bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–09–06
sixty-nine papers selected by
Cédric Chaveroux, CNRS
  1. Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA.
  2. Rewiring the ribosome to translate proteins encoded in its own RNA.
  3. [Research progress on the involvement of N6-methyladenosine modification in the regulation of immune response in sepsis].
  4. Characterization of METTL3/14-mediated m6A modification in human transcriptome using Nanopore direct RNA sequencing.
  5. RNA Labeling of Nucleolar Transcripts by 5-Ethynyl Uridine Click Chemistry.
  6. Fluorescence-Based mRNA Translation Reporter.
  7. The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress.
  8. Growth-dependent tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis.
  9. Mechanisms and therapeutic opportunities of the ribotoxic stress response in cancer.
  10. Dynamics of Aspartate Isomerization and Its Cellular Implications: Evidence for Isoaspartate Formation in ER-Folded Proteins and Stress-Responsive Regulation of PCMT1.
  11. SF3B4 "reads" RNA that is methylated by METTL16.
  12. Target-Directed miRNA Degradation: Mechanisms and Significance.
  13. A Co-Chaperone Mimetic Perturbs Cellular Nitrogen Metabolism in Mycobacteria.
  14. Assay for In-Vitro Arginine Methylation of RNA Binding Proteins Followed by RNA Binding.
  15. PTBP1 at the host-virus interface: mechanistic roles in viral RNA translation, replication, and immune modulation.
  16. Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues.
  17. Translational control by RPL22L1-specific ribosomes enhances DNA repair and chemoresistance.
  18. Hot and Sp(l)icy phosphatase: A potential thermosensor in mammals.
  19. Activation of mTOR pathway by human cytomegalovirus promoting host ribosomal protein expression by coordinated transcriptional and translational controls.
  20. The m⁶A reader YTHDF2 regulates mRNA transport and axon outgrowth in developing neurons.
  21. Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.
  22. Complementary Approaches for Accurate Detection of tRNA-Derived Small RNAs (tsRNAs): Small RNA Northern Blotting and Dumbbell PCR.
  23. A Dual-Color Electrophoretic Mobility Shift Assay to Examine RNA-Binding and RNA Chaperone Activity Simultaneously.
  24. Proteins as Regulators of Metabolic Changes in Sepsis: Alterations in Body Fluids, Immune Cells, and Organs through the Eyes of Proteomics.
  25. Reciprocal regulation of m6A RNA methylation and protein post-translational modifications: implications for disease pathogenesis and therapy.
  26. How Epitranscriptomic Machinery Senses Environmental Cues.
  27. Spermidine in Colorectal cancer: friend or foe?
  28. Repurposing ribavirin for oncology: Integrating metabolism, signaling, and translational control.
  29. Guanosine 10 methylation by TRMT11-TRMT112 optimizes human mitochondrial tRNAs for efficient translation.
  30. Isolation and Analysis of Bacterial Ribosomes Through Sucrose Gradient Ultracentrifugation.
  31. Post-transcriptional regulation of Profilin-2 by microRNAs and RNA-binding proteins forms a critical regulatory node for early embryonic cell fate decisions.
  32. Phase separation in neurodegenerative disorders: a metabolic perspective on protein aggregation and therapeutic targeting.
  33. Characterization of RNA Structure Dynamics with Trans-Factors Using Single-Molecule Optical Tweezers.
  34. The m6A reader IGF2BP2 promotes proinflammatory signaling in Lupus nephritis by recognizing STAT1 m6A modifications.
  35. In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles.
  36. Analysis of tRNA Aminoacylation by Northern Blotting and Multiplex Small RNA-Seq.
  37. FMRP promotes gastric cancer progression via m6A-dependent stabilization of DVL2 and activation of the Wnt/PCP-JNK pathway.
  38. Deep3MVPF: Multiview Deep Framework for the Prediction of Stability and m6A in mRNA 3'UTR.
  39. The integrated stress response in pancreatic β-cell failure in diabetes: from molecular mechanisms to precision therapeutics.
  40. Micro- and macro- heterogeneity of N-glycoproteome remodeling in endoplasmic reticulum stress.
  41. ERN1 inhibition modifies hypoxic regulation of EGLN1 expression in U87MG glioblastoma cells.
  42. A multi-omics systems toxicology framework reveals amino acid-mediated stress adaptation to deltamethrin exposure in a yeast model.
  43. Serine: From Metabolic Intermediate to Signaling Entity.
  44. Insights into the regulation of the HOTAIR proximal promoter.
  45. HNRNPC contributes to ccRCC progression by stabilizing AURKB mRNA in an m6A-dependent manner.
  46. Oxidative stress-driven epigenetic reprogramming of immune cells in COPD: from epitranscriptomic and metabolic crosstalk to treatable traits.
  47. RNA Triple Helices: From Structures and Mechanisms to Therapeutic Targets.
  48. Chloramphenicol stress triggers oxidative adaptation in Acinetobacter baumannii ATCC19606 devoid of RND efflux pumps AdeAB or AdeIJ.
  49. Isoform-resolved 14-3-3/YWHA networks in colorectal cancer: phospho-adaptor mechanisms, biomarker contexts and therapeutic opportunities.
  50. DNTTIP2 coordinates RNA exosome activities to ensure fidelity of human ribosome assembly.
  51. RNA m⁶A modification and its regulatory factors are altered in granulosa cells from women with PMOS.
  52. Local synthesis of CaMKII does not contribute to activity-dependent generation of ghost boutons.
  53. Synergies and trade-offs in the heat shock response mechanism.
  54. ANGII Initiated HSF2 Trans-Activating HIF-1α Through Induction of ER Stress to Promote Cardiac Hypertrophy.
  55. Functional Prediction of Epitranscriptome.
  56. How to Validate miRNA Targeting: Western Blot Analysis.
  57. Mass spectrometry-based mapping of the ubiquitin chaperone code.
  58. Lysine methylation is an endogenous post-translational modifications of tau protein in human brain and a modulator of aggregation propensity.
  59. Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La.
  60. Ribosomal protein S3: a critical regulator of human disease mechanisms.
  61. Autophagy in testicular physiology and male fertility: Mechanisms, dysregulation, and translational opportunities.
  62. SPRTN preserves RNA polymerase I transcription under genotoxic drug stress in lung adenocarcinoma.
  63. Mitophagy in neuronal health and disease: from mechanisms to neurodegeneration.
  64. Fructose induces PERK-dependent ER stress and mitochondrial dysfunction via nucleotide depletion in clear cell renal cell carcinoma.
  65. An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch.
  66. mRNA Microinjection for Gene Expression Studies in Xenopus laevis and Xenopus tropicalis.
  67. Endoplasmic Reticulum Stress Drives Copper-Induced Reticulophagy in Porcine Hepatocytes.
  68. Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.
  69. E3 Ubiquitin Ligase RNF126 Promotes Ovarian Cancer Progression and Cisplatin Resistance Through Targeting Numb/Notch1 Axis.
  1. Elife. 2026 Sep 04. pii: RP102752. [Epub ahead of print]13
    Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA.
    Zhuo Bi, Yu-Xiang Chen, Iris D Young, Mohamad T Dandan, Hemant Joshi, Hong-Wei Su, Yuemeng Chen, Jiayao Hong, James S Fraser, Babak Javid.
      Despite redundant cellular pathways to minimize translational errors, errors in protein synthesis are common. Pathways and mechanisms to minimize errors are classified as pre-ribosomal or ribosomal. Pre-ribosomal pathways are primarily concerned with the appropriate charging of tRNAs with their cognate amino acids. By contrast, the ribosomal decoding center is considered 'blind' to mischarged tRNAs since these have cognate codon•anti-codon pairing. Here, we identified that in mycobacteria, deletion of the 16S ribosomal RNA methyltransferase gidB led to increased ribosomal discrimination of mischarged tRNAs. Discrimination only occurred in mycobacteria enriched from environments or genetic backgrounds with high rates of mistranslation. GidB deletion was necessary, but not sufficient for reducing mistranslation due to misacylation. Analysis of new cryo-EM structures of the M. smegmatis ribosomes derived from wild-type and gidB-deleted strains point to the interaction between the base methylated by GidB on the 16S RNA and an asparagine on the ribosomal S12 protein that, when mistranslated to aspartate, may be involved in altering translational fidelity. Our data suggest a mechanism by which mycobacterial ribosomes can discriminate mischarged tRNAs and that 16S rRNA differential methylation by GidB may act to prevent catastrophic translational error.
    Keywords:  GidB; Mycobacterium; antibiotic tolerance; chromosomes; gene expression; infectious disease; microbiology; mistranslation; ribosome
    DOI:  https://doi.org/10.7554/eLife.102752
  2. Nature. 2026 Sep 02.
    Rewiring the ribosome to translate proteins encoded in its own RNA.
    Kasra Alizadeh, Dorota Klepacki, Nora Vázquez-Laslop, Alexander S Mankin.
      Cellular protein synthesis relies on random encounters between ribosomes and mRNAs, limiting optimization of the translation machinery for production of a single protein-a key need in biotechnology. One potential solution is integrating the protein-coding sequence into the ribosome itself, thereby committing the ribosome to synthesis of a single polypeptide. The feasibility of such integration could also address a long-standing challenge in RNA world models: explaining how early protein synthesis could function reliably despite the scarcity and poor organization of its components1. Whether a ribosome can translate its own ribosomal RNA (rRNA) has remained unclear. Here we show that bacterial ribosomes can synthesize proteins encoded within their own RNA. We engineered a chimeric messenger-ribosomal RNA (mrRNA) by appending a protein-coding sequence to 16S rRNA. The hybrid mrRNA assembles into a small ribosomal subunit that binds to the large subunit to form Ribo-M, a ribosome capable of translating mrRNA-encoded proteins. Translation is abolished by mutations or antibiotics that impair the function of the small subunit, demonstrating that mrRNA translation is carried out in cis by ribosomes assembled on the chimeric mrRNA. Incorporating mrRNA into a ribosome with tethered subunits yielded Ribo-TM, in which encoding, decoding and peptide synthesis are united within a single RNA scaffold. These findings establish the mechanistic feasibility of a ribosome translating its own rRNA in vivo and in vitro, offering a versatile platform for orthogonal protein production and insights into the origin of translation.
