bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–03–15
forty-four papers selected by
Cédric Chaveroux, CNRS
  1. Structural potential of the 5' noncoding regions of the mRNAs encoding p53 isoforms.
  2. Roles of the integrated stress response in regulation of inflammatory reactions.
  3. Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.
  4. Standing on the Shoulders of Giant Ribosomes: UPF1-dependent Surveillance of Translation Dynamics to Proteostasis.
  5. PRRC2A, PRRC2B and PRRC2C are Stress Granule Proteins that Promote Translation Through Association with the eIF3 complex.
  6. Translational regulation by oxidative desulfuration of tRNA modifications.
  7. A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.
  8. Long non-coding RNA isoform specificity and chemical modification on tRNA-Derived fragments leading to divergent functions.
  9. Alternative polyadenylation releases PCBP1-mediated suppression of CFIm25 during macrophage differentiation.
  10. EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.
  11. Stoichiometry-induced differential selection on codon optimization among ribosomal protein genes in bacterial species.
  12. Mycobacterium tuberculosis MutT4/RppH is an RNA pyrophosphohydrolase that forms condensate-like bodies and impacts mRNA degradation.
  13. La protein binding to telomerase RNA supports an evolutionary relationship between plant and ciliate telomerase pathways.
  14. Pathways of mRNA decay in trypanosomes.
  15. Molecular insights into dynamic RNA quaternary assemblies.
  16. The key m6A methylation regulator IGF2BP1 possesses potential prognostic value in papillary thyroid carcinoma.
  17. m6A RNA methylation orchestrates spermatogenesis: decoding the synergistic regulatory network of signaling pathways and ubiquitination modifications.
  18. Epitranscriptomic signatures of malignancy: how RNA modifications shape breast and ovarian tumor progression.
  19. Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells.
  20. Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes.
  21. Phosphoproteomic Landscape of HDLBP: Insights into Function and Disease Associations.
  22. Desmosomes compartmentalize mRNA and translation in the skin.
  23. Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems.
  24. Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer.
  25. Untangling Responses of A-to-I RNA Editing to Heat Stress in the Mussel Mytilus galloprovincialis.
  26. DNMT1 stabilizes MAPK10 via m5C RNA methylation to ameliorate hepatic steatosis and mitochondrial dysfunction in non-alcoholic fatty liver disease.
  27. ZNF460 Promotes the m6A Modification of COPS6 to Facilitate Immune Escape in Colorectal Cancer.
  28. The anti-viral protein Shiftless blocks p-body formation during KSHV infection.
  29. Forces That Shape the Transcriptome: Linking Cellular Mechanosensing to mRNA splicing.
  30. TRMT6-directed m1A modification initiates lung squamous cell carcinoma via YTHDF3-stabilized cell cycle genes.
  31. METTL14 Aggravates Sepsis-Induced Acute Kidney Injury by Promoting Ferroptosis Through m6A Modification of BMAL1.
  32. SlYTH3 regulates tomato leaf senescence via recognition of N6-methyladenosine-modified SlHDZIV2 transcripts.
  33. FUS condensed phase unfolds model RNA G-quadruplex.
  34. The function of mRNA quality control in aging and age-related diseases.
  35. Decoding the functions of nuclear speckles in neurodegeneration.
  36. m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.
  37. mRNA-based SARS-CoV-2 vaccines: intracellular processing and aggregation of the encoded spike protein as a mechanistic contributor to cardiac cellular stress.
  38. RNA-triggered innate immunity: friend and foe.
  39. Nuclear-m6A-Label-Seq Enables Transcriptome-Wide Nuclear m6A Profiling at Single-Base Resolution.
  40. Targeting dengue virus infection through a translation-modulator small-molecule screen.
  41. Host ESCRT machinery orchestrates the assembly of tomato spotted wilt virus ribonucleoproteins.
  42. UGA4 and YBR062C Regulate Oxidative Stress Tolerance Under Heavy Metal Toxicity.
  43. The strategies and advances of mRNA translation booster.
  44. Synergistic targeting of eIF4A-mediated translation initiation and apoptosis in acute myeloid leukemia.
  1. Acta Biochim Pol. 2026 ;73 15861
    Structural potential of the 5' noncoding regions of the mRNAs encoding p53 isoforms.
    Mariola Dutkiewicz, Paulina Zydowicz-Machtel.
      Famous for its nickname "guardian of the genome," the p53 protein acts, among other things, as a transcription factor in the form of a tetramer, which may consist of different types of p53 isoforms. They differ in length and content of specific domains that are responsible for their functions. The way this factor acts, sometimes opposite to what we would expect from the main protein isoform, depends on which isoforms form the tetramer. There are over a dozen isoforms of the human p53 protein encoded by a single gene, thanks to the use of different transcriptional promoters (DNA level), alternative splicing (pre-mRNA level), and different translation initiation sites (mRNA level). In vitro studies have demonstrated that the use of different translation initiation sites on full-length p53FL mRNA is possible due to specific RNA structures, and that these structures are also responsible for the rate and efficiency of target protein isoform formation. This affects the proportions between the different p53 isoforms present in the cell at a given moment and, consequently, the further fate of the cell. This paper summarizes the knowledge about the importance of the RNA structure (I-III order) of individual p53 transcripts for the fate of the cell and the organism.
    Keywords:  RNA interactions; RNA structure; mRNA structure; p53 isoforms; translation regulation
    DOI:  https://doi.org/10.3389/abp.2026.15861
  2. Front Immunol. 2026 ;17 1747401
    Roles of the integrated stress response in regulation of inflammatory reactions.
    Fan Jiang, Guei-Sheung Liu, Junjun Liu, Xiaopei Cui, Yanqiu Xing.
      The integrated stress response (ISR) is a conserved cyto-protective mechanism, which has fundamental roles in maintaining cell viability under various conditions when intracellular and/or extracellular homeostasis is disrupted. ISR features phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α), leading to a global reduction in protein synthesis. Emerging evidence suggests that activation of ISR may have anti-inflammatory effects. In this concise review, we summarize the current experimental evidence in this regard from both in vitro and in vivo studies. It is suggested that ISR may represent a potential drug target for developing novel anti-inflammatory therapies.
    Keywords:  ATF4; GADD34; anti-inflammation; eIF2a; inflammatory disease; integrated stress response; phosphorylation; protein translation
    DOI:  https://doi.org/10.3389/fimmu.2026.1747401
  3. RNA. 2026 Mar 10. pii: rna.080884.125. [Epub ahead of print]
    Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.
    Oluwasegun T Akinniyi, Aswathy Sebastian, Shardul Kulkarni, Istvan Albert, Joseph C Reese.
      Yeast Def1 is well known for its role in regulating RNA polymerase II elongation and degrading the large subunit of polymerase during transcriptional stress. It is an abundant cytoplasmic protein that undergoes stress-induced processing and is then transported to the nucleus. Previous research from our lab has shown that Def1 interacts with various proteins involved in mRNA decay and translation control, and that it regulates mRNA half-lives, suggesting an important role in the cytoplasm. In this study, we report that Def1 binds polyribosomes and that its null mutant strain exhibits phenotypes indicating a role in translation. Ribo-seq analysis revealed that deleting DEF1 altered ribosome footprints on mRNAs and increased the dwell time of ribosomes at non-optimal codons in the A-site. Additionally, results from a codon-optimality reporter assay suggest that Def1 facilitates the degradation of mRNAs containing non-optimal codons. The Ccr4-Not complex links codon optimality to mRNA decay, and Def1's binding to ribosomes depends on its ubiquitin-binding domain, as well as the ubiquitylation of eS7a in the small ribosomal subunit by the Ccr4-Not complex. Moreover, the polyglutamine-rich, unstructured C-terminus of Def1 is crucial for its interaction with RNA decay and translation factors. This indicates that Def1 functions as a ubiquitin-dependent scaffold that connects translation status to mRNA decay. In summary, we have identified a cytoplasmic function for Def1 in translation and established it as a regulator of gene expression that spans both transcription and translation processes.
    Keywords:  Ccr4-Not; Def1; co-translational decay; posttranscriptional control; ubiquitylation
    DOI:  https://doi.org/10.1261/rna.080884.125
  4. J Mol Biol. 2026 Mar 10. pii: S0022-2836(26)00125-7. [Epub ahead of print] 169752
    Standing on the Shoulders of Giant Ribosomes: UPF1-dependent Surveillance of Translation Dynamics to Proteostasis.
    Heeju Park, Chunghun Lim.
      Up-frameshift 1 (UPF1) is best known as a key factor in nonsense-mediated mRNA decay (NMD), a well-conserved surveillance pathway that degrades mRNAs harboring premature termination codons (PTCs). The ATP-dependent RNA helicase UPF1 is recruited to ribosomes terminating at PTCs and triggers mRNA decay. Canonical NMD thereby limits the accumulation of truncated, potentially harmful polypeptides by rapidly eliminating faulty transcripts after the initial rounds of translation. However, emerging evidence from yeast to mammals indicates that UPF1 activity extends beyond simple degradation of PTC-containing mRNAs. Recent work links UPF1 to translating ribosomes, connecting translation dynamics with mRNA surveillance, co-translational quality control of nascent polypeptides, and aggresome targeting of aberrant translation products. These UPF1 functions beyond canonical NMD are increasingly recognized as important for cellular homeostasis. This review focuses on how UPF1 engages ribosomes to influence translation dynamics and coordinates the quality control of mRNA substrates and aberrant translation products. We further discuss the implications of these ribosome-coupled activities for diverse aspects of cellular physiology and disease.
    Keywords:  UPF1; co-translational quality control; nonsense-mediated mRNA decay (NMD); proteostasis; ribosome surveillance
    DOI:  https://doi.org/10.1016/j.jmb.2026.169752
  5. bioRxiv. 2026 Feb 25. pii: 2026.02.24.707808. [Epub ahead of print]
    PRRC2A, PRRC2B and PRRC2C are Stress Granule Proteins that Promote Translation Through Association with the eIF3 complex.
    Jie Qi Huang, Eileigh Kadijk, Karl J Schreiber, Zi Hao Liu, Rachel W Chiang, Zhixin Zhang, Kevin Guttman, Tian Hao Huang, Sylvia M T Almeida, Olena Zhulyn, Alan Moses, Julie D Forman-Kay, John L Rubinstein, Ji-Young Youn.
