconazole against C. neoformans. The design of NMD inhibitors is an active pharmaceutical pipeline for use in treating human genetic diseases. Even though NMD is conserved across eukaryotes, underlying components and regulatory roles of NMD differ between humans and fungi. Therefore, understanding NMD within C. neoformans will inform the design and repurposing of NMD inhibitors to enhance the antifungal activity of fluconazole as a treatment for Cryptococcosis.
    DOI:  https://doi.org/10.64898/2026.02.19.706931
  54. bioRxiv. 2026 Feb 20. pii: 2026.02.19.706891. [Epub ahead of print]
    Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis.
    Esteban A Orellana, Isobel E Bowles, Xin Yang, Anais Torres, Sally R Jamieson, Raja H Ali, Alejandro Gutierrez, Richard I Gregory.
      tRNAs play a critical role in protein synthesis, influencing mRNA translation dynamics to shape proteomes. Emerging evidence links dysregulated tRNA activity to cancer progression, with tRNA-Arg-TCT identified as an oncogenic driver when ectopically overexpressed in non-malignant cells. The requirement of endogenous tRNA-Arg-TCT in cancer biology, however, remains untested. Moreover, considering that the tRNA-Arg-TCT family comprises six genes in humans, the importance of an individual tRNA isodecoder in cancer remains unknown. Here, we find elevated levels of tRNA-Arg-TCT-4-1 isodecoder are associated with poor patient prognosis across multiple cancer types. We demonstrate that, using different antisense RNA strategies, specific inhibition of tRNA-Arg-TCT-4-1 suppresses the growth of glioblastoma (GBM) and liposarcoma (LPS) cancer cells. Mechanistically, we find that tRNA-Arg-TCT-4-1 inhibition leads to a codon-biased remodeling of mRNA translation and the proteome, preferentially suppressing expression of growth-promoting genes and pathways encoded by mRNAs enriched in arginine AGA codons. Strikingly, intratumoral delivery of an antisense oligonucleotide (ASO) targeting tRNA-Arg-TCT-4-1 suppresses tumor growth and extends survival in mouse xenograft experiments performed using either a human LPS cell line or a patient-derived soft tissue sarcoma model. This study provides a foundation for targeting tRNA dysregulation as a novel therapeutic approach for cancer.
    One Sentence Summary: This study identifies tRNA-Arg-TCT-4-1 as a new anti-cancer therapeutic target and demonstrates that an antisense oligonucleotide (ASO) targeting this tRNA effectively suppresses tumorigenesis and extends survival in mouse xenograft models.
    DOI:  https://doi.org/10.64898/2026.02.19.706891
  55. Nucleic Acids Res. 2026 Feb 24. pii: gkag123. [Epub ahead of print]54(5):
    CELF1 is a non-canonical eIF4E binding protein that promotes translation of epithelial-mesenchymal transition effector mRNAs.
    Arindam Chaudhury, Natee Kongchan, Shebna A Massey, Rajesh Sharma, Rituraj Pal, Na Zhao, Phoebe Tsoi, Yingmin Zhu, Emuejevoke Olokpa, Sufeng Mao, Sonia Del Rincon, Lucas C Reineke, Richard E Lloyd, Marco Sardiello, Jeffrey M Rosen, Choel Kim, Josephine C Ferreon, Joel R Neilson.
      Mounting evidence is revealing an increasing complexity of gene regulation at the level of messenger RNA (mRNA) translation. Within mammalian cells, canonical cap-dependent mRNA translation depends on the eIF4F complex, consisting of the m7G mRNA cap-binding protein eukaryotic initiation factor 4E (eIF4E), the helicase eIF4A (eIF4A), and the eIF4G (eIF4G1) scaffolding protein. eIF4G1 additionally binds poly(A) binding protein (PABPC1) to facilitate mRNA circularization and nucleates pre-translation initiation complex assembly to initiate ribosomal scanning. In breast epithelial cells, the CELF1 RNA-binding protein specifically promotes the translation of select epithelial-to-mesenchymal transition (EMT) effector mRNAs by binding GU-rich elements (GREs) within their 3' untranslated regions (UTRs). Here we show that CELF1 directly binds to both eIF4E and PABPC1 to promote eIF4G1-independent translation of GRE-containing mRNAs in mesenchymal cells. Disruption of this CELF1/eIF4E interaction inhibits both EMT induction in vitro and experimental metastasis in vivo. Our findings define a novel, non-canonical mode of translational regulation underlying cellular de-differentiation, raising the possibility that analogous non-canonical modes of translation impact additional transitional cellular states within development and disease.