    DOI:  https://doi.org/10.1038/s41586-026-10962-1
  3. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2026 Aug;38(8): 771-775
    [Research progress on the involvement of N6-methyladenosine modification in the regulation of immune response in sepsis].
    Long Yang, Zerui Ma, Shaoqi Sun, Ling Zhang.
      Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection, its exact pathogenesis has not yet been fully elucidated, and the clinical mortality rate remains high. N6-methyladenosine (m6A) modification is a common form of post-transcriptional chemical modification in eukaryotes. By influencing RNA splicing, nuclear-cytoplasmic transport, and translation, it plays a role in regulating various pathophysiological processes. Recent studies have revealed that dynamic changes in m6A modifications are associated with damage caused by the immune response in sepsis. During the progression of sepsis, alterations in the activity of m6A modification-associated methyltransferases, demethylases and recognition proteins within immune cells can influence the RNA metabolism of key downstream signalling molecules. m6A modification may participate in the chemotaxis of macrophages and neutrophils by regulating the expression of relevant transcription factors. Furthermore, m6A modification is also involved in regulating the RNA metabolic re-editing process of adaptive immune cells in sepsis. Focusing on the aforementioned pathophysiological processes, this review summarises the current state of research on the involvement of m6A modifications in macrophage polarisation, neutrophil migration, and the regulation of RNA metabolism and immune cell re-editing in sepsis. It aims to provide a reference for understanding the role of m6A modifications in immune regulation within the pathogenesis of sepsis and their potential clinical therapeutic applications.
    DOI:  https://doi.org/10.3760/cma.j.cn121430-20250807-00724
  4. PLoS Genet. 2026 Sep;22(9): e1012278
    Characterization of METTL3/14-mediated m6A modification in human transcriptome using Nanopore direct RNA sequencing.
    Emily Kurtyan, Andrew J Stein, Kelly J Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim.
      Post-transcriptional RNA modifications modulate diverse aspects of RNA metabolism. N6-methyladenosine (m6A), one of the most abundant internal RNA modifications, is deposited by the core methyltransferase complex, METTL3 and METTL14. Oxford Nanopore Technologies (ONT) platform permits direct, single RNA molecule sequencing while preserving native modifications. However, without rigorous benchmarking, the accuracy and reproducibility of modification detection remain uncertain. Here, we leveraged ONT to comprehensively profile bona fide m6A modifications in cellular RNAs at single-nucleotide resolution by integrating two direct RNA sequencing chemistries (RNA002 and RNA004) with the m6Anet and Dorado modification-detection models. We independently depleted METTL3 and METTL14 in human cells and rigorously validated modification calls through several assays and independent orthogonal methods (GLORI and miCLIP). We find that Dorado detected a higher number of m6A events and enabled simultaneous detection of other RNA modifications (5-methylcytosine, pseudouridine, and inosine). Pairing Dorado with an in vitro transcribed, unmodified control under stringent filtering, we provide compelling evidence supporting a global reduction in m6A sites and stoichiometry within coding sequences and across genes, particularly in highly modified genes and sites, and at consensus DRACH motifs. We report a differential and complex regulation of modified transcripts, accompanied by a global reduction in poly(A) tail length. Notably, METTL3 and METTL14 depletion produced distinct transcript-specific effects, supporting non-redundant roles within the m6A writer complex. Together, our study illustrates a notable advancement of ONT capabilities and establishes a robust transcriptome-wide framework for RNA modification detection, thereby laying the groundwork for exploring the contribution of METTL3/METTL14 to cellular functions and disease.
    DOI:  https://doi.org/10.1371/journal.pgen.1012278
  5. Methods Mol Biol. 2026 ;3047 109-116
    RNA Labeling of Nucleolar Transcripts by 5-Ethynyl Uridine Click Chemistry.
    Juyeon Lee, Kyung-Ha Lee.
      The nucleolus is a dynamic membraneless organelle where ribosomal RNA (rRNA) transcription, processing, and ribonucleoprotein assembly occur. Visualizing nascent RNA within nucleolar condensates reveals how RNA metabolism and phase separation reorganize under stress. This chapter provides a practical protocol to label nascent RNA using 5-ethynyl uridine (5-EU), followed by copper-catalyzed azide-alkyne cycloaddition for fluorescent detection. The method is straightforward, works across mammalian cells, and robustly reports nucleolar transcription under basal and stress conditions (heat shock; low-dose actinomycin D). Step-by-step instructions, reagent setup, image analysis metrics, troubleshooting, safety, and expected results are included so that researchers can reproducibly implement the assay.
    Keywords:  5-ethynyl uridine; Actinomycin D; Click chemistry; Condensates; Heat shock; Nascent RNA; Nucleolar stress; Nucleolus; RNA labeling
    DOI:  https://doi.org/10.1007/978-1-0716-5352-4_9
  6. Methods Mol Biol. 2026 ;3047 203-223
    Fluorescence-Based mRNA Translation Reporter.
    Jemima Riess, Gunhild Sommer, Tilman Heise.
      Herein, we describe a fluorescence reporter assay for investigating regulatory elements in the 5'-UTR of mRNA that modulate translational initiation. The canonical translation initiation process generally begins with the assembly of the eIF4F complex at the cap structure, the formation of the ternary complex, which is loaded with the initiator tRNA, and finally, the preinitiation complex. The preinitiation complex then scans the 5'-UTR to identify the authentic translation start site, which is typically characterized by an AUG codon within a sequence context known as the Kozak sequence. It is well established that the 5'-UTR varies extensively in length and contains regulatory, structural, and sequence elements. To investigate these elements, we use a green fluorescence protein (GFP)- and a luciferase-based mRNA reporter. These reporters can be quickly generated by ordering gBlocks or by PCR-based template generation for in vitro transcription, capping and polyadenylation, to produce synthetic mRNAs. These mRNAs can be transfected into cells, and expression can be monitored via GFP fluorescence or by measuring luciferase activity. In this chapter, we provide a step-by-step protocol for designing gBlocks, generating the reporter mRNA, transfecting the cells, and analyzing the results.
    Keywords:  5′-untranslated region; Cell-based assay; Fluorescence; Luciferase; RNA structure; RNA-binding; RNA-binding protein; Reporter; Translation
    DOI:  https://doi.org/10.1007/978-1-0716-5352-4_16
  7. RNA. 2026 Sep 02. pii: rna.081099.126. [Epub ahead of print]
    The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress.
    Laura Monaghan, Chetan Srinath, Abigail R Mann, Nila Roy Choudhury, Graeme R Grimes, Dasa Longman, Javier F Caceres.
      The nonsense-mediated decay pathway (NMD) is an RNA quality control mechanism that regulates the stability of target RNAs. We previously identified the ER-localized SEC13 protein as a novel NMD factor in C. elegans and in HeLa cells; raising the possibility that it could be involved in regulating the stability of mRNAs translated at the ER. SEC13 is a component of several cellular complexes, including the COPII vesicle coat, the nuclear pore complex (NPC) and the nutrient sensing GATOR2 complex. Here, we show that SEC13 interacts with core NMD factors and using a newly developed dual-color fluorescent NMD sensor in U2OS cells, we assessed SEC13 NMD activity, at a single-cell level. Transcriptomic profiling revealed that unlike the previously described ER-NMD factor, NBAS, SEC13 co-regulates the stability of substrates translated both in the cytoplasm and at the ER. We also show that SEC13 function in NMD is largely independent of its function in other cellular complexes. Altogether, these results show that SEC13 is a bona fide NMD factor in mammalian cells. Finally, we utilized an ER stress-activated indicator (ERAI) in U2OS cells to demonstrate that SEC13, together with canonical NMD factors, has a role in the regulation of the unfolded protein response (UPR) at the ER. Thus, the moonlighting functions of SEC13 include a role in NMD pathway and the regulation of ER stress.
    Keywords:  Moonlighting; RNA-quality control; SEC13; Stress response; nonsense-mediated decay (NMD)
    DOI:  https://doi.org/10.1261/rna.081099.126
  8. mBio. 2026 Aug 31. e0147426
    Growth-dependent tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis.
    Michelle M Mitchener, Caleb M Anderson, Mark Veleba, Kayla Teo, Mélanie Roch, Ruixi Chen, Yifeng Yuan, Isaiah Han, Agnieszka Dziergowska, Kevin Pethe, Thomas J Begley, Kimberly A Kline, Peter C Dedon.
      Enterococcus faecalis is a gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis, how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem-loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.IMPORTANCEEnterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism's physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for posttranscriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.
    Keywords:  Enterococcus faecalis; posttranscriptional control mechanisms; tRNA; tRNA modification
    DOI:  https://doi.org/10.1128/mbio.01474-26
  9. Mol Oncol. 2026 Sep 02.
    Mechanisms and therapeutic opportunities of the ribotoxic stress response in cancer.
    Anastassiya Kim, Maryam Aslam, Elouise Torruella, Alphons Sony, Asif Rahman, Simira Smith, Columba de la Parra, Moira Sauane.
      Various environmental and endogenous stressors, including ultraviolet (UV) radiation, cytotoxins, and dysregulated translation, can induce ribosome stalling and collisions, disrupting protein homeostasis. The ribotoxic stress response (RSR) is a cellular surveillance mechanism that senses translational stress and activates stress signaling via the MAP3 kinase ZAKα and the stress-activated protein kinases (SAPKs) p38 and JNK. This review outlines the molecular mechanisms behind RSR, distinguishes RSR from other translational stress response pathways, such as the well-studied integrated stress response (ISR), discusses the role of RSR in key cellular processes, and presents new evidence linking RSR to cancer biology. We explore how ribotoxic stress is exploited by chemotherapeutic agents and other compounds to induce cancer cell death, and the potential limitations of such therapeutic strategy. Finally, we highlight future considerations for inducing the RSR pathway in cancer, highlighting both therapeutic potential and the challenges in this emerging field.