      Regulation of mRNA translation is essential for cellular homeostasis, and its dysregulation contributes to cancer, neurodegeneration, and developmental disorders. Stress granules are cytosolic condensates that form during stress-induced translation arrest and are enriched in mRNAs, translation factors, and RNA-binding proteins, but how stress granule proteins modulate translation remains poorly understood. Here, we identify the stress granule components Proline-Rich Coiled-Coil A, B, and C (PRRC2 proteins) as translation regulators. PRRC2 proteins are large, intrinsically disordered paralogs conserved across jawed vertebrates. Functional proteomics revealed that all PRRC2 proteins associate with the 48S translation initiation complex (PIC), whereas PRRC2B additionally interacts with nuclear proteins. Under stress, the proximal interaction network of PRRC2 proteins undergoes dynamic remodeling, including increased interactions with the stress granule scaffold G3BP1. Genetic perturbation shows that the PRRC2 proteins influence stress granule assembly in a context-specific manner, and are collectively required for cell growth in basal conditions due to their essential role in translation. Cells with reduced PRRC2 proteins exhibit a significant reduction in the abundance of more than half of the proteome, with a bias toward translational targets of eIF3d and eIF4G2. Interaction domain mapping and AlphaFold3 modeling revealed that an α helix within the putative coiled-coil domain of PRRC2C mediates interactions with the eIF3 core complex. This modeling places the PRRC2C α helix in a previously unassigned region of a published cryo-EM density map, validating the protein interaction and the mechanistic role of PRRC2C in translation control. Together, these findings establish PRRC2 proteins as components of the translation initiation machinery that regulate translation through their interactions with the eIF3 complex and other components of the 48S PIC factors, providing a direct mechanistic link between stress granule proteins and translational control.
    DOI:  https://doi.org/10.64898/2026.02.24.707808
  6. Nat Commun. 2026 Mar 10. pii: 2125. [Epub ahead of print]17(1):
    Translational regulation by oxidative desulfuration of tRNA modifications.
    Yufeng Mo, Kensuke Ishiguro, Kenjyo Miyauchi, Yuriko Sakaguchi, Yosei Hanzawa, Naho Akiyama, Ayaka Murayama, Kodai Machida, Hiroaki Imataka, Akio Yamashita, Takayuki Ohira, Mikako Shirouzu, Tsutomu Suzuki.
      Modifications in the anticodon region of transfer RNA (tRNA) are essential for accurate and efficient protein synthesis. 5-Methyl-2-thiouridine derivatives (xm5s2U) are major modifications at the wobble position of tRNA anticodons decoding purine-ending two-codon sets. Although the thiocarbonyl group of xm5s2U enhances decoding efficiency, it is chemically susceptible to oxidative desulfuration, yielding 4-pyrimidinone derivatives (xm5h2U). Here, we identify xm5h2U derivatives in human cells and mouse tissues and confirm their cellular formation by spike-in experiments. Desulfurized tRNAs carrying 5-methoxycarbonylmethyl-4-pyrimidinone (mcm5h2U) show impaired codon recognition in a human reconstituted in vitro translation system. The mcm5h2U modification reduces aminoacylation of tRNAs for lysine, glutamate, and glutamine, but not arginine. Cryogenic electron microscopy reveals the structural basis of altered AAA/AAG decoding by mcm5h2U at the ribosomal A-site. These findings reveal a mechanism by which oxidative desulfuration of tRNA modifications dynamically regulates codon recognition and protein synthesis under oxidative stress conditions in human and mammalian cells.
    DOI:  https://doi.org/10.1038/s41467-026-70126-7
  7. Nucleic Acids Res. 2026 Feb 24. pii: gkag207. [Epub ahead of print]54(5):
    A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.
    Julita Gumna-Mikina, Angelika Andrzejewska-Romanowska, Maciej Antczak, Ewa Tykwińska, Marta Szachniuk, Katarzyna Pachulska-Wieczorek.
      Activity-regulated cytoskeleton-associated protein (ARC) is an RNA-binding protein that also serves as a central hub for neuronal protein-protein interactions. It is essential for intercellular signaling and contributes to synaptic plasticity. ARC includes Gag-like sequences of Ty3/Gypsy retrotransposons and retains the ability to self-assemble into capsid-like structures containing Arc mRNA. Here, we employ an integrative approach to provide the first detailed in vitro analysis of ARC-RNA interactions. Using quantitative binding assays, RNA structure mapping, and ribonucleoprotein (RNP) footprinting, complemented by extensive computational analyses, we identified Arc mRNA regions specifically and non-specifically bound by ARC, as well as ARC amino acid residues involved in RNA interactions. We show that ARC recognizes RNA sequence and structure. A specific GC-rich motif is common to all bound RNA sequences, and the binding preferentially occurs near highly stable, solvent-exposed helices in the 5' region of Arc mRNA. Surprisingly, the conserved coding sequence seems more relevant to binding specificity than the 5'-untranslated region. Our predictions suggest that ARC binding to RNA through positively charged regions of matrix and capsid domains exposes an oligomerization motif, enhancing binding cooperativity. We also provide evidence that ARC acts as a nucleic acid chaperone and can locally destabilize Arc mRNA structure.
    DOI:  https://doi.org/10.1093/nar/gkag207
  8. Am J Pathol. 2026 Mar 05. pii: S0002-9440(26)00057-X. [Epub ahead of print]
    Long non-coding RNA isoform specificity and chemical modification on tRNA-Derived fragments leading to divergent functions.
    Xiaoxiao Hao, Zhangli Su, Anindya Dutta.
      Non-coding RNAs (ncRNAs) are important regulators of gene expression in development, immunity, and disease. Among them, long non-coding RNA (lncRNAs) and tRNA-derived fragments (tRFs) represent two major types of ncRNA that differ in size, structure, and function. As regulators, lncRNAs display remarkable structural complexity and extensive isoform diversity. Discrete motifs (such as hairpins, triple helices, G-quadruplexes, scaffold domains) harbored by a given isoform govern interactions with DNA, RNA and proteins, yet isoform-specific structures are rarely addressed, leading to contradictory findings across studies. In contrast, tRFs (14-35 nt) arise from precise cleavage of precursor or mature tRNAs and regulate translation, stress responses, and epigenetic inheritance. Their limited length constrains large-scale structural isoform diversity, but their functions are strongly shaped by chemical modifications, which affect stability, localization, and association with RNA binding proteins. Here, we highlight two underappreciated principles: (i) isoform- and structure-resolved mechanisms are essential for truly understanding lncRNA biology; and (ii) modification-driven rules diversify tRF functions. We propose an integrated framework that combines sequence, structure, isoform, and modification to refine mechanisms of action of ncRNAs and accelerate ncRNA-based diagnostics and therapeutics.
    DOI:  https://doi.org/10.1016/j.ajpath.2026.02.005
  9. FEBS Lett. 2026 Mar 13.
    Alternative polyadenylation releases PCBP1-mediated suppression of CFIm25 during macrophage differentiation.
    María Del Pilar Mendoza-Martín, Salwa Mohd Mostafa, Atish Barua, Claire L Moore, Srimoyee Mukherjee.
      CFIm25, a key component of the cleavage factor Im (CFIm) complex needed for mRNA 3' end processing, shows increased protein expression during monocyte-to-macrophage differentiation despite stable mRNA levels. We demonstrate that poly(C)-binding protein 1 (PCBP1) suppresses CFIm25 translation in monocytes by binding to its long 3' untranslated region (UTR). During differentiation, alternative polyadenylation generates a shorter CFIm25 3'UTR lacking PCBP1 binding sites. RNA immunoprecipitation confirms PCBP1 binding to the long 3'UTR, while ribosome association analysis shows enhanced ribosome recruitment upon PCBP1 depletion. PCBP1 knockdown increases CFIm25 protein in undifferentiated cells and induces macrophage differentiation markers without stimulation. These findings reveal how alternative polyadenylation controls CFIm25 expression during immune cell differentiation by modulating RNA-binding protein interactions and provide insight into post-transcriptional regulation of RNA processing factors. Impact statement This work reveals how a key regulator of mRNA processing is itself controlled through a previously uncharacterized mechanism during immune cell differentiation. Our findings provide insights into the molecular circuits governing macrophage development and identify potential therapeutic targets for inflammatory disorders where myeloid cell differentiation is dysregulated.
    Keywords:  CFIm25; NUDT21; PCBP1; RNA‐binding proteins; alternative polyadenylation; mRNA processing; monocyte–macrophage differentiation; translational regulation
    DOI:  https://doi.org/10.1002/1873-3468.70313
  10. Elife. 2026 Mar 10. pii: RP106846. [Epub ahead of print]14
    EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.
    Alan Monziani, Juan Pablo Unfried, Todor Cvetanovic, Igor Ulitsky.
      Mammalian genomes are pervasively transcribed into long noncoding RNAs (lncRNAs), whose functions and modes of action remain poorly understood. EPB41L4A-AS1 is an evolutionarily conserved, broadly and highly expressed lncRNA that produces the H/ACA snoRNA SNORA13 from one of its introns. We studied the consequences of EPB41L4A-AS1 perturbation in breast cancer cells and found that it acts both in cis, to enhance transcription of the proximal EPB41L4A gene and additional genes in its two flanking topologically associated domains, and in trans by broadly regulating gene expression, including expression of snoRNAs, transcription of genes involved in nucleolar biology and the distribution of nucleolar proteins. These effects are phenocopied by the loss of SUB1, an interactor of EPB41L4A-AS1, and are observed following transient perturbations of EPB41L4A-AS1 that do not affect steady-state SNORA13 levels or the rRNA modification it helps install. Exogenous expression of the full-length EPB41L4A-AS1 locus but not SNORA13 expression can rescue the trans-acting transcriptional effects of its perturbation. The EPB41L4A-AS1 gene is thus a versatile locus producing RNA molecules acting on multiple levels for key cellular functions.
    Keywords:  chromosomes; gene expression; gene regulation; genetics; genomics; human; long noncoding RNA; nucleolus; snoRNAs
    DOI:  https://doi.org/10.7554/eLife.106846
  11. Mol Biol Evol. 2026 Mar 08. pii: msag062. [Epub ahead of print]
    Stoichiometry-induced differential selection on codon optimization among ribosomal protein genes in bacterial species.
    Xuhua Xia.