    DOI:  https://doi.org/10.1093/nar/gkag123
  56. JACS Au. 2026 Feb 23. 6(2): 1001-1011
    Site-Directed Modification of mRNA with Functionalized Platinum(IV)-Ammines.
    Edward Miller, Charlotte E Farquhar, Jacob Rodriguez, Andrei Loas, Bradley L Pentelute.
      Developing chemical toolkits for mRNA modification has remained an immense challenge, driven by the inherent difficulties in targeting mRNA molecules. Antisense oligonucleotides (ASOs) offer a promising framework for targeting specific mRNA sequences, yet they do not possess the capacity to alter the structure of mRNA except through enzyme-mediated hydrolysis. We developed a platinum-(IV)-ASO strategy that combines the sequence specificity of ASOs with the reactivity of platinum to functionalize nucleic acids, including short RNA and mRNA, in a selective enzyme-free manner. Access to Pt-(IV)-ASO constructs was made possible by an equatorial Pt-(IV) ammine derivatization strategy, allowing for the conjugation of carboxylic acids directly to the Pt core. Reactivity with 21-mer RNA and full-length mRNA by Pt-ASO constructs was demonstrated, and the conjugated products were characterized using a suite of orthogonal techniques, such as electrophoretic mobility shift assay, MALDI-TOF MS, temperature-dependent dissociation assay, and RT-qPCR. Constructs were optimized for their reactivity and selectivity, allowing for Pt-(IV)-PMO constructs with subnanomolar IC50 values in an RNA competition assay. This Pt-(IV)-ASO platform facilitates new avenues for RNA modification by providing a strategy for functionalizing nucleic acids with potential applications in molecular biology research.
    Keywords:  Pt(IV)−prodrugs; antisense oligonucleotides; bioconjugation; coordination chemistry; mRNA
    DOI:  https://doi.org/10.1021/jacsau.5c01369
  57. bioRxiv. 2026 Feb 09. pii: 2025.12.26.696633. [Epub ahead of print]
    Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons.
    Martín Escamilla Del Arenal, Lauren C Tang, Albana Kodra, Hani Shayya, Aileen Ugurbil, Olga Stathi, Keskin Abdurrahman, Adan Horta, Joan Pulupa, Junqiang Ye, Marko Jovanovic, Stavros Lomvardas, Rachel Duffié.
      During the switch from progenitor to differentiated cell, cellular physiology must change to accommodate increased translation and trafficking of membrane-bound proteins. We identify RNA-binding and E3 ubiquitin ligase Mex3a as a key driver of proper neuronal differentiation by regulating mRNA translation and trafficking of cell surface proteins in the context of Unfolded Protein Response (UPR) signaling. Loss of Mex3a in immature olfactory sensory neurons (OSNs) leads to defects in cilia structure, cell surface protein expression, and planar cell polarity in mature OSNs. Proteomics reveal a Mex3a-dependent decrease in proteins related to vesicle transport, lipid metabolism, and ribosome biogenesis. We identify RNA and ubiquitin targets of Mex3a and provide evidence that Mex3a may confer K27 ubiquitin linkage on substrates. Finally, modulating cellular levels of Mex3a changes the recruitment of translation factors Serbp1 and p-eEF2 to ribosomes with possible effects on translation. Our data reveal how a stemness factor regulates development post-transcriptionally and post-translationally to ensure robust differentiation.
    Highlights: Loss of stemness factor Mex3a in immature olfactory neurons leads to defects in mature olfactory neurons.Translation/Trafficking of cell surface proteins, cilia structure, and planar cell polarity are compromised in the absence of Mex3a.Mex3a may confer K27 ubiquitination on stress granule protein Serbp1 and ribosome protein Rps7.Mex3a levels are associated with Serbp1 and p-eEF2 recruitment to ribosomes.
    DOI:  https://doi.org/10.64898/2025.12.26.696633
  58. J Transl Med. 2026 Feb 23.
    m6A RNA modification and its emerging roles in diseases: recent advances and therapeutic implications.
    Radhika Kansal, Vrashti Sharma, Payal Potraje, Malabika Datta.
      
    Keywords:  Export; Metabolic disease; RNA; Splicing; Stability; Translation; m6A modification
    DOI:  https://doi.org/10.1186/s12967-026-07805-y
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