    Keywords:  ZAKα; cancer; ribosome collision; ribosome stalling; ribotoxic stress response; stress‐activated protein kinase
    DOI:  https://doi.org/10.1002/1878-0261.70323
  10. Biochemistry (Mosc). 2026 Aug;91(8): 1449-1459
    Dynamics of Aspartate Isomerization and Its Cellular Implications: Evidence for Isoaspartate Formation in ER-Folded Proteins and Stress-Responsive Regulation of PCMT1.
    Burcu Biterge.
      Spontaneous isomerization of aspartate and deamidation of asparagine residues into isoaspartate (isoAsp) constitute major non-enzymatic post-translational modifications that alter protein structure, stability, and turnover. The repair enzyme protein L-isoaspartate O-methyltransferase (PCMT1) catalyzes methylation of isoAsp residues, thereby preventing their accumulation and preserving proteome integrity. Although PCMT1 has been studied extensively in cytoplasm and nucleus, its relationship to endoplasmic reticulum (ER) proteostasis remains poorly understood. Here, we investigated dynamics of aspartate isomerization within the cell, focusing on isoAsp accumulation and the regulation of PCMT1 localization under physiological and stress conditions. Using immunofluorescence, subcellular fractionation, and in vitro methylation assays, we detected isoAsp-modified proteins within the ER-enriched fractions of HeLa cells. We found that ER stress induction enhanced formation of isoAsp-containing proteins, with MG132 treatment producing the highest accumulation. PCMT1 expression increased under both stress conditions, accompanied by distinct subcellular redistribution between the cytoplasmic and nuclear compartments. These observations indicate that ER-folded proteins are susceptible to spontaneous aspartate isomerization, and that PCMT1 activity dynamically responds to proteostatic stress. Our findings provide the first experimental evidence linking isoAsp formation within the ER to PCMT1-mediated protein repair, thereby integrating chemical instability with cellular quality-control pathways. This study establishes a structural and cellular framework for understanding the dynamics of aspartate isomerization in the cell and underscores significance of PCMT1 in maintaining proteostasis under stress conditions.
    Keywords:  ER stress; PCMT1; aspartate isomerization; isoAspartate; protein damage; proteostasis
    DOI:  https://doi.org/10.1134/S0006297926600894
  11. Biochem J. 2026 Sep 02. pii: BCJ20260340. [Epub ahead of print]
    SF3B4 "reads" RNA that is methylated by METTL16.
    Fen Yang, Yin Li, Yuanqi Zhang, Wentao Sun, Xue-Jun Wang, Junxia Qi, Cari Sagum, Mark T Bedford.
      N6-methyladenosine (m6A) is a prevalent RNA modification that regulates multiple aspects of RNA metabolism, including RNA localization, stability, decay, and translation. m6A deposition is catalyzed by distinct methyltransferase complexes, including the METTL3/14 complex and METTL16, which recognize different RNA sequence motifs. The biological effects of m6A are mediated by effector proteins that selectively recognize m6A-modified RNA. To identify previously uncharacterized m6A binding proteins, we developed an RNA-binding protein domain array to systematically screen for candidate m6A effectors. Using this approach, we identified the spliceosomal protein SF3B4 as a potential m6A reader. RNA pull-down assays using m6A-modified RNA probes demonstrated selective enrichment of endogenous SF3B4, supporting its ability to recognize m6A RNA. To define the RNA targets of SF3B4, we performed SF3B4 RIP-seq alongside m6A RIP-seq, followed by RIP-qPCR validation of overlapping targets. Motif analysis revealed that SF3B4 preferentially associates with the conserved GRAGRA (R=A/G) motif, consistent with the RNA sequence recognized by the METTL16 methyltransferase. Notably, transcripts of the BCR and MET oncogenes were identified as shared targets of SF3B4 and METTL16. Together, these findings identify SF3B4 as a previously unrecognized m6A effector and suggest that it participates in RNA metabolic processes downstream of METTL16-mediated m6A modification.
    Keywords:  METTL16; RNA modification; SF3B4; m6A reader
    DOI:  https://doi.org/10.1042/BCJ20260340
  12. Methods Mol Biol. 2026 ;3056 21-37
    Target-Directed miRNA Degradation: Mechanisms and Significance.
    Michael Attathikhun, Ancuta Jurj, George A Calin.
      MicroRNAs are small noncoding RNAs that regulate gene expression within cells through the translational repression or degradation of targeted mRNA. miRNAs undergo a multiphase synthesis that includes conformational changes mediated by Drosha, Dicer, and Argonaute to integrate mature miRNA into the RNA-induced silencing complex to target messenger (m)RNA. miRNAs have been characterized through their transcription and biogenesis; however, the mechanism regarding miRNA turnover is less comprehensible because of the stability of each miRNA. Target-directed miRNA degradation (TDMD) is dependent on the stability of miRNAs, which modulates the decay rate of miRNAs. This mechanism is initiated through target RNAs' engagement with miRNAs via the 3' end complements, which induces Argonaute rearrangement. These rearrangements of Argonaute can be induced through tailing and trimming, with one of the central initiators being the ZSWIM8 E3 ubiquitin ligase. Tailing and trimming are often associated with TDMD, and the mechanistic role is context-dependent. This mechanism provides a regulation process in which mRNA is actively repressed and silenced by the miRNA. The significance of TDMD lies in its role in post-transcriptional regulation of miRNA expression, its implications for therapeutic treatments, and its association with various diseases.
    Keywords:  Cancer; TDMD; miRNA
    DOI:  https://doi.org/10.1007/978-1-0716-5392-0_2
  13. Chembiochem. 2026 Sep 14. 27(17): e70504
    A Co-Chaperone Mimetic Perturbs Cellular Nitrogen Metabolism in Mycobacteria.
    Brock Nelson, Tania J Lupoli.
      Protein quality control in bacteria relies on dynamic chaperone networks that rapidly respond to environmental stresses. In mycobacteria, a central Hsp70 chaperone, DnaK, and its co-chaperones, J-domain proteins (JDPs), play essential roles in the cellular response to stress and antibiotics. Conserved "J-domain" sequences of JDPs are known to mediate transient interactions with Hsp70s and other protein partners. We have previously shown that a rationally designed proteomimetic of a J-domain is toxic to stressed mycobacterial cells. Here, we aimed to trap J-domain mimetic interaction partners to potentially reveal vulnerabilities in cellular stress-response pathways. To do so, we modified a J-domain proteomimetic of the mycobacterial JDP DnaJ1 (J1C) with a photoaffinity label moiety, resulting in J1C-PAL. In heat-shocked mycobacteria, J1C-PAL crosslinked to DnaK in cells, confirming retention of canonical Hsp70-binding activity under proteotoxic stress. Chemoproteomic profiling revealed additional cellular targets, namely a conditionally essential mycobacterial protein, glutamine synthetase (GS). Biochemical assays demonstrated that J1C-PAL bound GS and inhibited its enzymatic activity. Cellular studies validated that J1C perturbed nitrogen metabolism mediated by GS in mycobacteria. Together, these findings establish J1C-PAL as a cell-permeable chemoproteomic tool for mapping protein targets and uncover a surprising link between a co-chaperone mimetic and bacterial metabolism.
    Keywords:  J‐domain proteins; chemoproteomics; glutamine synthetase; molecular chaperones; mycobacteria; proteomimetics
    DOI:  https://doi.org/10.1002/cbic.70504
  14. Methods Mol Biol. 2026 ;3047 189-199
    Assay for In-Vitro Arginine Methylation of RNA Binding Proteins Followed by RNA Binding.
    Sakshi Dewasthale, Gayatri Mohanan, Purusharth I Rajyaguru.
      Arginine methylation is a prevalent post-translational modification that plays a critical role in regulating the function of RNA-binding proteins [RBPs]. RBPs are the largest class of arginine methylated proteins. Catalyzed by protein arginine methyltransferases [PRMTs], this modification influences RNA recognition, binding affinity, and the formation of RNA-protein complexes. This impacts diverse cellular processes such as RNA splicing, transport, stability, and translation. Arginine methylation of RGG motifs modulates RBP behavior, with implications for normal physiology and disease states, including neurodegeneration, cancer, and immune disorders. In vitro methylation assays combined with RNA binding studies offer a powerful approach to elucidate how arginine methylation affects RNA-protein interactions. These techniques allow precise manipulation of methylation states and controlled assessment of binding dynamics, providing mechanistic insights into regulatory pathways. The protocols described in this chapter outline methods for recombinant protein expression, enzymatic methylation, and RNA binding assays, offering adaptable tools for researchers studying the functional consequences of arginine methylation in RNA biology. Together, these methodologies provide a framework to explore the interplay between post-translational modifications and RNA regulation, deepening our understanding of cellular processes.
    Keywords:  Arginine methylation; RGG-motif; RNA-binding; RNA-protein interaction
    DOI:  https://doi.org/10.1007/978-1-0716-5352-4_15
  15. Mol Biol Rep. 2026 Sep 04. pii: 1526. [Epub ahead of print]53(1):
    PTBP1 at the host-virus interface: mechanistic roles in viral RNA translation, replication, and immune modulation.
    Kajal, Achyut Pandey, Rajesh Yadav, Rishikesh Shukla, Shruti Mishra.
      Viruses require the involvement of host RNA binding proteins for completion of important steps of their life cycle. Polypyrimidine tract binding protein 1 (PTBP1) is an RNA-binding protein found ubiquitously which performs important regulatory functions like alternative splicing, RNA stability, RNA localization, and translation by virtue of its four RRMs and shuttling between nucleus and cytoplasm. There is increasing evidence showing that many viruses make use of such regulatory roles of PTBP1 to facilitate their gene expression and replication. This review describes the existing mechanistic knowledge about the PTBP1 functions during viral infection, paying attention to the role of PTBP1 in viral RNA translation, viral RNA genome replication, and regulation of host antiviral response. Special attention is paid to the regulation by PTBP1 of IRES-dependent translation of enteroviruses and hepatitis C virus, as well as to the PTBP1 contribution to RNA stabilization, long-distance RNA interactions, and genome cyclization of flaviviruses such as dengue virus and Japanese encephalitis virus. Recent data on the PTBP1 function in coronavirus RNA metabolism are discussed as well. Furthermore, the role of PTBP1 in being both proviral and antiviral is reviewed in terms of innate immunity signalling pathways, stress granule biology, and virus-host interaction. Finally, we will explore the possibility of PTBP1 being used as a host-directed antiviral drug target despite the hurdles in doing so considering its multifunctionality as an essential cellular RNA-binding protein.