      While it is well established that highly expressed genes in bacteria exhibit stronger codon optimization than lowly expressed ones, whether codon-anticodon adaptation shows fine-scale differentiation among highly expressed genes themselves remains unexplored. Ribosomal proteins, which are expressed in stoichiometric amounts and often co-transcribed in polycistronic operons, provide an ideal system for testing such differential selection. Here, I demonstrate that in Escherichia coli, Bacillus subtilis, and Vibrio natriegens, codon usage is more optimized in long ribosomal protein genes compared to short ones. This pattern persists even among genes within individual operons such as S10, spc, and α operons. A ribosome in E. coli or B. subtilis needs four copies of L7/L12 (encoded by rplL) but only one copy each of the other ribosomal proteins. This high demand for L7/L12 leads to my prediction that the rplL gene should be translated more actively than its operonic partner, rplJ, encoding L10. This prediction is also strongly supported by empirical evidence from representative bacterial species. Actively translated mRNAs are protected from endonucleolytic cleavage and degradation. If rplL mRNA is more actively translated than rplJ mRNA, then rplL mRNA would be degraded less and become more abundant than rplJ mRNA, which is true. These results demonstrate that translation optimization reflects functional stoichiometry and protein length constraints. This is the first demonstration of natural selection operating predictably and precisely among ribosomal protein genes in the same operon, fine-tuning translational output to achieve efficient ribosomal assembly.
    Keywords:  Ribosomal proteins; codon optimization; differential selection; stoichiometry and selection; translation initiation and elongation
    DOI:  https://doi.org/10.1093/molbev/msag062
  12. Nucleic Acids Res. 2026 Feb 24. pii: gkag200. [Epub ahead of print]54(5):
    Mycobacterium tuberculosis MutT4/RppH is an RNA pyrophosphohydrolase that forms condensate-like bodies and impacts mRNA degradation.
    J Hilario Cafiero, Junpei Xiao, Irene Lepori, Abigail R Rapiejko, Manchi Reddy, Opeyemi I Ibitoye, Louis A Roberts, James C Sacchettini, M Sloan Siegrist, Scarlet S Shell.
      Bacterial adaptation to stress involves changes in transcription and messenger RNA (mRNA) degradation. In Escherichia coli, the Nudix hydrolase RppH initiates mRNA degradation by removing pyrophosphate from mRNA 5'-ends, converting 5'-triphosphates to 5'-monophosphates. We aimed to identify the RppH homolog in the globally important pathogen Mycobacterium tuberculosis (Mtb). We identified the protein encoded by Rv3908, previously annotated as a nucleotide pool cleanser mutT4, as the predominant mycobacterial RppH. Deletion of rppHMtb increased the relative abundance of 5'-triphosphates on myriad mRNAs across the transcriptome. Purified RppHMtb converted mRNA 5'-triphosphates into monophosphates, and stimulated degradation by RNase E and RNase J in vitro to varying extents. Surprisingly, deletion of rppHMtb had mixed impacts on mRNA degradation in vivo, suggesting that it may not sensitize most transcripts to degradation. RppHMtb has intrinsically disordered regions (IDRs), which often participate in biomolecular condensate formation. Microscopy showed that RppHMtb forms condensate-like bodies that localize with RNases and dissociate upon addition of rifampicin. The N-terminal IDR is sufficient for condensate-like body formation. Deletion of rppHMtb leads to higher outer membrane permeability and resistance to oxidative stress. We conclude that MutT4 is the mycobacterial RppH, assembling in condensate-like bodies with RNases but having unexpectedly complex impacts on mRNA degradation rates.
    DOI:  https://doi.org/10.1093/nar/gkag200
  13. Nucleic Acids Res. 2026 Feb 24. pii: gkag216. [Epub ahead of print]54(5):
    La protein binding to telomerase RNA supports an evolutionary relationship between plant and ciliate telomerase pathways.
    Leon Jenner, Dzmitry Pruchkouski, Barbora Štefanovie, Olga Nováková, Monika Kubíčková, Petr Fajkus, Marie Brázdová, Jan Paleček, Eva Sýkorová.
      The Arabidopsis thaliana La1 (AtLa1) protein is a member of the genuine La family of RNA biogenesis proteins, which are structurally similar to the La-related protein 7 (LARP7) family. LARP7 proteins participate in the biogenesis of the telomerase ribonucleoprotein complex in model systems, but are absent in plants. We show that AtLa1 binds to telomerase RNA in a manner reminiscent of the Tetrahymena LARP7 protein p65. Classical in vitro methods and microscale thermophoresis (MST) were used to specify the molecular structures involved in this multi-surface interaction. AtLa1 also enhances the binding of TR to the telomerase reverse transcriptase RNA binding domain. We therefore propose that biogenesis of telomerase RNA in plants and ciliates is achieved by a similar pathway, differing in the employment of genuine La or LARP7-like proteins, respectively. We also report that the domain of unknown function (DUF3223, DeCL) found in the AtLa1 protein binding partner, Domino, is an RNA binding domain with modest TR-binding capacity. This domain is also found in plant and ciliate proteins, including plant polymerases IV/V and the Tetrahymena La protein Mlp1. Together, these suggest that RNA biogenesis pathways in plants and ciliates have a conserved evolutionary relationship, with parallels between their La proteins.
    DOI:  https://doi.org/10.1093/nar/gkag216
  14. Curr Opin Microbiol. 2026 Mar 10. pii: S1369-5274(26)00022-6. [Epub ahead of print]91 102728
    Pathways of mRNA decay in trypanosomes.
    Michał Małecki, Christoph Wenzl, Luisa M Figueiredo.
      Messenger RNA (mRNA) decay is a central determinant of gene expression in eukaryotes, functioning both as a quality control mechanism and as a regulatory layer that shapes transcript abundance. In trypanosomes, including Trypanosoma brucei, gene expression relies almost entirely on post-transcriptional mechanisms due to polycistronic transcription and the near absence of promoter-specific transcriptional regulation. As a result, mRNA stability plays a dominant role in controlling protein output and developmental gene expression programs. In this review, we summarize current knowledge of the major nuclear and cytoplasmic mRNA decay pathways and surveillance mechanisms operating in T. brucei, highlighting both conserved and parasite-specific features of the RNA degradation machinery. We discuss the roles of the principal exonucleases, as well as deadenylation and decapping processes, and outline proposed strategies for mRNA stabilization and destabilization. Despite significant progress, direct mechanistic links between cis-regulatory elements, RNA-binding proteins, and specific decay pathways remain poorly understood. We conclude by outlining key open questions and emerging experimental approaches that promise to advance our understanding of mRNA decay as a central regulatory axis in trypanosome biology.
    DOI:  https://doi.org/10.1016/j.mib.2026.102728
  15. RNA Biol. 2026 Dec;23(1): 1-13
    Molecular insights into dynamic RNA quaternary assemblies.
    Zirui Huang, Weijun Lin, Liu Wang, Zhaoming Su.
      Quaternary assembly of proteins frequently plays essential roles in biological processes. In contrast, natural RNA oligomers have rarely been reported. The majority of observed RNA quaternary structures are symmetric homodimers, while recent studies have also revealed structures of heterodimers and symmetric homooligomers with more than two protomers. These higher-order assemblies adopt various intermolecular motifs including kissing-loops, pseudoknots, palindromic base-pairing, stacking, minor-groove interactions, and metal ion coordination that are found in RNA dimers. The dynamics in oligomerization vary across different segments of a single RNA as well as among different RNAs within the same family, which are primarily enabled by variable secondary structures, intermolecular motifs, and shape complementarity. These structural insights deepen our understanding of RNA multimerization mechanisms, paving the way for potential applications in condensate formation, RNA structure prediction, and therapeutic targeting and delivery.
    Keywords:  RNA oligomerization; RNA structure; cryo-EM; dynamic quaternary assembly; intermolecular interface
    DOI:  https://doi.org/10.1080/15476286.2026.2644525
  16. Sci Rep. 2026 Mar 10. pii: 8699. [Epub ahead of print]16(1):
    The key m6A methylation regulator IGF2BP1 possesses potential prognostic value in papillary thyroid carcinoma.
    Jinqiu Wang, Chen Dai, Mingze Wei, Weida Fu, Jin Luo, Yongping Dai.
      Papillary thyroid carcinoma (PTC) poses a risk of recurrence, and the efficacy of existing treatments is limited. Consequently, there is an urgent need to identify new prognostic markers and potential therapeutic targets. N6-methyladenosine (m6A) mRNA methylation is involved in tumorigenesis and progression, yet the role of m6A RNA methylation regulators in PTC remains unclear. The Cancer Genome Atlas database was utilized to analyze 17 m6A regulators in PTC. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was markedly down-regulated in PTC, yet higher IGF2BP1 expression predicts better 5-year survival, acting as an independent prognostic marker with high accuracy. Elevated IGF2BP1 also indicated greater sensitivity to doxorubicin and sunitinib. Clinically, low IGF2BP1 correlated with central lymph-node metastasis and BRAFV600E mutation. Additionally, IGF2BP1 overexpression suppresses thyroid carcinoma cell proliferation, invasion, and migration. In conclusion, High expression of IGF2BP1 was associated with a favorable prognosis in PTC, and it served as an independent prognostic factor and a potential therapeutic target for PTC.
    Keywords:  IGF2BP1; N6-methyladenosine; Papillary thyroid carcinoma; Predictive factor
    DOI:  https://doi.org/10.1038/s41598-026-43501-z
  17. J Assist Reprod Genet. 2026 Mar 13.
    m6A RNA methylation orchestrates spermatogenesis: decoding the synergistic regulatory network of signaling pathways and ubiquitination modifications.
    Zongxi Zhao, Junhu Su.
      N6-methyladenosine (m6A), the most prevalent epitranscriptomic modification in eukaryotic mRNA, dynamically regulates mRNA stability, splicing, and translational efficiency through a sophisticated "writer-eraser-reader" network. This system comprises methyltransferase writers (e.g., METTL3/14, METTL16, WTAP), demethylase erasers (e.g., ALKBH5, FTO), and recognition readers (e.g., YTHDC2, YTHDF2, hnRNPC). This precise regulatory mechanism governs spermatogonial stem cell proliferation, meiotic initiation, and spermatid maturation by orchestrating cell cycle progression, meiotic timing, and sperm morphological functionality. The depth and breadth of its regulation are further demonstrated via deep integration with related signaling pathways, as it collaboratively regulates the PI3K/AKT/mTOR pathway that maintains the metabolic homeostasis of spermatogonial stem cells, the Wnt/β-catenin pathway that coordinates stem cell renewal and meiotic initiation, the GnRH pathway that connects neuroendocrine regulation, and the ERK1/2 pathway that mediates key events of cell proliferation and differentiation. This multipathway synergy jointly ensures the normal progression of spermatogenesis. Furthermore, an interplay exists between m6A modification and ubiquitination modification. While m6A regulates the expression of genes related to ubiquitination by influencing the protein degradation pathway, ubiquitination regulates the methylation of m6A either by directly modifying m6A or by participating in the activity of related enzymes indirectly. This review provides a novel perspective for understanding the epigenetic mechanisms of spermatogenesis and discusses intervention strategies for managing male infertility by systematically integrating the dynamic distribution of m6A, its core regulatory mechanisms, and its interaction with multidimensional signaling networks.