    Keywords:  Alternative splicing; Broad-spectrum antivirals; Flaviviruses; Genome cyclization; HIV-1 replication; Host-directed antiviral therapy; IRES-mediated translation; PTBP1; Picornaviruses; RNA chaperone; RNA-binding protein; SARS-CoV-2; Viral RNA metabolism
    DOI:  https://doi.org/10.1007/s11033-026-12713-x
  16. Genome Res. 2026 Sep 01. 36(9): 1902-1920
    Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues.
    Simeiyun Liu, Andrew D Holmes, Ruoxia Zhao, Cassandra Herbert, Patrick A Limbach, Todd M Lowe, Upasna Sharma.
      Transfer RNAs (tRNAs) are central to protein synthesis and are increasingly recognized as dynamic regulators of gene expression whose abundance and chemical modifications are subject to precise biological control. Here, we systematically investigate how two distinct dietary interventions, low-protein and high-fat diets, reshape the tRNA landscape across multiple mouse tissues, using RNA mass spectrometry and ordered two-template relay sequencing (OTTR-seq) to comprehensively profile cytosolic and mitochondrial tRNAs at single-nucleotide resolution. We reveal pronounced tissue-specific biases in tRNA isodecoder expression, including the unexpected presence of full-length cytosolic tRNAs in mature sperm with a distinct isotype composition. In somatic tissues such as liver and heart, dietary conditions alter both tRNA abundance and key modifications known to regulate decoding efficiency, whereas in reproductive tissues diet primarily affects the abundance of select tRNAs with comparatively limited changes in modification profiles. We further demonstrate that mitochondrial tRNAs are subject to diet-responsive changes in both abundance and modification status and that even subtle differences in dietary fat composition are sufficient to alter tRNA modification signatures. Together, these findings establish the tRNA epitranscriptome as a sensitive and tissue-specific sensor of nutritional state and provide a resource for understanding how dietary cues interface with translational regulation in somatic and reproductive tissues.
    DOI:  https://doi.org/10.1101/gr.281159.125
  17. Nat Commun. 2026 08 04. pii: 9367. [Epub ahead of print]17(1):
    Translational control by RPL22L1-specific ribosomes enhances DNA repair and chemoresistance.
    Saisai Wei, Wentao Yu, Yilin Shen, Yu Qian, Ye Wang, Tiezheng Li, Jiaqi Cao, Xiangwei Gao, Xiujun Cai.
      Ribosome heterogeneity has emerged as a regulatory layer in gene expression, yet its biological roles in cancers remain poorly characterized. Here, we identify RPL22L1, a paralog of the ribosomal protein RPL22, as a key modulator of DNA damage response (DDR) in colorectal cancer cells. DNA damage induces RPL22L1 upregulation and ribosomal incorporation, forming RPL22L1-specific ribosomes. Ribosome profiling reveals that RPL22L1-containing ribosomes preferentially translate mRNAs with highly structured 5' untranslated region (5'UTR). In particular, RPL22L1 enhances the translation of ATRX through a cap-independent mechanism. ATRX subsequently recruits DNA-PKcs to DNA damage sites, thereby enhancing the DNA repair capacity. RPL22L1 loss creates exploitable DDR vulnerabilities, sensitizing cancer cells to cisplatin and PARP inhibitors in vitro and in vivo. Collectively, these findings uncover a specialized ribosome-mediated translational program in DDR and highlight RPL22L1 as a potential therapeutic target in DDR-based cancer therapy.
    DOI:  https://doi.org/10.1038/s41467-026-76283-z
  18. Mol Cell. 2026 Sep 03. pii: S1097-2765(26)00556-3. [Epub ahead of print]86(17): 3359-3361
    Hot and Sp(l)icy phosphatase: A potential thermosensor in mammals.
    Márton Szabó, Ritwick Sawarkar.
      Adaptation to thermal stress requires cells to interpret temperature changes in molecular terms to initiate biochemical responses. In this issue of Molecular Cell, Ueno et al.1 uncover a protein phosphorylation circuit as a potential thermosensor, linking stress to changes in global mRNA splicing.
    DOI:  https://doi.org/10.1016/j.molcel.2026.08.009
  19. Virulence. 2026 Dec;17(1): 2724626
    Activation of mTOR pathway by human cytomegalovirus promoting host ribosomal protein expression by coordinated transcriptional and translational controls.
    Yang Li, Zhongwei Zhao, Xiangjing Meng, Yujing Huang, Te Qi, Ying Qi, Zhongyang Liu, Qiang Ruan, Yanping Ma.
      Human cytomegalovirus (HCMV) profoundly reprograms host transcription and RNA metabolism, yet its impact on transcription start site (TSS) regulation of host genes remains poorly understood. Here, we employed NanoCap Analysis of Gene Expression sequencing (NanoCAGE-seq) to investigate HCMV-driven changes in alternative TSS usage across the host transcriptome. We identified widespread TSS switching, with ribosomal protein genes (RPGs) emerging as a highly enriched category. Alternative TSS usage produced isoforms with distinct 5'untranslated regions (UTRs), thereby altering cis-regulatory elements that shape translational efficiency. Integrative transcriptomic and proteomic analyses revealed a paradoxical accumulation of RPG proteins despite transcriptional downregulation during infection. Using 5' Rapid Amplification of cDNA Ends (5'RACE), we characterized four RPGs of RPL4, RPS11, RPS23, and RPS24 that generated 5'UTR variants through alternative TSS usage. Notably, isoforms containing a 5'terminal oligopyrimidine (5'TOP) motif were significantly enriched, correlating with mTOR activation induced by HCMV. Functional assays with bicistronic reporter constructs in HEK293 cells and infection models in human embryonic lung fibroblasts demonstrated that the RPL4 5'TOP isoform exhibited enhanced mTORC1-driven translation compared with non-5'TOP counterparts. Importantly, RPL4 upregulation facilitated viral protein synthesis and boosted production of infectious virions. Together, our findings reveal that dynamic TSS switching of RPGs provides a simple, yet effective, mechanism for fine-tuning mTORC1-responsive translation. By co-opting host transcriptional and translational programs, HCMV enhances ribosome function to optimize the cellular environment for productive viral replication.
    Keywords:  Human cytomegalovirus; RPGs; TSS switching; mTOR; transcription regulation; translational regulation
    DOI:  https://doi.org/10.1080/21505594.2026.2724626
  20. Nat Commun. 2026 07 30. pii: 9255. [Epub ahead of print]17(1):
    The m⁶A reader YTHDF2 regulates mRNA transport and axon outgrowth in developing neurons.
    Bonsang Koo, Ajeet Kumar, Huiseon Hwang, Minyeong Park, Sung-Min Lee, Sung Ho Boo, Ki-Heon Lee, Ji-Hoon Moon, Jaewon Yang, Chan-Woo Park, Saebom Lee, Hee-Jung Jo, Woo-Il Kim, Eunji Cho, Hagyeong Lee, Chang-Won Lee, Jae-Sung Woo, Jong Hyuk Yoon, Yoon Ki Kim, Ki-Jun Yoon.
      Proper nervous system development is critical for brain function, and deficits in neural development are implicated in many brain disorders. Neurons are distinctly polarized cells where mRNA can be transported to distal structures like axons and dendrites. Recent discoveries of widespread mRNA chemical modifications raise the question of their post-transcriptional regulatory role in brain development and function. N6-methyladenosine (m6A), installed by the METTL3/METTL14 methyltransferase complex, is the most prevalent internal mRNA modification, influencing stability, translation, splicing, and localization. However, the impact of m6A modification on RNA transport in developing neurons is not well understood. In this study, we find that the ablation of Mettl14 in postmitotic neurons leads to impaired axonal projection during corticogenesis. RNA-seq and single-molecule in situ hybridization reveal mislocalization of mRNAs in neurites of neurons with m6A loss-of-function. Furthermore, m6A-SAC-seq to identify a single nucleotide resolution m6A maps in the perinatal brain uncovers m6A-tagged transcripts associated with synapse organization, mRNA processing, and axonogenesis. We also identify YTHDF2 as the reader protein responsible for mRNA transport in callosal projection axons. YTHDF2 interacts with motor proteins, translational regulators, and microtubules to facilitate distal transport of m6A-tagged mRNA. Our data suggest that FMRP may serve as a context-guiding interactor that reshapes the YTHDF2 complex by recruiting specific cofactors and motor proteins, thereby promoting transport rather than degradation of m⁶A-tagged transcripts. Together, these findings provide insight into the epitranscriptomic mechanisms governing axon projection and guidance during mammalian cortical neurogenesis.
    DOI:  https://doi.org/10.1038/s41467-026-76161-8
  21. Nat Commun. 2026 Aug 06. pii: 9475. [Epub ahead of print]17(1):
    Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.
    Cristina Gutierrez-Vargas, Lee S Izhaki-Tavor, Diana G Calvopina-Chavez, Caroline D Keroack, Pablo Copello, Manoj T Duraisingh, Mélissa Léger-Abraham.
      Babesia are tick-borne intracellular apicomplexan parasites that infect a wide range of wild and domestic animals (e.g., cattle), resulting in significant economic losses to the livestock industry. Humans are considered accidental hosts for a few Babesia species. Babesia microti and B. divergens are the most prevalent causes of human babesiosis that are showing a broadening geographic distribution. Due to the complex life cycle of Babesia species, their survival depends on the precise control of gene expression, which is primarily regulated by epigenetic, transcriptional, and post-transcriptional mechanisms. High-resolution structural information on key components of the translation machinery, such as ribosomes, could aid in the development of antiparasitic drugs. Here, we report cryogenic electron microscopy ribosome structures from B. divergens, showing associated tRNAs, an mRNA fragment, and RACK1, a signaling scaffold crucial to translation regulation. Density map analysis displays ribosome regions at high resolution, which, when combined with nanopore sequencing, enabled the comprehensive identification of rRNA modifications. The rRNA modifications localize not only to the reduced B. divergens rRNA expansion segments but also to functionally essential ribosomal sites.