    Keywords:  M6A modification; Signaling pathway; Spermatogenesis; Ubiquitination modification
    DOI:  https://doi.org/10.1007/s10815-026-03846-w
  18. Biochem Pharmacol. 2026 Mar 08. pii: S0006-2952(26)00204-2. [Epub ahead of print]248 117872
    Epitranscriptomic signatures of malignancy: how RNA modifications shape breast and ovarian tumor progression.
    Pankaj Garg, Ravi Salgia, Sharad S Singhal.
      Breast and ovarian cancers are still one of the most prevalent causes of cancer death among the women in all parts of the world, mostly occurring at a later stage with high recurrence rate and resistance to treatment. Beyond the well-known genetic and epigenetic modifications, the new branch of study is epitranscriptomics that investigates reversible chemical modifications of RNA has brought a new aspect of cancer regulation to light. Modifications such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Psi), and N1-methyladenosine (m1A) have dramatic effects on RNA stability, splicing, localization, and translation, which alter oncogenic signalling, immune evasion, and drug resistance. Reprogramming of the transcriptome and proteome with dysregulation of the respective corresponding writers, erasers, and readers of these RNA scripts, enhance tumor proliferation, epithelial-mesenchymal transition (EMT), angiogenesis, and metastasis. Recent developments highlight the putative clinical value of targeting RNA modifying enzymes using small-molecule inhibitor, CRISPR-based editing technology, and delivery systems based on nanotechnology. In addition, RNA modification patterns are emerging as promising diagnostic and prognostic biomarkers, with growing applications in liquid biopsy and precision oncology. A combination of epitranscriptomic data and multi-omics solutions, artificial intelligence (AI), and personalized medicine frameworks offers an effective way of optimizing cancer classification and treatment. This review highlights, how decoding of epitranscriptomic signatures of malignancy can help transform the concept of tumor biology and provide with new avenues of diagnosis, prognosis, and targeted therapy options of breast and ovarian malignancies, representing a new era of patient-centred oncology.
    Keywords:  Breast cancer; Epitranscriptomics; Ovarian cancer; Pseudouridine; RNA modifications; Therapy resistance; m5C; m6A
    DOI:  https://doi.org/10.1016/j.bcp.2026.117872
  19. Biochem Biophys Rep. 2026 Mar;45 102528
    Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells.
    L Cruz-Garcia, Philip Davies, Veronika Goriacha, Mustafa Najim, Stanislav Polozov, Maria Polozova, Christophe Badie.
      A cell's transcriptome is regulated through the integration of external and internal signals that activate intracellular signal pathways, epigenetic modifications and post-translational changes. Post-transcriptional regulation through RNA methylation has emerged as an important mechanism in cancer development, and informative for diagnosis and treatment. The most abundant one, N6-methyladenosine (m6A), regulates gene expression in eukaryotes. In the present study m6A RNA modifications have been characterized in response to ionizing radiation (IR) exposure in the HT1080 human cell line. Cells were exposed to a dose of 10 Gy of X-rays and harvested 1, 2, 10 min, 1 and 24 h after exposure. m6A sites were identified using long read nanopore direct RNA sequencing. A pipeline was designed using m6Anet to estimate m6A stoichiometries transcriptome-wide, which were then analysed by a beta-binomial regression model with moderated dispersion estimates and independent filtering to detect differentially methylated (DM) sites between treated and control samples. We found that IR modifies m6A sites in a dynamic way, inducing site specific increase of methylation. Remarkably, it peaks within the first minute after exposure, followed by a sharp decrease at 1 h without returning to baseline, increasing again after 24 h. Two transcripts of the nuclear encoded gene UQCR10, a subunit of the respiratory chain protein, sharing the same site presented a stable hypermethylation over time, confirmed by a modified quantitative PCR assay. Moreover, we generated Knockouts (KO) cell lines for 3 key enzymes involved in m6A methylation, a writer, a reader and an eraser namely METTL3, YTHDF2 and FTO, to better understand mechanistically IR driven m6A dynamics. Importantly, all three KOs presented a transcriptome wide decrease in RNA methylation following IR exposure. Lastly, m6A modifications were also confirmed in human skin biopsies exposed to IR, with the UQCR10 gene site also hypermethylated 24 h after a lower 2 Gy X-rays dose. To summarise, we provide evidence that IR modulates RNA m6A levels in a site-specific and dynamic way, with DM sites enriched in genes involved in bioenergetics, cell signalling/migration and apoptosis pathways, thus representing a rapid cellular response to radiation. Considering the essential role of m6A in controlling gene expression and physiological activities, this study established the basis for further studies assessing IR driving m6A with a potential role in radiation oncology and protection.
    DOI:  https://doi.org/10.1016/j.bbrep.2026.102528
  20. Genome Res. 2026 Mar 12. pii: gr.280820.125. [Epub ahead of print]
    Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes.
    Zohar Rosenwasser, Roni Cohen-Fultheim, Ofir Shliefer, Erez Y Levanon, Eli Eisenberg.
      A-to-I RNA editing, catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome. ADARs bind to double-stranded RNA (dsRNA) and their specificity and efficiency are affected by the structural properties of these substructures. In most cases, the dsRNA structure arises from homology between two segments of the same RNA molecule that fold into RNA stem structures. Another possible source of dsRNA is cotranscription of sense and antisense strands of the same genomic region. Binding of these complementary, naturally occurring, antisense transcripts (NATs) results in a perfect RNA duplex, which may be targeted by ADARs. To explore the scope of ADAR editing of NAT-derived dsRNA, we examined editing levels at genome locations where both strands are transcribed. Our findings indicate that editing is rare in regions for which both strands cotranscribe. Moreover, even when RNA editing does occur in NAT regions, it is typically associated with secondary structures on a single strand, suggesting that editing depends on intramolecular structures rather than binding of NATs.
    DOI:  https://doi.org/10.1101/gr.280820.125
  21. Int J Mol Sci. 2026 Feb 25. pii: 2147. [Epub ahead of print]27(5):
    Phosphoproteomic Landscape of HDLBP: Insights into Function and Disease Associations.
    Pathiyil Sajini Sekhar, Amal Fahma, Suhail Subair, Leona Dcunha, Althaf Mahin, Athira Perunally Gopalakrishnan, Rajesh Raju, Sowmya Soman.
      High-density lipoprotein-binding protein (HDLBP), also called Vigilin, is a multifunctional RNA-binding protein with established roles in RNA transport and regulation, chromosome segregation, lipid homeostasis, and translational regulation. Frequently detected to be perturbed in phosphoproteome analysis, phosphorylation is indicated as a major mechanism in the regulation of HDLBP functions; however, its phosphorylation landscape remains unexplored. We performed a meta-phosphoproteome analysis of HDLBP to map site-specific functional and regulatory roles of its two most frequently detected phosphosites, S31 and S944. Co-occurrence analysis across multiple datasets indicated that they can be phosphorylated together, suggesting potential co-ordinated regulation. Site-specific co-regulation analysis revealed distinct phospho-regulatory networks, with upstream kinases identified exclusively for S944. Functional enrichment of co-regulated protein phosphosites (CPPs) highlighted its role in RNA metabolism, chromosome organization, and nucleoplasmic transport, while functional annotation of site-specific phosphorylation of CPPs indicates its involvement in cell cycle regulation, apoptosis, and carcinogenesis. Additionally, the potential role of CPPs in the lipid homeostasis network was explored. Furthermore, the differential expression of HDLBP phosphosites across multiple cancers was observed using UALCAN, suggesting a potential role for phospho-regulation of HDLBP in tumor-associated pathways. Together, these findings provide the first integrated view of HDLBP phosphorylation and could serve as a valuable framework for future targeted studies to elucidate the mechanistic roles of site-specific HDLBP phosphorylation in cellular and pathophysiological processes.
    Keywords:  HDLBP; cancer; co-regulation; phosphoproteomics; phosphosites
    DOI:  https://doi.org/10.3390/ijms27052147
  22. Dev Cell. 2026 Mar 12. pii: S1534-5807(26)00078-X. [Epub ahead of print]
    Desmosomes compartmentalize mRNA and translation in the skin.
    Alec D'Alessandro, Kwabena Badu-Nkansah, Sophia Link, Daniel Hlavaty, Glenn Bjerke, Christopher V Nicchitta, Rui Yi, Terry Lechler.
      Subcellular compartmentalization allows cells to spatially control molecular functions. We show that in mouse and human epidermal cells, translational machinery is enriched at the cell cortex, where a large subset of mRNAs is also localized, defining a previously unrecognized axis of mRNA organization. The desmosomal protein desmoplakin is required for the cortical recruitment of both ribosomes and mRNAs via distinct mechanisms. Surprisingly, many cortex-localized transcripts are not actively translated but instead are translationally repressed. This spatially restricted regulation involves the RNA-induced silencing complex (RISC), which is also enriched at the cortex in a desmoplakin-dependent manner. Under homeostatic conditions, cortical RISC associates with mRNAs encoding cell adhesion and cytoskeletal proteins. Following wounding, these RISC-associated transcripts become translationally activated. Together, our findings reveal a dynamic, desmosome-dependent cortical compartmentalization of translation that responds to epithelial barrier disruption.
    Keywords:  RISC; compartmentalization; desmoplakin; desmosome; mRNA localization; ribosome; translation; translatome
    DOI:  https://doi.org/10.1016/j.devcel.2026.02.013
  23. Nucleic Acids Res. 2026 Feb 24. pii: gkag208. [Epub ahead of print]54(5):
    Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems.
    Evan M Kalb, Jose L Alejo, Leticia Dias-Fields, Isaac Knudson, Joshua A Davisson, Efren Maldonado, Kanokporn Chattrakun, Shangsi Lin, Jung Yeon Lee, Tianchen He, Alanna Schepartz, Shenglong Zhang, Scott C Blanchard, Aaron E Engelhart, Katarzyna P Adamala.