    DOI:  https://doi.org/10.1038/s41467-026-75282-4
  22. Methods Mol Biol. 2026 ;3047 15-27
    Complementary Approaches for Accurate Detection of tRNA-Derived Small RNAs (tsRNAs): Small RNA Northern Blotting and Dumbbell PCR.
    Chankyung Kim, Mark A Kay, Hak Kyun Kim.
      tRNA-derived small RNAs (tsRNAs) are generated by specific cleavage of transfer RNAs that are essential for delivering amino acids during protein synthesis. They have emerged as important regulators of gene expression across diverse biological contexts and have been implicated in multiple diseases, including cancers and neurological disorders. Advances in next-generation sequencing (NGS) have enabled high-throughput profiling of tsRNA abundance; however, extensive base modifications and heterogeneous termini frequently lead to inaccurate outcomes in small RNA sequencing. These technical limitations highlight the need for reliable validation strategies. Here, we present two complementary methods for tsRNA validation: small RNA northern blotting, which allows direct visualization of RNA size and abundance, and dumbbell PCR, which enables isoform-specific quantification with single-nucleotide resolution. Together, these approaches provide robust tools to validate tsRNA expression and facilitate mechanistic studies of their biological functions.
    Keywords:  Dumbbell PCR (Db-PCR); Real-time PCR; Small RNA northern blot; tRNA-derived small RNAs (tsRNA)
    DOI:  https://doi.org/10.1007/978-1-0716-5352-4_2
  23. Methods Mol Biol. 2026 ;3051 89-100
    A Dual-Color Electrophoretic Mobility Shift Assay to Examine RNA-Binding and RNA Chaperone Activity Simultaneously.
    Tobias Schmidt.
      RNA-binding proteins that rearrange RNA structure often undergo complicated reaction pathways including multivalent interactions with itself and the RNA substrates. For detailed mechanistic understanding of these reactions, it is essential to get insight into the individual complexes formed during the reaction that can guide answering questions regarding sequence or stoichiometry of the reaction. Meanwhile high-resolution structural approaches allow discrimination of multiple conformations and complexes in a heterogeneous sample; however, these approaches are cost- and time-intensive and require extensive technical experience. Traditional electrophoretic mobility shift assays are cheap and require no specialized equipment, and can give valuable insight into reaction pathways resolving both RNA-RNA and protein-RNA interactions.In this chapter, I present an adaptation of a gel electrophoretic mobility shift assay using individually fluorescently labelled RNAs in a discontinuous gel system that can resolve protein-RNA and RNA-RNA complexes from a single reaction in the same gel. The method is applied and discussed based on the example of the RNA-unwinding activity of the RNA helicase eIF4A1 including a small molecule eIF4A1-modulator silvestrol. The example demonstrates the capacity of the assay to provide detailed mechanistic insight into rearrangement of RNA structure and protein-RNA interactions.
    Keywords:  Annealing; RNA chaperone; RNA folding; Strand displacement
    DOI:  https://doi.org/10.1007/978-1-0716-5372-2_5
  24. J Proteome Res. 2026 Sep 04. 25(9): 4380-4392
    Proteins as Regulators of Metabolic Changes in Sepsis: Alterations in Body Fluids, Immune Cells, and Organs through the Eyes of Proteomics.
    Giuseppe G F Leite, Felipe Dal-Pizzol, Tom van der Poll, Reinaldo Salomão.
      Sepsis is a life-threatening syndrome characterized by a dysregulated host response to infection and profound metabolic alterations that contribute to immune dysfunction and organ failure. This Review synthesizes proteomic evidence on sepsis-associated alterations in proteins involved in metabolic pathways across circulating biofluids, immune cells, and organs. Across plasma and urine, proteomic studies identify disturbances in lipoprotein-associated pathways, redox homeostasis, mitochondrial function, and substrate metabolism, indicating that protein signatures of metabolic dysregulation are systemic and detectable across biofluids. In immune cells, monocytes and neutrophils, proteomic analyses reveal a shift toward glycolysis with concurrent impairment of mitochondrial pathways alongside phenotype-dependent differences in lipid and redox-related programs. Organ-level studies further show that metabolic responses are heterogeneous, with distinct trajectories in the kidney, heart, liver, lung, skeletal muscle, and brain. These observations support the concept that sepsis involves compartment-specific remodeling of metabolism-associated protein networks rather than a single convergent metabolic state. Proteomics also highlights potential translational opportunities by identifying metabolism-associated proteins linked to disease severity, clinical phenotypes, and biologically distinct patient subgroups, although the current evidence remains largely exploratory and context-dependent. Overall, proteomics provides a complementary framework for understanding the molecular regulation of sepsis-associated metabolic dysfunction and may refine biological stratification and therapeutic targeting, particularly when integrated with longitudinal sampling and multiomic data.
    Keywords:  immunometabolism; lipoproteins; mitochondria and biomarkers
    DOI:  https://doi.org/10.1021/acs.jproteome.6c00386
  25. Biochim Biophys Acta Mol Basis Dis. 2026 Sep 01. pii: S0925-4439(26)00312-1. [Epub ahead of print]1873(1): 168446
    Reciprocal regulation of m6A RNA methylation and protein post-translational modifications: implications for disease pathogenesis and therapy.
    Xinyi Li, Liting Yang, Xianmin Zhou, Gongxing Chen, Shuiping Liu.
      N6-methyladenosine (m6A) is a prevalent epitranscriptional modification in RNA that is crucial for RNA metabolism and biogenesis. Accumulating evidence reveals a complex interplay between m6A and protein post-translational modifications (PTMs)-covalent additions of chemical groups or structural alterations to nascent proteins during or after biosynthesis. This crosstalk involves in disease development and drug response by altering protein properties and functions. However, comprehensive discussion about the roles and mechanisms of m6A and PTMs crosstalk is limited. Here, we present an up-to-date review of this emerging and complex interplay in disease and therapeutic response. We first summarize the crosstalk between m6A and PTMs such as ubiquitination, lactylation, acetylation, phosphorylation, and methylation, organizing our discussion around the three major regulatory factors m6A writers, erasers, and readers. Next, we explore the mechanism of m6A-PTMs crosstalk involved in the pathogenesis and development of diseases, including various cancers, metabolic disorders, and inflammatory diseases. Moreover, we discuss the role of m6A-PTMs crosstalk in drug response, focusing on chemotherapy drugs. In summary, this review provides a framework for understanding the regulatory networks of m6A-PTMs crosstalk in disease pathogenesis, development, and therapeutic response, highlighting potential treatment strategies based on this interplay and suggesting future research directions.
    Keywords:  Crosstalk; Inflammatory responses; Metabolic diseases; Protein post-translational modifications; Tumors; m(6)A
    DOI:  https://doi.org/10.1016/j.bbadis.2026.168446
  26. Adv Biol (Weinh). 2026 Sep;10(9): e70154
    How Epitranscriptomic Machinery Senses Environmental Cues.
    Shayan Jalali, Ehsan Pashay Ahi.
      Environmental fluctuations remodel RNA modification landscapes, yet the routes that connect cue detection to writer-eraser-reader control remain dispersed across disciplines. Here, we consolidate upstream mechanisms capable of driving epitranscriptomic change and organize them by response speed. At the fastest proximal level, catalytic output can be modulated through shifts in substrate and cofactor availability, redox and ionic state, temperature, and direct chemical or metal interference with enzyme active sites, although transcriptome-wide RNA readouts may appear later. Over minutes to hours, cue-responsive signaling can reach the machinery through post-translational modification, partner switching, subcellular trafficking, and stress-induced condensates that may gate access to modified transcripts. Across hours to days, regulator abundance and specificity are reshaped by transcriptional programs, translational control, and protein quality-control pathways, enabling adaptation and, in some contexts, persistence. We propose a kinetics-to-sensors approach for interpreting time-resolved epitranscriptomic datasets and prioritizing perturbations that discriminate among candidate upstream inputs. We also outline conceptual gaps and experimental practices needed to establish causal cue-to-mark chains.
    Keywords:  RNA modifications; environmental cues; epitranscriptomics; metabolic coupling; post‐translational modifications; signal‐dependent regulation
    DOI:  https://doi.org/10.1002/adbi.70154
  27. Amino Acids. 2026 Aug 26. pii: 47. [Epub ahead of print]58(1):
    Spermidine in Colorectal cancer: friend or foe?
    Sonia Coni, Rosa Bordone, Luca Campea, Shohei Ohno, Gianluca Canettieri, Enzo Agostinelli.
      Colorectal cancer (CRC) is a leading cause of cancer-related mortality, and its incidence is rising among individuals, especially young, underscoring the need for novel therapeutic strategies. CRC development is driven by genetic and epigenetic alterations in key oncogenic pathways and is accompanied by profound reprogramming of polyamine metabolism. In this context, spermidine (SPD), a central polyamine produced downstream of the MYC-ODC axis, is regarded as a pro-tumorigenic metabolite that sustains CRC growth by fueling eIF5A hypusination and MYC translation, thereby establishing a feed-forward MYC-ODC-polyamine-eIF5A circuit that promotes tumorigenesis. Recent studies also show that combined inhibition of polyamine biosynthesis and eIF5A hypusination synergistically impairs MYC translation and suppresses CRC growth in preclinical models, outperforming single-agent strategies such as ornithine decarboxylase (ODC) blockade with difluoromethylornithine (DFMO) and highlighting the translational potential of dual targeting of this axis. Conversely, other lines of evidence indicate that excessive SPD or altered flux through the polyamine pathway can be cytotoxic: multiple reports demonstrate that high-dose SPD triggers apoptosis, while experimental models suggest that SPD and epithelial eIF5A hypusination can protect against colitis and colitis-associated cancer by supporting the translation of detoxifying enzymes. Overall, the literature points to a dual role of SPD, and the aim of this review is to dissect the functions of SPD in CRC, to summarize and critically discuss the potential benefits of this polyamine, and to evaluate how it might be rationally exploited as a therapeutic agent in cancer.