      Transfer RNAs (tRNAs) are utilized by the ribosome to decode the nucleic acid alphabet. tRNA structure, stability, aminoacylation efficiency, and decoding efficacy are governed by their extensive post-transcriptional modifications. In most studies, individual tRNAs are generated using in vitro transcription, which produces tRNAs devoid of these critical site-specific modifications, negatively affecting translation yields and fidelity. To address this challenge, we have developed a purification method that couples tRNA overexpression to DNA hybridization-based purification. Using this approach, we produced native tRNAs from Escherichia coli in high yield and purity while retaining their complement of native post-transcriptional modifications and translational activity. We extend this technique to the purification of Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$, tRNAs of critical importance for genetic code expansion. We confirmed that both Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$ contain native E. coli post-transcriptional modifications and provide the first complete modification profiles of each. Moreover, we found that in vivo-generated Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}\ $significantly outperform their in vitro-generated counterparts in amber codon suppression in cell-free translation reactions. Finally, we purified an engineered variant of E. coli$tRNA_{CCA}^{Trp}$, extending our studies to synthetic tRNAs. We present a flexible method that generates modified tRNAs in high yield and purity, addressing a critical and persistent challenge in RNA biochemistry.
    DOI:  https://doi.org/10.1093/nar/gkag208
  24. Sci Adv. 2026 Mar 13. 12(11): eaea9061
    Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer.
    Heather Karner, Tabea C Mittmann, Vicky W Chen, Ashir A Borah, Andreas Langen, Hassan Yousefi, Lisa Fish, Balyn W Zaro, Albertas Navickas, Hani Goodarzi.
      Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet the extent of contribution from posttranscriptional regulation remains unclear. Here, we systematically measured messenger RNA (mRNA) dynamics across diverse breast cancer models, revealing that mRNA stability substantially shapes gene expression variability. To decipher these dynamics, we developed GreyHound, an interpretable multimodal deep-learning framework integrating RNA sequence features and RNA binding protein (RBP) expression. GreyHound identified an extensive network of RBPs and their regulons underlying variations in mRNA stability, including a regulatory axis centered on RBP RBMS3 and redox regulator TXNIP. RBMS3 depletion resulted in targeted transcript destabilization-associated with poor clinical outcomes and enhanced metastatic potential in xenograft models. In vivo epistasis studies confirmed that RBMS3-mediated regulation of TXNIP mRNA stability drives this metastasis-suppressive program. These findings identify a key posttranscriptional mechanism in breast cancer and illustrate how interpretable models of RNA dynamics can uncover regulatory programs in disease.
    DOI:  https://doi.org/10.1126/sciadv.aea9061
  25. Integr Zool. 2026 Mar 10.
    Untangling Responses of A-to-I RNA Editing to Heat Stress in the Mussel Mytilus galloprovincialis.
    Yajie Zhu, Mingling Liao, Guodong Han, Qiaoling Su, Long Zhao, Ying Su, Yunwei Dong.
      RNA editing is a post-transcriptional modification that can have important effects on mRNA translation and, thereby, on the composition of the proteome. RNA editing exhibits complex responses to temperature and thus may be important in ectothermic species' capacities to cope with thermal stress. To investigate the temperature-dependent patterns and potential functions of RNA editing events in intertidal mollusks, we conducted a genome-wide identification and analysis of RNA editing sites in the mussel Mytilus galloprovincialis exposed to various temperatures. Our results showed that the number of sites where adenosine (A) was converted to inosine (I) decreased significantly with increasing temperatures and correlated positively with the expression level of the enzyme adenosine deaminase acting on RNA. Furthermore, the shared edited genes among all temperatures were enriched significantly in some key biological processes (e.g., negative regulation of apoptotic processes), and the unique edited genes at the sublethal temperature of 31°C were enriched significantly in some cellular signaling pathways (e.g., GTPase activator activity). Luciferase assays showed that protein translation efficiency was positively correlated with the number of edited A-to-I sites in the 3' untranslated region (3'UTR). Our study demonstrates that temperature-sensitive A-to-I editing events may play an important role in allowing mollusks like M. galloprovincialis to rapidly acclimatize to stressful thermal environments.
    Keywords:  A‐to‐I RNA editing; adenosine deaminases acting on RNA (ADAR); mussel; thermal acclimation/acclimatization
    DOI:  https://doi.org/10.1111/1749-4877.70079
  26. Integr Biol (Camb). 2026 Jan 16. pii: zyag006. [Epub ahead of print]18
    DNMT1 stabilizes MAPK10 via m5C RNA methylation to ameliorate hepatic steatosis and mitochondrial dysfunction in non-alcoholic fatty liver disease.
    Jing Liu, Chuang Liu, Huanzhi Xiao, Peng Cao, Sufang Zhou.
       BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) represents a highly prevalent metabolic disorder; however, the functional role of mitogen-activated protein kinase 10 (MAPK10) in the initiation and progression of NAFLD remains incompletely understood. This study investigated MAPK10's role in NAFLD and its regulatory mechanisms.
    MATERIALS AND METHODS: Bioinformatics analysis was performed on the GSE89632 dataset to screen for differentially expressed genes (DEGs) associated with NAFLD. An in vivo NAFLD model was established in C57BL/6 J mice by feeding a high-fat diet (HFD), and subsequent lentiviral transduction was used to achieve hepatic overexpression or knockdown of MAPK10 and DNA methyltransferase 1 (DNMT1). In vitro, HepG2 cells were transfected with DNMT1 overexpression plasmids. Molecular analyses, including RT-qPCR and Western blot, were used to measure gene and protein expression levels. RNA immunoprecipitation (RIP) and dual-luciferase reporter assays were employed to assess the m5C modification of MAPK10 mRNA and its transcriptional activity, respectively. An RNA stability assay was used to evaluate mRNA half-life.
    RESULTS: MAPK10 expression was significantly reduced in the liver tissues of HFD-fed mice. Overexpression of MAPK10 alleviated hepatic steatosis, oxidative stress, and mitochondrial damage in vivo. Mechanistically, DNMT1 enhanced MAPK10 expression and stability in an m5C-dependent manner. RIP assay confirmed increased m5C modification of MAPK10 mRNA upon DNMT1 overexpression. Luciferase reporter assay demonstrated that DNMT1 specifically enhanced the activity of wild-type, but not m5C-site-mutated, MAPK10. RNA stability assay further showed that DNMT1 overexpression stabilized MAPK10 mRNA. Rescue experiments indicated that MAPK10 knockdown reversed the protective effects (improved lipid accumulation, oxidative stress, and mitochondrial function) induced by DNMT1 overexpression in HFD-fed mice.
    CONCLUSION: MAPK10 plays a protective role in NAFLD by ameliorating hepatic steatosis and mitochondrial dysfunction. Its expression is positively regulated by DNMT1 via m5C-mediated RNA stabilization. This study highlights the DNMT1-MAPK10 axis as a potential therapeutic target for NAFLD. Insight Box This study uncovers a previously unrecognized RNA epigenetic regulatory axis in NAFLD, demonstrating that DNMT1 post-transcriptionally regulates MAPK10 expression and stability through m5C RNA methylation. We establish MAPK10 as a key metabolic protector against NAFLD, ameliorating hepatic steatosis, oxidative stress, and mitochondrial dysfunction. By integrating bioinformatics, molecular biology, and functional validation across in vivo and in vitro models, we delineate a mechanistic pathway where m5C modification critically modulates MAPK10 activity. These findings not only provide fresh insight into the RNA-centric regulatory layer of NAFLD pathogenesis but also spotlight the therapeutic potential of modulating the DNMT1-MAPK10 axis, underscoring the value of integrative research strategies in elucidating complex metabolic diseases. Main points MAPK10 expression was significantly reduced in the liver tissues of HFD-induced NAFLD mice. MAPK10 overexpression alleviated hepatic steatosis and mitochondrial damage in HFD-fed mice. DNMT1 positively regulates MAPK10 expression and mRNA stability in an m5C RNA methylation-dependent manner.
    Keywords:  DNMT1; MAPK10; hepatic steatosis; m5C; mitochondrial dysfunction; non-alcoholic fatty liver disease
    DOI:  https://doi.org/10.1093/intbio/zyag006
  27. FASEB J. 2026 Mar 31. 40(6): e71640
    ZNF460 Promotes the m6A Modification of COPS6 to Facilitate Immune Escape in Colorectal Cancer.
    Weijian Lun, Yongjia Liu, Canhua Luo, Huihuan Wu.
      Colorectal cancer (CRC) continues to be a significant global health concern. Emerging studies emphasize the tumor microenvironment (TME) as a key regulator of therapeutic response, particularly in its ability to suppress CD8+ T cell-mediated tumor clearance under chronic stimulation. However, the precise mechanisms responsible for this immunosuppressive effect remain unclear and require further exploration. Functional experiments evaluated CRC cell proliferation, migration, and invasion. CD8+ T cell infiltration and cytotoxicity were assessed using flow cytometry and LDH cytotoxicity assays. Mechanistic studies involved RNA immunoprecipitation (RIP), methylated RNA immunoprecipitation (MeRIP), chromatin immunoprecipitation (ChIP), and dual-luciferase reporter assays to investigate the METTL5/YTHDF1-mediated regulation of COPS6 and the transcriptional activation of METTL5 by ZNF460. An in vivo CRC mouse model was established. The results indicated COPS6 was significantly upregulated in CRC and associated with poor prognosis. Knockdown of COPS6 suppressed CRC proliferation, migration, and invasion while enhancing CD8+ T cell infiltration and cytotoxicity. METTL5 was identified as an upstream regulator of COPS6, stabilizing its mRNA via m6A modification in a YTHDF1-dependent manner. ZNF460 bound to the METTL5 promoter, enhancing its transcription. In vivo, depletion of ZNF460 or METTL5 inhibited tumor growth and increased CD8+ T cell activity, whereas METTL5 overexpression reversed these effects. The ZNF460/METTL5/COPS6 axis promotes CRC progression and immune evasion by regulating COPS6 stability and CD8+ T cell infiltration. Targeting this pathway may offer new therapeutic strategies for CRC treatment.
    Keywords:  COPS6; METTL5; ZNF460; colorectal cancer; immune escape
    DOI:  https://doi.org/10.1096/fj.202503485R
  28. J Gen Virol. 2026 Mar;107(3):
    The anti-viral protein Shiftless blocks p-body formation during KSHV infection.
    David Hatfield, William Rodriguez, Timothy Mehrmann, Mandy Muller.
      Processing bodies (P-bodies/PBs) are non-membranous foci involved in coordinating RNA fate by regulating translation and mRNA decay. In this study, we characterize the anti-viral factor Shiftless (SHFL) as a potent disruptor of PB dynamics. We show SHFL expression restricts PB accumulation even in the context of oxidative stress, suggesting that SHFL expression impedes PB formation. Mutational approaches revealed that SHFL RNA-binding activity is not required to restrict PB formation. However, we have identified a new region of SHFL, a bridge between two distant SHFL domains, as necessary for SHFL-mediated PB disruption. Furthermore, we show that SHFL's ability to disrupt PB formation also impacts its anti-viral activity during infection by the gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV). While WT SHFL efficiently restricts KSHV lytic reactivation, SHFL mutants defective in PB disruption no longer restrict KSHV reactivation. SHFL-mediated PB disruption also leads to increased expression of several anti-viral cytokines, further emphasizing the connection among SHFL, PB dynamics and the SHFL-dependent anti-viral state. Taken together, our observations suggest a role of SHFL in inhibiting PB formation to restrict KSHV lytic replication, reinforcing the importance of crosstalk between RNA fate and the innate immune response to viral infection.
    Keywords:  Kaposi’s sarcoma-associated herpesvirus (KSHV); RNA decay; Shiftless (SHFL); herpesvirus; processing body (P-body)
    DOI:  https://doi.org/10.1099/jgv.0.002229
  29. J Biol Chem. 2026 Mar 06. pii: S0021-9258(26)00222-X. [Epub ahead of print] 111352
    Forces That Shape the Transcriptome: Linking Cellular Mechanosensing to mRNA splicing.
    Pavel Simara, Cristina Mazzotti, Gokula Narayanan, Marco Cassani, Stefania Pagliari, Giancarlo Forte.
      Mechanical signaling has been well documented in certain cell types such as muscle cells, osteoblasts, fibroblasts, and other cells historically defined as mechanocytes for their ability to receive and respond to mechanical stimuli. However, recent data suggest that mechanical signaling is not restricted to given cell types, but it is rather a universal feature of most of the eukaryotic cells that, similarly to extracellular chemical signaling, controls basic metabolic and intracellular signaling processes. Several studies published in recent years provided evidence that mRNA maturation is altered in cells exposed to mechanical stress. These data indicate that the process might be closely related to the three-dimensional (3D) spatial re-organization of RNA-binding proteins. With mounting evidence for the mechanical control of mRNA splicing, this review aims to provide an overview of the available literature and offer a comprehensive vision of this phenomenon that stands out as a fundamental process in cellular biology.
    Keywords:  Mechanosensing; RNA maturation; RNA-binding proteins; alternative splicing; mechanical stress
    DOI:  https://doi.org/10.1016/j.jbc.2026.111352
  30. NPJ Precis Oncol. 2026 Mar 10.
    TRMT6-directed m1A modification initiates lung squamous cell carcinoma via YTHDF3-stabilized cell cycle genes.
    Weihao Xue, Liqiang Zhu, Xiaolong Wei, Jinqi Sun, Weihao Lin, Shaomin Huang, Lianpin Wu, Donghong Zhang.
      N1-Methyladenosine (m1A) is a prevalent RNA modification that governs RNA metabolism, structure, stability, and translation. Yet its cancer-wide landscape and functional impact remain largely unexplored. Here, we delineate the m1A regulatory network in lung squamous cell carcinoma (LUSC). The dominant m1A writer of TRMT6 emerged as the most up-regulated regulator in LUSC through a comprehensive pan-cancer analysis; both TRMT6 expression and global m1A levels significantly distinguished LUSC from normal tissue, serving as potent diagnostic biomarkers. Functionally, TRMT6 installs m1A marks and facilitates their cellular export. Both the in vitro and in vivo experiments reveal that TRMT6 accelerates LUSC proliferation by orchestrating cell-cycle gene expression. Mechanistically, TRMT6 binds cell-cycle transcripts, most notably TOPBP1 and DSN1, promotes the formation of m1A, and stabilizes these mRNAs via the YTHDF3 reader pathway. A single, critical m1A site in each target mRNA is sufficient to boost TOPBP1 and DSN1 expression. Using dCasRx-TRMT6, we further show that site-specific m1A deposition on DSN1 mRNA is a potent strategy to modulate its expression and drive proliferation. Collectively, our findings uncover a previously unrecognized m1A-dependent regulatory axis that underpins LUSC diagnosis and progression.
    DOI:  https://doi.org/10.1038/s41698-026-01361-w
  31. Clin Exp Pharmacol Physiol. 2026 Mar;53(3): e70107
    METTL14 Aggravates Sepsis-Induced Acute Kidney Injury by Promoting Ferroptosis Through m6A Modification of BMAL1.
    Yishu Wang, Yang Li, Na Wu, Xinyue Xu, Xiaoxuan Fan, Haifeng Wang.
       BACKGROUND: Acute kidney injury (AKI) is a common and severe complication of sepsis and represents an independent risk factor for mortality in septic patients. Despite its clinical significance, the mechanisms of sepsis-induced AKI (Sepsis-AKI) remain incompletely understood. This study investigates the role of methyltransferase like 14 (METTL14)-mediated m6A modification in regulating brain and muscle ARNT-like protein-1 (BMAL1) stability and its effect on tubular epithelial cell injury and ferroptosis.
    METHODS: Human renal proximal tubular epithelial (HK-2) cells were treated with lipopolysaccharide (LPS) to establish an in vitro model of Sepsis-AKI. Cell proliferation and viability were assessed using EdU and CCK-8 assays; apoptosis was evaluated by TUNEL staining, and inflammatory cytokines Interleukin-6 (IL-6) and IL-1β were measured by ELISA. Ferroptosis indices were detected using corresponding kits. RT-qPCR and Western blotting were used to detect mRNA and protein expression. MeRIP and RIP assays were used to evaluate BMAL1 m6A modification and RNA-protein interaction. The stability of BMAL1 mRNA was determined using an Actinomycin D chase assay. A Sepsis-AKI model was established to examine the effect of METTL14 silencing on renal injury.
    RESULTS: BMAL1 overexpression significantly alleviated LPS-induced apoptosis, inflammatory responses, and ferroptosis in HK-2 cells. Furthermore, METTL14 silencing reduced BMAL1 m6A modification, stabilized BMAL1 mRNA, and consequently improved HK-2 cell injury. In addition, YTHN6-methyladenosine RNA binding protein 1 (YTHDF1) was identified as the critical m6A reader mediating BMAL1 mRNA degradation. Consistently, in vivo experiments demonstrated that METTL14 knockdown mitigated Sepsis-AKI and ferroptosis in mice.
    CONCLUSION: METTL14 enhanced BMAL1 m6A modification and promoted YTHDF1-mediated BMAL1 degradation, thereby facilitating ferroptosis and aggravating Sepsis-AKI.
    Keywords:  acute kidney injury; brain and muscle ARNT‐like protein‐1; lipopolysaccharide; methyltransferase like 14; sepsis
    DOI:  https://doi.org/10.1111/1440-1681.70107
  32. Plant Cell. 2026 Mar 12. pii: koag064. [Epub ahead of print]
    SlYTH3 regulates tomato leaf senescence via recognition of N6-methyladenosine-modified SlHDZIV2 transcripts.
    Mengzhuo Li, Xingguan Zhang, Xiuyang Si, Yue Sun, Changtian Pan, Gang Lu.
      N 6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic mRNA, with essential roles in plant development and stress adaptation. However, its regulatory function in leaf senescence remains poorly defined. Here, we demonstrate that tomato (Solanum lycopersicum) leaf aging is accompanied by dynamic changes in m6A levels and that YT521-B homology (YTH) domain protein 3 (SlYTH3) acts as an m6A reader to preserve leaf longevity by recognizing m6A-modified transcripts of HOMEODOMAIN-LEUCINE ZIPPER IV 2 (SlHDZIV2). Loss of SlYTH3 accelerates dark-induced leaf senescence, leading to chloroplast disruption, photosynthetic impairment, and premature activation of senescence-associated genes. Mechanistically, SlYTH3 binds to the canonical m6A motif (RRACH) within SlHDZIV2 mRNA, enhancing both its transcript stability and translation efficiency. Genetic analyses confirmed that SlHDZIV2 functions downstream of SlYTH3. Furthermore, SlHDZIV2 directly activates transcription of autophagy-related 5 (SlATG5), thereby sustaining autophagic activity during senescence. Disruption of this regulatory cascade in slhdziv2 or slatg5 mutants results in precocious leaf senescence. Together, these findings unveil an m6A-dependent regulatory module, SlYTH3-SlHDZIV2-SlATG5 that integrates RNA methylation and autophagy to modulate leaf senescence, providing mechanistic insights into epitranscriptomic control of plant aging.
    Keywords:   N 6-methyladenosine; HD-ZIP; SlATG5; SlHDZIV2; SlYTH3; autophagy; leaf senescence; m6A reader
    DOI:  https://doi.org/10.1093/plcell/koag064
  33. J Mol Biol. 2026 Mar 05. pii: S0022-2836(26)00112-9. [Epub ahead of print] 169739
    FUS condensed phase unfolds model RNA G-quadruplex.
    Tongyin Zheng, Nicolas L Fawzi.
      RNA G-quadruplexes (rG4s) are remarkably stable secondary structures with critical regulatory roles in gene expression, RNA metabolism, and telomere maintenance. However, their behavior within cells remains controversial, partly due to challenges in detecting rG4s in complex environments. Here, we use solution NMR spectroscopy to investigate how condensates formed by the low-complexity and RGG domains of the RNA-binding protein FUS affect the structure of TERRA, a highly stable model rG4 RNA. We show that FUS LC-RGG1 interacts with TERRA in dilute solution and that binding perturbs, but does not disrupt, the G-quadruplex structure. When co-phase separated with FUS LC-RGG1, however, NMR signatures of TERRA's folded state disappear, and the remaining observable resonances indicate an unfolded conformation, even in buffer containing potassium where TERRA rG4 is exceptionally stable when outside a condensate. Quantitative comparisons with a mutant form of TERRA, used as a baseline for fully unfolded RNA, suggest that at minimum a third of TERRA RNA becomes unfolded in the condensed phase. Thus, our results demonstrate that condensates can shift the structural ensemble of rG4 towards unfolded species, offering a potential mechanistic explanation for their apparent lack of stability in vivo and revealing how phase-separated environments may actively modulate RNA structure and function.
    Keywords:  FUS; NMR spectroscopy; RNA G-quadruplex; biomolecular condensates; phase separation; telomere RNA
    DOI:  https://doi.org/10.1016/j.jmb.2026.169739
  34. J Biol Chem. 2026 Mar 06. pii: S0021-9258(26)00221-8. [Epub ahead of print] 111351
    The function of mRNA quality control in aging and age-related diseases.