    Keywords:  Colorectal cancer; Polyamines; Spermidine
    DOI:  https://doi.org/10.1007/s00726-026-03554-w
  28. J Pharmacol Exp Ther. 2026 Aug 03. pii: S0022-3565(26)01201-2. [Epub ahead of print]393(9): 105001
    Repurposing ribavirin for oncology: Integrating metabolism, signaling, and translational control.
    Amrita Talukder Mohini, Chibuike Emmanuel Okafor, Joseph M Schober, Bhargav A Patel.
      Repurposing of approved drugs offers a rapid and cost-effective strategy for the identification of new therapeutic applications, particularly for difficult-to-treat and therapy-resistant cancers. Ribavirin, which is a synthetic guanosine analog and used as an antiviral drug, has demonstrated promising anticancer activity. To that end, the literature has presented varied anticancer mechanisms of action for ribavirin. This review integrates the current mechanistic evidence and proposes a working hypothesis in which ribavirin may influence interconnected metabolic, signaling, and translational processes that collectively induce its anticancer activity. Ribavirin inhibits inosine monophosphate dehydrogenase and depletes GTP, which may influence small GTPase-dependent signaling such as Ras-driven pathways. More recently, modulation of metabolic signaling by ribavirin has been proposed through the inhibition of AMP-activated protein kinase-associated pathways. These upstream perturbations may propagate through oncogenic signaling networks and complement the suppression of eukaryotic translation initiation factor 4E-dependent mRNA export and protein synthesis. Further, ribavirin treatment indirectly influences epigenetic regulators, inflammatory mediators, and immune checkpoint pathways, contributing to broader reprogramming of tumor cell behavior. Ultimately, ribavirin's effects lead to cell cycle arrest, apoptosis, and enhanced chemosensitivity across diverse cancer types. Taken together, the available evidence supports the hypothesis that ribavirin may function as a multilevel modulator of cellular growth networks, although the mechanistic relationships among these pathways remain incompletely defined. SIGNIFICANCE STATEMENT: This review theorizes ribavirin as a systems-level anticancer agent by integrating its effects on guanine nucleotide metabolism, oncogenic signaling, and eukaryotic translation initiation factor 4E-dependent translation into a unified metabolic-signaling-translation axis. In addition, it identifies the disparities in the mechanistic literature, which may assist in designing future studies.
    Keywords:  AMP-activated protein kinase; Drug repurposing; Eukaryotic translation initiation factor 4E; Inosine monophosphate dehydrogenase; Ribavirin; Translational reprogramming
    DOI:  https://doi.org/10.1016/j.jpet.2026.105001
  29. Nucleic Acids Res. 2026 Aug 24. pii: gkag859. [Epub ahead of print]54(16):
    Guanosine 10 methylation by TRMT11-TRMT112 optimizes human mitochondrial tRNAs for efficient translation.
    Jonny Petrosyan, Mehmet Yilmaz, Carolin P M Scheitl, Nicolas Lemus-Diaz, Angela Boshnakovska, Laurianne L E Tay, Wanwan Hu, Olga Beine-Golovchuk, David Touboul, Ricarda Richter-Dennerlein, Claudia Höbartner, Marc Graille, Peter Rehling, Katherine E Bohnsack.
      Modified nucleotides are essential determinants of RNA function, and identifying the enzymes that install them is fundamental to understanding their cellular roles. Here, we show that the human RNA methyltransferase TRMT11 and its cofactor TRMT112 are imported into mitochondria via N-terminal targeting signals. Using a recently developed N2-methylguanosine (m2G)-sensitive DNAzyme, we demonstrate that TRMT11 catalytic activity and interaction with TRMT112 are required for installation of m2G at position 10 in 13 mitochondrial (mt-)tRNAs. The crosslinking profile of TRMT11 on mt-tRNAs experimentally supports a model of the TRMT11-TRMT112-mt-tRNATrp complex in which the THUMP domain contacts the 3' end of the acceptor stem, and G10 is flipped into the S-adenosylmethionine binding pocket for methylation. Transcriptome-wide mapping reveals that TRMT11 interacts with most nuclear-encoded and mt-tRNAs, but only methylates a subset. In vitro reconstitution of TRMT11-TRM112-mediated methylation defines key structural requirements for m2G10 installation across different mt-tRNAs, and reveals how pathogenic mutations influence this modification. TRMT11-TRMT112 recognizes folded mt-tRNAs, and in the degenerate mt-tRNALys, m1A9 strongly enhances m2G10 methylation efficiency. Loss of m2G10 modifications alters the conformation of numerous mt-tRNAs, perturbs mitochondrial protein synthesis, and impairs oxidative phosphorylation, highlighting an essential role of this modification in maintaining mitochondrial function.
    DOI:  https://doi.org/10.1093/nar/gkag859
  30. Methods Mol Biol. 2026 ;3051 301-313
    Isolation and Analysis of Bacterial Ribosomes Through Sucrose Gradient Ultracentrifugation.
    Ricardo F Dos Santos, Cátia Bárria, Alda F Q Silva, João P Sousa, Cecília M Arraiano, José M Andrade.
      Ribosomes are large macromolecular complexes responsible for the translation process. During the course of ribosome biogenesis and protein synthesis, extra-ribosomal factors interact with the ribosome or its subunits to assist in these vital processes. Here we describe a method to isolate and analyze not only bacterial ribosomes but also their associated factors, providing insights into translation regulation. This detailed protocol allows the separation and monitoring of the ribosomal species and their interacting partners along a sucrose density gradient. Simultaneously, fractionation of the gradient allows for the recovery of 70S ribosomes and its subunits enabling a wide range of downstream applications. This protocol can be easily adapted to ribosome-related studies in other species or for separating other macromolecular complexes.
    Keywords:  Ribosome isolation; Ribosome profiles; Ribosomes; Sucrose gradient; UV analysis; Ultracentrifugation
    DOI:  https://doi.org/10.1007/978-1-0716-5372-2_18
  31. PLoS Genet. 2026 Sep;22(9): e1012279
    Post-transcriptional regulation of Profilin-2 by microRNAs and RNA-binding proteins forms a critical regulatory node for early embryonic cell fate decisions.
    Carolyn Sangokoya, Isabella R Rosso, Rana Ghandehari-Alavijeh, Robert Blelloch.
      Post-transcriptional control by RNA binding proteins (RBPs) and microRNAs play central roles in mRNA stability and translation, yet how RBPs and microRNAs coordinate in developmental time to regulate cell fate remains poorly understood. Here, we demonstrate that post-transcriptional regulation of the Profilin 2 (Pfn2) transcript is essential for differentiation of embryonic stem cells (ESCs) into the primary germ layer lineages. The Pfn2 3'untranslated region has both an Iron Regulatory Protein binding site (IRE) and a nearby binding site for ESC enriched microRNAs. Deletion of this microRNA site leads to increased PFN2 and reduced FGF signaling during pluripotency transition prior to germ layer formation. In contrast, deletion of the IRE leads to decreased PFN2, a Wnt signaling defect, reduced nuclear beta-catenin, and a subsequent block in mesendodermal lineages during early germ layer formation. We further find that loss of the IRE site results in a cell autonomous defect in Wnt signaling and mesendodermal differentiation. The IRE site acts to stabilize beta-catenin, as disruption of the site leads to reduced nuclear beta-catenin levels. Together, these findings reveal the Pfn2 microRNA-IRE regulatory axis as a critical post-transcriptional regulatory node governing the switch from pluripotency to somatic differentiation.
    DOI:  https://doi.org/10.1371/journal.pgen.1012279
  32. Transl Neurodegener. 2026 Aug 31. pii: 43. [Epub ahead of print]15(1):
    Phase separation in neurodegenerative disorders: a metabolic perspective on protein aggregation and therapeutic targeting.
    Shujun Peng, Hui Chen, Guowei Yin, Alexei Verkhratsky, Chenju Yi.
      Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are increasingly recognised as dynamic organisers of intracellular biochemistry, particularly in neurons where spatially restricted signalling, RNA metabolism, and proteostasis are essential. Aberrant phase transitions of disease-associated proteins, including TDP-43, FUS, tau, and α-synuclein, contribute to protein aggregation and neurodegenerative pathology. Beyond protein-intrinsic sequence features, metabolic state has emerged as an important contextual regulator of condensate assembly, material properties, and liquid-to-solid maturation. Metabolic cues, including ATP availability, NAD+/NADH balance, redox state, lipid composition, enzyme-mediated post-translational modifications, and cellular stress responses, can influence the phase behaviour across biochemical, cellular, and disease-model systems. However, direct causal evidence in neurons, animal models, and human neurodegenerative diseases remains uneven and protein-specific. Here, we review LLPS in neurodegenerative disorders from the metabolic perspective, distinguishing established mechanisms from plausible but incompletely validated links. We discuss how pathological condensates may impair RNA metabolism, synaptic function, proteostasis, and cognition, and critically evaluate emerging therapeutic strategies that aim to modulate aberrant phase behaviour. This review therefore provides a cautious framework in which metabolic dysregulation is considered a potential upstream contributor to pathological phase transitions rather than an established master regulator.
    Keywords:  Cognition; Metabolic enzymes; Neurodegenerative diseases; Pathological protein aggregation; Phase separation
    DOI:  https://doi.org/10.1186/s40035-026-00575-z
  33. Methods Mol Biol. 2026 ;3051 43-56
    Characterization of RNA Structure Dynamics with Trans-Factors Using Single-Molecule Optical Tweezers.
    Alexandria Smart, Neva Caliskan.
      RNA folding is a dynamic process that is essential and has a regulatory function in many cellular processes. Additionally, RNA structure and function can be modulated by the binding of trans-acting factors such as translation machinery, RNA-binding proteins, small molecules, or other RNAs. These mechanisms, which add layers of regulation, can exist in many different states that can be difficult to resolve in ensemble methods alone. For this reason, single-molecule methods to monitor RNA folding dynamics in the presence of regulatory factors are crucial in identifying subpopulations, transient intermediates, and understanding the underlying mechanisms of RNA structure, function, and regulation. In this chapter, we describe methods for RNA structure analysis using single-molecule optical tweezers (OTs). This technique can be widely applied to explore diverse RNA-protein complexes or trans-acting factors regulating RNA-folding pathways or chaperones as they undergo phase separation under changing conditions.