    Seokjun G Ha, Hyunwoo C Kwon, Jongsun Lee, Hyung-Jun Kim, Seung-Jae V Lee.
      Aging is a complex biological process characterized by the gradual decline of physiological and molecular functions and increased susceptibility to age-associated diseases. Emerging evidence indicates the role of mRNA quality control mechanisms in the regulation of aging and longevity. This review focuses on the function of mRNA surveillance mechanisms, including nonsense-mediated mRNA decay (NMD), nonstop decay (NSD), and no-go decay (NGD), in aging and age-related diseases. We discuss the critical roles of these pathways in maintaining mRNA quality and preventing the accumulation of aberrant transcripts, which can contribute to aging and age-related disorders. Specifically, we discuss the function of NMD in aging processes and age-related diseases, including cancer and neurodegenerative disorders. We also review the safeguarding roles of NSD and NGD in preventing the accumulation of faulty mRNAs and proteins associated with various diseases. We explore the potential functions of additional mRNA surveillance and the associated signaling pathways, such as ribosome-associated quality control (RQC), in aging and age-related diseases. Understanding the intricate relationship between mRNA surveillance mechanisms and aging may provide key information for developing potential therapeutics that boost these pathways for delaying aging and treating age-related diseases.
    DOI:  https://doi.org/10.1016/j.jbc.2026.111351
  35. Trends Neurosci. 2026 Mar 06. pii: S0166-2236(26)00013-5. [Epub ahead of print]
    Decoding the functions of nuclear speckles in neurodegeneration.
    Xu Chen, Bokai Zhu.
      Nuclear speckles, traditionally considered mainly as reservoirs of splicing factors, are increasingly recognized as dynamic biomolecular condensates essential for RNA metabolism, transcriptional regulation, and chromatin organization. Recent advances reveal their phase separation properties, compositional complexity, and stress-responsive remodeling, positioning nuclear speckles as key regulators of proteostasis and stress adaptation. Here, we synthesize emerging evidence linking nuclear speckle dysfunction to neurodegenerative proteinopathies, particularly amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD) and tauopathies. We highlight how disease-associated repeat RNAs, dipeptide repeat proteins, and hyperphosphorylated tau disrupt nuclear speckle integrity, driving transcriptional and splicing defects. Finally, we discuss therapeutic strategies to rejuvenate nuclear speckles, emphasizing their potential as novel targets for restoring proteostasis and mitigating neurodegeneration. This review underscores nuclear speckles as critical yet underexplored regulators of neuronal resilience.
    Keywords:  ALS/FTD; RNA metabolism; cellular stress response; nuclear condensates; proteinopathy; tauopathy
    DOI:  https://doi.org/10.1016/j.tins.2026.01.010
  36. Front Genet. 2026 ;17 1776616
    m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.
    Jiajie Lu, Yanan Li, Yuxiang Hong, Dongshan Liao, Guanhua Fang.
       Introduction: Cardiovascular disease (CVD) is a major threat to health, with high incidence rates and a trend toward younger age groups. RNA modifications are an important component of epigenetics, widely present and indispensable in cells. Increasing evidence suggests that RNA modifications are key regulatory factors involved in cardiac physiological and pathological changes. Understanding the role of RNA modifications in heart-related diseases can help us to identify new drug targets.
    Methods: To systematically investigate the role of m6A modification in different cardiac diseases, we integrated m6A epitranscriptome profiles from five cardiac pathological conditions (three drug-induced cardiac toxicity models-Evodiamine, Matrine, and TKI, hypertrophy, and heart calcification) and their control groups to construct the first predictive model for abnormal m6A modification in cardiac diseases. We constructed separate models for upregulated and downregulated modifications under different pathological conditions, performed feature selection and parameter optimization, and validated the performance of our models using an independent test set.
    Results: m6AHD demonstrated excellent performance on the independent test set, with AUROC scores ranging from 0.728 to 0.880 across various pathological conditions. Cross-validation across different conditions and model interpretability demonstrated that m6A modifications exhibit similar patterns under different pathological conditions and are potentially regulated by similar factors, providing new clues for identifying targets in cardiovascular diseases at the epitranscriptome level. Furthermore, we validated our findings using a zebrafish model of Evodiamine-induced cardiotoxicity. The experimental results revealed significant morphological defects and a broad downregulation of m6A methyltransferase complex components, confirming the involvement of aberrant m6A machinery in the pathology of cardiotoxicity.
    Discussion: m6AHD is the first dedicated framework for predicting multi-condition cardiac m6A dysregulation. Our findings underscore the critical role of m6A homeostasis in cardiomyocyte function and demonstrate that aberrant methylation patterns can serve as reliable indicators of cardiac pathology. This framework provides a robust computational tool for identifying potential therapeutic targets at the epitranscriptome level for cardiovascular diseases.
    Keywords:  RNA modification; bioinformatics framework; cardiac disease; m6A; machine learning
    DOI:  https://doi.org/10.3389/fgene.2026.1776616
  37. Front Immunol. 2026 ;17 1635478
    mRNA-based SARS-CoV-2 vaccines: intracellular processing and aggregation of the encoded spike protein as a mechanistic contributor to cardiac cellular stress.
    Rolf Schreckenberg, Nadine Woitasky, Nadja Itani, Laureen Czech, Anita C Windhorst, Malte Juchem, Christian Bär, Thomas Thum, Péter Ferdinandy, Rainer Schulz.
       Introduction: The trimeric spike (S) protein on the envelope of the SARS-CoV-2 virus is the primary target structure for currently approved corona vaccines. For this reason, the two mRNA-based corona vaccines Comirnaty (BNT162b2, Pfizer/BioNTech) and Spikevax (mRNA-1273, Moderna) first induce the production of a spike monomer in body cells. After enzymatic cleavage by the endoprotease furin, two S subunits are formed, which are supposed to trigger the desired immune response following secretion. Based on this concept, a preventive measure against symptomatic SARS-CoV-2 infections became available within one year of the pandemic's onset. mRNA-based vaccines have proven highly effective in reducing severe disease and mortality. However, both the virus itself and mRNA vaccines have been associated with cardiac symptoms, which are commonly classified as myocarditis, pericarditis, or a combination thereof based on clinical presentation. Although vaccine-induced myocarditis remains a rare adverse event, recent longitudinal studies have raised questions regarding its long-term impact.
    Objective: To better understand the molecular mechanisms potentially involved in vaccine-associated cardiac side effects, we investigated the translation and proteolytic processing of the encoded spike monomers in human AC16 cardiomyocytes, as well as (for comparative purposes) in HEK-293 and HeLa cells.
    Results: In all three cell types, both BNT162b2 and mRNA-1273 produced two divergently sized monomer translation products from which one S1 subunit was formed after enzymatic cleavage. However, the number of identified S2 subunits varied between two and four depending on the cell line and mRNA used. Within a few hours, covalently bonded high-molecular complexes formed from both the spike monomers and their subunits. The arrangement of these complexes always adhered to a consistent pattern in each cell type. Particularly in AC16 cardiomyocytes, the various spike protein derivatives impaired not only cell proliferation, but also induced a pro-inflammatory response and oxidative stress. Only the secreted S1 subunit was detected as an immunogen in the supernatant of all three cell lines.
    Conclusion: Our findings may help to improve the safety and specificity of future mRNA platform technologies by emphasizing the importance of evaluating intracellular protein processing and the potential cellular effects of translated immunogens already during preclinical development.
    Keywords:  SARS-CoV-2; cardiac inflammation; cardiotoxicity; mRNA vaccines; off-target effects; oxidative stress; spike (S) protein; vaccine safety
    DOI:  https://doi.org/10.3389/fimmu.2026.1635478
  38. Front Genet. 2026 ;17 1775625
    RNA-triggered innate immunity: friend and foe.
    Maike Henschel, Maria R Conte, Rocio T Martinez-Nunez.
      Endogenous, or 'self', vs. microbial, or 'non-self', RNA sensing can tip the scales between immune pathology and effective immunity. Cells are equipped to sense RNA, fundamental to trigger an innate immune response to clear viral infection that should not generate a harmful immune response against endogenous RNA. Multiple chemical modifications in RNA fine-tune its cellular sensing and are exploited by pathogens to evade immunity. Likewise, perturbations triggering self RNA sensing cause immune pathologies. This underscores the clinical need for a better understanding of self RNA recognition. Here, we address nucleic acid sensing in the innate immune response from an RNA-centric view. We discuss how self RNA is shielded from sensing by chemical modifications and subcellular compartmentalization, possible mechanisms and consequences of self-RNA sensing, and how this knowledge has been harnessed to revolutionize vaccine development.
    Keywords:  RNA modifications; RNA sensing; host vs pathogen; immune pathology; innate immunity; mRNA therapeutics
    DOI:  https://doi.org/10.3389/fgene.2026.1775625
  39. ACS Chem Biol. 2026 Mar 10.
    Nuclear-m6A-Label-Seq Enables Transcriptome-Wide Nuclear m6A Profiling at Single-Base Resolution.
    Chenyang Huang, Xiner Ying, Xiao Shu, Jianzhao Liu.
      N6-Methyladenosine (m6A) on mature mRNA has been extensively characterized, yet its precise mapping and functions in nuclear noncoding RNAs remain elusive. To address this issue, we recently developed Nuclear-m6A-label-seq, a metabolic labeling-based method for transcriptome-wide nuclear m6A profiling at single-base resolution. This approach builds on the prototypical m6A-label-seq principle, in which an allyl group, instead of methyl group, is metabolically installed at N6-position at supposed RNA m6A-generating adenosines and the resultant N6-allyl adenosine is subsequently converted into 1, N6-cyclized adenosine (cyc-A) by mild iodination reaction. During RNA reverse transcription, HIV reverse transcriptase is employed to introduce a base misincorporation at cyc-A sites while enabling a template switch to incorporate adapter sequences to the complementary DNA end in a single step. Through this strategy, library construction is shortened to about 6 h, and the required cell-labeling total RNA input is reduced to 5 μg of total nuclear RNA, representing a 100-fold reduction compared to the prototypical protocol. Both polyadenylated and nonpolyadenylated nuclear transcripts are captured through the sequential nuclear RNA isolation and rRNA depletion. Following high-throughput sequencing, reads from human cells are aligned with the complete T2T-CHM13 genome, enabling accurate mapping of repetitive regions. Aligned reads are then analyzed using the user-friendly rMATS-DVR pipeline to identify high-confidence m6A sites based on cyc-A-induced misincorporation patterns. Here, we provide a detailed step-by-step protocol for Nuclear-m6A-label-seq, which stands for a direct and high-resolution approach for profiling the nuclear m6A epitranscriptome.
    DOI:  https://doi.org/10.1021/acschembio.6c00014
  40. Antiviral Res. 2026 Mar 06. pii: S0166-3542(26)00052-5. [Epub ahead of print]249 106393
    Targeting dengue virus infection through a translation-modulator small-molecule screen.
    Rodolfo Katz, Yarden Moalem, Rina Rosin-Arbesfeld, Ella H Sklan.
      Dengue virus (DENV), a mosquito-borne RNA virus, poses a significant global health concern due to the lack of effective antivirals and the limitations of current vaccines. To uncover host-targeted vulnerabilities, we performed a functional screen of small-molecule translation modulators. Elongation inhibitors consistently produced the most potent antiviral effects, markedly reducing viral RNA levels, nonstructural protein 3 (NS3) levels, and infectious virus production. Compounds targeting cap-dependent initiation were largely ineffective, except for eIF4E:eIF4G inhibitors, which exerted moderate suppression. This may likely be due to the internal ribosome entry site (IRES)-like activity reported in the DENV 5' untranslated region (UTR). Rocaglamide A strongly suppressed DENV, consistent with an eIF4A helicase-specific vulnerability. Two clinically relevant inhibitors, homoharringtonine (HHT) and bruceantin (BCT), blocked DENV propagation at low nanomolar doses in cell lines and reduced viral RNA and titers in primary human macrophages, underscoring their translational potential. Similar effects were observed with the related Zika virus (ZIKV) in cell lines. These pharmacological data suggest that translation elongation and eIF4A helicase activity are candidate host dependencies for orthoflaviviruses, motivating stage-resolved and in vivo evaluation studies.
    Keywords:  Dengue virus; Host-targeted antivirals; Translation elongation; Translation modulators; Zika virus
    DOI:  https://doi.org/10.1016/j.antiviral.2026.106393
  41. Proc Natl Acad Sci U S A. 2026 Mar 17. 123(11): e2518109123
    Host ESCRT machinery orchestrates the assembly of tomato spotted wilt virus ribonucleoproteins.
    Kikyo Watanabe, Chihiro Oda-Yamamizo, Kazuhiro Ishibashi.
      The genomic RNA of negative-strand RNA viruses is encapsidated by nucleocapsid proteins and associates with RNA polymerase to form a ribonucleoprotein (RNP) complex. Lacking both a 5' cap and a 3' poly (A) tail, viral RNAs are highly unstable and prone to degradation by cellular nucleases. Therefore, newly synthesized genomic and complementary-strand RNAs must be rapidly protected through RNP formation. However, the molecular mechanisms governing RNP assembly in cytoplasm-replicating negative-strand RNA viruses remain largely unknown. Here, we screened a yeast knockout library and isolated mutants in several components of the endosomal sorting complexes required for transport (ESCRT) genes that affected RNA replication of tomato spotted wilt virus (TSWV). In wild-type (WT) yeast cells, TSWV nucleocapsid (N) and RNA polymerase (L) proteins colocalize at the trans-Golgi network (TGN) in a replicon-RNA-dependent manner, suggesting that TSWV RNPs accumulate at the TGN. However, in the snf7Δ, bro1Δ, and doa4Δ mutant cells, N localization to TGN and RNP formation were impaired. Another RNA replication-defective mutant, vps36Δ, showed normal N localization, and SNF7, BRO1, and DOA4 were recruited to the TGN by TSWV N or L proteins, implying that the ESCRT components have additional roles in TSWV RNA replication beyond facilitating N transport. These findings suggest that ESCRT components play multifaceted roles in TSWV RNA replication, including the intracellular transport of N to the TGN-where RNA replication takes place-thereby ensuring accurate and efficient RNP assembly.
    Keywords:  Trans-Golgi network (TGN); endosomal sorting complexes required for transport (ESCRT); tomato spotted wilt virus; viral replication
    DOI:  https://doi.org/10.1073/pnas.2518109123
  42. FASEB J. 2026 Mar 31. 40(6): e71662
    UGA4 and YBR062C Regulate Oxidative Stress Tolerance Under Heavy Metal Toxicity.
    Mustafa Al-Gafari, Houman Moteshareie, Thomas D D Kazmirchuk, Jiashu Wang, Sarah Takallou, Parvin Khosravifar, Mohsen Hooshyar, Bahram Samanfar, Ashkan Golshani.
      Heavy metals impose a major cellular stress by promoting protein dysfunction and the accumulation of reactive oxygen species (ROS). In Saccharomyces cerevisiae, the glutathione S-transferase Ure2p is a key determinant of resistance to metal-induced oxidative stress and can be synthesized through a stress-responsive, cap-independent internal ribosome entry site (IRES) in the URE2 5' UTR. Much has been learned about the cellular responses to heavy metal exposure; however, the mechanistic details of how response genes are regulated in response to stress require further investigation. Here, we identify two previously unrecognized contributors to heavy metal tolerance, UGA4, a 4-aminobutyric acid GABA permease, and YBR062C, a poorly characterized gene previously linked to filamentous growth. Deletion of UGA4 or YBR062C caused notable sensitivity when cells were exposed to sub-inhibitory concentrations of cadmium (Cd), arsenite (As(III)), and nickel (Ni), with colony-forming units reduced by approximately 50%-80% relative to the wild-type strain. Genetic analysis positioned both genes in the URE2 pathway. Double mutants ure2Δ uga4Δ and ure2Δ ybr062cΔ were not more sensitive than the single mutant ure2Δ. URE2 overexpression restored metal resistance in uga4Δ and ybr062cΔ backgrounds, whereas UGA4 or YBR062C overexpression did not rescue ure2Δ. Mechanistically, UGA4 and YBR062C acted post-transcriptionally. URE2 mRNA abundance was unchanged, but Ure2p protein levels were reduced, particularly under Cd stress. Polysome profiling revealed decreased ribosomal association of URE2 mRNA in both mutants, and a URE2-IRES-dependent β-galactosidase reporter showed approximately 80% lower activity without affecting cap-dependent translation or altering reporter mRNA levels. Together, these data demonstrate that UGA4 and YBR062C promote heavy metal tolerance by enabling IRES-mediated translation of URE2 mRNA.
    Keywords:  IRES; URE2; heavy metals; oxidative stress; translation; yeast
    DOI:  https://doi.org/10.1096/fj.202503701R
  43. Asian J Pharm Sci. 2025 Dec;20(6): 101090
    The strategies and advances of mRNA translation booster.
    Yingying Shi, Kedong Sun, Yilong Hu, Zeliang Lou, Yi Wang, Jian You.
      The therapeutic efficacy and safety of mRNA-based drugs in immunological and nonimmunological applications are critically dependent on the translated protein yield, which requires precise modulation of mRNA expression kinetics. Among the factors influencing mRNA translation, immunogenicity and stability are pivotal in determining the longevity of protein production. Current optimization strategies have integrated (1) molecular engineering (e.g., modified nucleotides), (2) advanced delivery systems (e.g., lipid nanoparticles), and (3) adjuvant drug synergy. This review focuses on co-delivered adjuvant drugs and introduces the concept of "mRNA translation boosters" for the first time. mRNA translation boosters are classified as small-molecule compounds and macromolecular agents that improve translational fidelity through mechanisms including blockade of pattern recognition receptors, modulation of inflammatory cascades, facilitation of endosomal escape, and protection against enzymatic degradation. As clinically validated with COVID-19 mRNA vaccines, these boosters have now demonstrated expanded utility in gene editing therapies and protein replacement applications. This review addresses the immunological challenges encountered during mRNA transfection and translation while summarizing existing mRNA translation boosters that optimize protein expression kinetics. By establishing a mechanistic framework for booster selection and employment, this work provides translational guidance for advancing nucleic acid therapeutics towards their maximum clinical potential.
    Keywords:  Immunogenicity; Nucleic acid therapeutics; Translation boosters; mRNA expression
    DOI:  https://doi.org/10.1016/j.ajps.2025.101090
  44. Blood Neoplasia. 2026 May;3(2): 100202
    Synergistic targeting of eIF4A-mediated translation initiation and apoptosis in acute myeloid leukemia.
    Yoke Seng Lee, Jonathan D Good, Noha Awais, Benjamin K Eschle, Maia S Lineberry, Jingting Lin, Mark Wunderlich, Jenna Thibodeau, Holly Edwards, Jessica L Teo, Sarah Bibeau, Morgan Wollman, George Karadimov, Nurefsan Sariipek, Basit Salik, Jean Acosta, Jenny Noel, David G J Cucchi, Erica A K DePasquale, Prafulla C Gokhale, Jerome Ritz, Yubin Ge, Peter G Miller, Fadi J Najm, Richard M Stone, Jacqueline S Garcia, Andrew A Lane, Courtney L Jones, Peter van Galen.
      Targeted therapies, such as the BCL-2 inhibitor venetoclax, have expanded the treatment options for patients with acute myeloid leukemia (AML), but survival remains poor because of drug resistance and disease relapse. We found that the translation initiation factor EIF4A1, which unwinds complex messenger RNA structures in the 5' untranslated region (UTR) of oncogenic transcripts, is highly expressed in AML stem- and progenitor-like cells relative to healthy hematopoietic stem and progenitor cells. Inhibition of eukaryotic initiation factor 4A (eIF4A) with the first-in-class small molecule zotatifin reduces the translation efficiency of transcripts related to the cell cycle and oncogenic signaling via the PI3K/AKT/mTOR pathway, as shown by ribosome profiling and gene set enrichment analysis. Western blot analysis corroborated these findings and demonstrated the downregulation of AKT, STAT-5, and MCL-1, factors implicated in resistance to venetoclax-based regimens. The combination of zotatifin and venetoclax synergistically kills AML cells in vitro and induces apoptosis across AML genotypes with selectivity toward progenitor-like cells in primary AML bone marrow (BM); however, its effect in primary healthy BM is limited. Using 3 in vivo xenograft models derived from patients with relapsed/refractory AML, the combination significantly suppressed the tumor burden and prolonged survival. These results support eIF4A-mediated protein translation as a therapeutic target in AML and highlight the potential of zotatifin and venetoclax in relapsed/refractory disease.
    DOI:  https://doi.org/10.1016/j.bneo.2026.100202
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