    Keywords:  Optical tweezers; RNA folding—trans-factor regulation; RNA structure; Single-molecule
    DOI:  https://doi.org/10.1007/978-1-0716-5372-2_3
  34. Autoimmunity. 2026 Dec 31. 59(1): 2724058
    The m6A reader IGF2BP2 promotes proinflammatory signaling in Lupus nephritis by recognizing STAT1 m6A modifications.
    ChangZhi Zheng, XianMei Xu, Di Wu, Run Cheng, YouWei Bai, DeGuang Wang.
      Characterized by renal inflammation and structural damage, lupus nephritis (LN) is a severe and often debilitating complication of systemic lupus erythematosus. The dynamic regulation of RNA processing, stability, and translation by N6-methyladenosine (m6A) modification has been implicated in the pathophysiology of LN. As an m6A reader, insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) plays a crucial role in the pathogenesis of various kidney diseases, yet its precise function in LN remains unclear. IGF2BP2 expression was measured in kidney specimens from LN patients and MRL/LPR mice. MRL/lpr mice were administered IGF2BP2 short hairpin RNA adeno-associated viral vectors, followed by evaluation of proteinuria, renal function, and histology. In vitro experiments employed lipopolysaccharide (LPS) stimulation of human kidney tubular epithelial cells (HK-2) to simulate LN inflammatory responses and further investigated the mechanism of IGF2BP2. Molecular interactions were validated via RNA immunoprecipitation and luciferase reporter assays. IGF2BP2 expression is significantly upregulated in LN and positively correlated with proinflammatory factor levels. Knockdown of IGF2BP2 significantly improved renal injury and alleviated renal inflammatory responses in MRL/LPR mice, as well as reduced LPS-induced inflammatory responses in HK-2 cells. Mechanistically, under LN pathological conditions, IGF2BP2 recognized m6A modifications on signal transducer and activator of transcription 1 (STAT1) mRNA and enhanced its stability, leading to the activation of proinflammatory signaling, exacerbation of renal inflammation, and ultimately renal injury. The m6A reader IGF2BP2 promotes proinflammatory signaling in LN by recognizing m6A-modified STAT1 mRNA. Targeting the IGF2BP2-STAT1 axis may represent a potential therapeutic strategy to ameliorate renal inflammatory responses in LN.
    Keywords:  IGF2BP2; Lupus nephritis; STAT1; inflammatory response; m6A
    DOI:  https://doi.org/10.1080/08916934.2026.2724058
  35. Elife. 2026 Sep 03. pii: RP110114. [Epub ahead of print]15
    In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles.
    Zahra Seraj, Ximena Zottig, ChunYing Huang, Anna B Loveland, Stephen Diggs, Emily Sholi, Nikolaus Grigorieff, Andrei A Korostelev.
      Cryogenic electron microscopy (cryo-EM) made impressive progress in resolving cellular macromolecules and their detailed interactions. Single-particle cryo-EM traditionally relies on purified macromolecules and lacks the complexity of cellular environments, whereas in situ cryo-EM and cryogenic electron tomography (cryo-ET) require extensive sample preparation and data acquisition, presenting challenges in achieving high resolution. We describe cryo-EM of cellular lysates-in extracto cryo-EM-allowing the flexibility and high-resolution of cryo-EM in the context of cellular components. High-resolution 2D template matching (2DTM) yields ~2.2 Å maps of the mammalian translational apparatus. Elongating ribosome abundances in primate cell lines (MCF-7 and BSC-1) and rabbit reticulocyte lysates range from ~70% to ~10%, reflecting translational stress responses. Non-translating (hibernating) ribosomes carrying no mRNA feature numerous proteins shielding ribosomal functional centers. Elongation factor 2 (eEF2) is the most abundant hibernation factor bound to >95% of 80S ribosomes and, unexpectedly, to 60S subunits. eEF2•GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature La-related protein 1 (LARP1) involved in initiation and mTOR signaling, eIF5A implicated in elongation and termination, and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of in extracto cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution.
    Keywords:  H. sapiens; Oryctolagus cuniculus; RRL; human; mammalian; molecular biophysics; rabbit; structural biology
    DOI:  https://doi.org/10.7554/eLife.110114
  36. Methods Mol Biol. 2026 ;3051 27-42
    Analysis of tRNA Aminoacylation by Northern Blotting and Multiplex Small RNA-Seq.
    Jennifer Porat, Christopher P Watkins, Mark A Bayfield.
      Measuring RNA folding is particularly challenging for tRNAs, where extensive structure and posttranscriptional modifications complicate traditional structure probing and reverse-transcriptase-based assays. Since tRNA folding is a prerequisite for aminoacylation, quantifying tRNA aminoacylation is often used as an indirect, though functionally relevant, measure of tRNA folding. Periodate oxidation and beta-elimination, resulting in the selective loss of the 3' terminal nucleotide of deacylated tRNAs, is an amino-acid-agnostic chemistry that enables differentiation of aminoacylated and deacylated tRNAs when coupled to high-resolution northern blotting or RNA sequencing. Quantification of tRNA aminoacylation has been used to demonstrate RNA chaperone activity for RNA-binding proteins that promote tRNA folding to increase the fraction of aminoacylated tRNAs, underscoring the utility of this assay in interrogating RNA chaperone-assisted tRNA folding and function.
    Keywords:  Aminoacylation; Northern blotting; Small RNA sequencing; tRNA
    DOI:  https://doi.org/10.1007/978-1-0716-5372-2_2
  37. J Transl Med. 2026 Aug 22. pii: 1139. [Epub ahead of print]24(1):
    FMRP promotes gastric cancer progression via m6A-dependent stabilization of DVL2 and activation of the Wnt/PCP-JNK pathway.
    Xiaoyu Hou, Jinlan Gao, Xuesha Xing, Qi Liu, Ming Yi, Chen Liu, Qi Chu, Mengdie Zou, Meirong Hu, Yang Luo.
       BACKGROUND: N6-methyladenosine (m6A) modification has emerged as a critical regulator in gastric cancer progression. Fragile X messenger ribonucleoprotein 1 (FMRP), an RNA-binding protein with tumorigenic potential, remains poorly characterized in gastric cancer.
    METHODS: FMRP expression in gastric cancer was assessed through bioinformatic analyses and tissue microarray-based immunohistochemistry. Its biological functions were examined through loss-of-function experiments in vitro and in vivo. Mechanistic investigations, including RNA interaction, m6A site mutation, and RNA stability analyses, were performed to identify downstream targets and pathways regulated by FMRP.
    RESULTS: Bioinformatic analyses and tissue microarray-based immunohistochemistry showed that FMRP was significantly upregulated in gastric cancer tissues. FMRP depletion suppressed tumor growth and metastasis. Subsequently, Dishevelled segment polarity protein 2 (DVL2) was identified as a candidate downstream target of FMRP. DVL2 was also significantly upregulated in gastric cancer tissues, and its expression positively correlated with FMRP expression. Mechanistically, FMRP bound to DVL2 mRNA and enhanced its stability in an m6A-dependent manner. Among the candidate sites tested, mutation of 1271A attenuated FMRP-mediated regulation of DVL2 reporter activity, supporting the involvement of this site. Functionally, FMRP promoted activation of the noncanonical Wnt/planar cell polarity (PCP) signaling pathway and enhanced the proliferative, migratory, and invasive capacities of gastric cancer cells via DVL2.
    CONCLUSIONS: These results define FMRP as an oncogenic driver in gastric cancer that operates via the DVL2/Wnt/PCP axis. Targeting this pathway may provide a potential therapeutic strategy for gastric cancer.
    Keywords:  DVL2; FMRP; Gastric cancer; Wnt/PCP-JNK pathway; m6A
    DOI:  https://doi.org/10.1186/s12967-026-08834-3
  38. J Chem Inf Model. 2026 Aug 24. 66(16): 10396-10411
    Deep3MVPF: Multiview Deep Framework for the Prediction of Stability and m6A in mRNA 3'UTR.
    Junyi Liu, Qi Zhang, Jiangning Song, Dong-Jun Yu.
      Accurate prediction of mRNA stability and identification of N6-methyladenosine (m6A) sites are central to understanding post-transcriptional regulation. Because the 3' untranslated region (3'UTR) contains both stability-associated cis-elements and many m6A sites, it provides a suitable context for modeling RNA regulatory effects. However, most existing methods rely primarily on linear sequence information and do not adequately capture higher-order topology or RNA structural context. Here, we present Deep3MVPF, a multiview deep learning framework for 3'UTR stability prediction and m6A site identification. Deep3MVPF integrates a multiscale convolutional neural network, a k-mer de Bruijn graph neural network, and a secondary-structure graph neural network to jointly model sequence, topological, and structural representations. For 3'UTR stability prediction, the model was trained and evaluated on a zebrafish (Danio rerio) mRNA degradation data set and achieved an MSE of 0.0049. For m6A site identification, it was evaluated on nine human cell line data sets and achieved an average AUC of 0.970. Attribution analysis further showed that Deep3MVPF recovered regulatory features consistent with known biology, including the destabilizing GCACUU motif and stabilizing G-rich/G-quadruplex-associated signals. These results demonstrate that integrating heterogeneous RNA representations can improve predictive modeling and facilitate interpretation of post-transcriptional regulatory grammar.
    DOI:  https://doi.org/10.1021/acs.jcim.6c01345
  39. Front Endocrinol (Lausanne). 2026 ;17 1855305
    The integrated stress response in pancreatic β-cell failure in diabetes: from molecular mechanisms to precision therapeutics.
    Yijun Huang, Yu Zeng, Xinying Zhong, Lin Li.
      Diabetes mellitus is a global metabolic disorder characterized by progressive pancreatic β-cell failure, which leads to inadequate insulin secretion, often in combination with insulin resistance, and ultimately disrupts glucose homeostasis. The Integrated Stress Response (ISR), a crucial signaling network that enables cells to maintain homeostasis under endogenous and exogenous pressures, has garnered increasing attention for its role in regulating islet β-cell function and contributing to their failure. In recent years, a growing body of evidence has revealed that the ISR acts as a dual-edged sword in the onset and progression of diabetes. On the one hand, ISR activation can transiently relieve biosynthetic stress and help preserve cellular homeostasis. On the other hand, persistent or dysregulated ISR signaling is increasingly associated with impaired insulin production, loss of β-cell identity, and cell death in diabetes. In this Review, we summarize the molecular architecture of the ISR, focus on its regulatory role in pancreatic β-cell stress biology, and examine how ISR-related pathways are engaged in monogenic diabetes, type 1 diabetes, and type 2 diabetes. We further evaluate current therapeutic strategies targeting ISR-associated pathways and highlight the central translational challenge in this field, aiming to provide a theoretical basis and novel insights for a deeper understanding of the molecular mechanisms driving diabetic β-cell failure and for the development of novel precision therapeutic approaches.
    Keywords:  diabetes mellitus; eIF2α phosphorylation; endoplasmic reticulum stress; integrated stress response (ISR); pancreatic β-cells
    DOI:  https://doi.org/10.3389/fendo.2026.1855305
  40. Mol Cell Proteomics. 2026 Sep 01. pii: S1535-9476(26)00149-0. [Epub ahead of print] 101653
    Micro- and macro- heterogeneity of N-glycoproteome remodeling in endoplasmic reticulum stress.
    Alexander Black, Tiffany Ngo, Boomathi Pandi, Andrew Mongin, Dominic C M Ng, Edward Lau, Maggie P Y Lam.
      N-glycosylation plays essential roles in the folding, trafficking, and maturation of proteins in the secretory pathways, but how individual protein- and site- specific glycosylation rewires under endoplasmic reticulum (ER) stress is unknown. Particularly, intact glycopeptide data that retain the connectivity between glycosylation sites and the attached glycans are needed to reveal the micro- and macro- heterogeneity of N-glycosylation sites and their permutations in stressed cells. Here, we developed and optimized a magnetic polyethyleneimine boronic acid-containing scaffold (mPBA) enrichment workflow to achieve sensitive and broad enrichment of intact glycopeptides for mass spectrometry analysis, requiring only 0.1 to 0.5 mg total peptide input. With this method, we performed a large intact glycopeptide comparative study, systematically analyzing 13,759 unique protein-, site-, and glycoform combinations, termed glycopeptidoforms, in normal and stressed human cells. The data reveals a dynamic rewiring of N-glycosylation involving hundreds of proteins with complex protein-, site-, and glycan- specific granularity. The magnitude of differential glycosylation far exceeds that of protein expression changes. Individual glycoform reconfigurations can be observed that indicate likely disruptions within specific steps in protein maturation and trafficking. Mannose trimming emerges as a shared disruption across multiple proteins, suggesting a processing bottleneck of the ER stress glycoproteome. Together, these results reveal molecular details into the remodeling of protein secretory pathways upon ER stress and highlight the utility of mPBA for sensitive N-glycoproteomics studies. The data can be visualized on https://glycoproteome.info.
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101653
  41. Endocr Regul. 2026 Jan 01. 60(1): 179-189
    ERN1 inhibition modifies hypoxic regulation of EGLN1 expression in U87MG glioblastoma cells.
    Oleh V Halkin, Dmytro O Minchenko, Yuliia M Viletska, Myroslava Y Sliusar, Olena O Khita, Taia V Feldman, Oleksandr H Minchenko.
      Objective. Glioblastomas are the most common and highly aggressive malignant brain tumors that are difficult to treat. Hypoxia is a significant factor in glioblastoma growth. Previous studies have shown that the inhibition of ERN1 (endoplasmic reticulum to nucleus signaling 1) significantly suppresses the glioblastoma cell proliferation and modifies the hypoxic regulation. The present study aimed to investigate the impact of hypoxia on the expression of endoplasmic reticulum stress-dependent genes including EGLN1 in U87MG glioblastoma cells in relation to ERN1 inhibition to reveal a possible role of the ERN1 signaling pathway in the hypoxic regulation of these genes' expression. Methods. The control U87MG glioblastoma cells (transfected by an empty vector) and ERN1 knockdown cells with inhibited ERN1 endoribonuclease and protein kinase (dnERN1) were used. Hypoxia was induced at normoxic conditions with dimethyloxalylglycine (0.5 mM for 4 h). RNA was extracted and reverse transcribed. The expression levels of EGLN1, HSPA5, DDIT4, PA2G4, XIAP, and MTOR genes were studied by real-time qPCR and normalized to ACTB mRNA. Results. It was established that hypoxia increases the expression level of EGLN1, HSPA5, DDIT4, and XIAP in glioblastoma cells with native ERN1. However, the expression levels of two other stress-dependent genes (PA2G4 and MTOR) were reduced in these glioblastoma cells under hypoxia. Furthermore, inhibition of ERN1 enzymatic activity attenuated the effects of hypoxia on the expression of most of the genes studied in glioblastoma cells, while XIAP gene expression was dramatically increased. Conclusion. The results of this study showed that hypoxia differentially affects the expression of genes related to endoplasmic reticulum stress in glioblastoma cells and is dependent on ERN1 activity. This reflected the ERN1-mediated reprogramming of hypoxic regulation of gene expression.
    Keywords:  DDIT4; EGLN1; ERN1 inhibition; HJSPA5; gene expression; glioblastoma cells; hypoxia; mTOR
    DOI:  https://doi.org/10.2478/enr-2026-0018
  42. Sci Rep. 2026 09 01. pii: 27411. [Epub ahead of print]16(1):
    A multi-omics systems toxicology framework reveals amino acid-mediated stress adaptation to deltamethrin exposure in a yeast model.
    Mustafa Yavuz, Hakime Gul Yavuz, Aytac Dursun Oksuzoglu, Ceyhun Bereketoglu, Adil Mardinoglu, Beste Calimlioglu.
      Deltamethrin (DLM) is a widely used synthetic pyrethroid insecticide known for its neurotoxic effects through interactions with voltage-gated sodium channels in insects. Despite its extensive application in agriculture, aquaculture, household settings, and animal husbandry, accumulating evidence indicates that DLM poses significant health risks to non-target organisms, including neurotoxicity, hepatotoxicity, nephrotoxicity, reproductive toxicity, metabolic disorders, and oxidative stress. Elucidating the cellular mode of action of DLM exposure is therefore critical. Previous studies have linked DLM exposure to endoplasmic reticulum (ER) stress and disrupted iron homeostasis; however, the metabolic adaptations underlying these responses remain poorly understood. In this study, we employed an integrated multi-omics approach to investigate the metabolic and transcriptomic responses of Saccharomyces cerevisiae exposed to non-lethal, chronic DLM doses over 30 days. Metabolomic profiling revealed significant alterations in amino acid metabolism, with notable accumulation of glycine and serine, amino acids known to mitigate ER stress. Transcriptomic analysis showed upregulation of iron deprivation response genes (FRE3, SIT1) and amino acid permease genes (PUT4, AGP1), indicating enhanced amino acid transport and iron uptake. Our findings demonstrate a coordinated adaptive response in which amino acid trafficking and iron homeostasis act in concert to alleviate DLM-induced ER stress, highlighting conserved stress adaptation mechanisms with potential relevance to human health.
    Keywords:   Saccharomyces cerevisiae ; Deltamethrin; Metabolomics; Toxicity; Transcriptomics
    DOI:  https://doi.org/10.1038/s41598-026-66841-2
  43. Biochemistry. 2026 Sep 01. 65(17): 2629-2643
    Serine: From Metabolic Intermediate to Signaling Entity.
    Sharon Spizzichino, Giovanni Maria Varchetta, Giulia Elizabeth Borsatti, Emma Chillemi, Marzia Arese, Alessio Paone, Serena Rinaldo, Francesca Cutruzzolà.
      Serine, a nonessential amino acid classically defined as a precursor for protein synthesis and one-carbon metabolism, is increasingly recognized as a signaling metabolite that links the cellular metabolic status to regulatory decision-making. Intracellular serine availability is shaped by nutrient conditions, glycolytic flux, and activity of the serine synthesis pathway, and these fluctuations are sensed to elicit coordinated metabolic and signaling responses. This review discusses mechanisms by which serine modulates cell growth and stress responses, with particular emphasis on its interaction with central nutrient-sensing pathways, including mTORC1 and the integrated stress response. In parallel, serine-driven one-carbon metabolism is examined for its role in supporting nucleotide biosynthesis, methylation reactions, and redox homeostasis through folate-dependent pathways and NADPH generation, thereby coupling anabolic processes to the maintenance of redox balance and genome integrity. In addition to intracellular functions, serine contributes to intercellular signaling. Conversion of l-serine to d-serine mediates neuromodulatory activity via N-methyl-d-aspartate receptors, while serine availability also influences immune cell function, inflammatory signaling, and host-microbe interactions. Dysregulation of serine metabolism and signaling is further considered in the context of disease states, including cancer, neurodegeneration, and metabolic disorders. Together, these observations support a framework in which serine functions as an information-bearing metabolic signal that coordinates the biosynthetic capacity with cellular adaptation and intercellular communication.
    Keywords:   N-methyl-d-aspartate (NMDA); 3-phosphoglycerate (3-PG); S-adenosylmethionine (SAM); phosphoenolpyruvate (PEP); reactive oxygen species (ROS)
    DOI:  https://doi.org/10.1021/acs.biochem.6c00353
  44. Biochem Soc Trans. 2026 Sep 23. 54(9): 1211-1219
    Insights into the regulation of the HOTAIR proximal promoter.
    Aritra Gupta, Kartiki V Desai.
      HOTAIR (HOX transcript antisense RNA) is a HOXC-cluster long intervening non-coding RNA (lincRNA) whose cancer relevance is tightly coupled to how its transcription is wired into hormone, hypoxia, inflammatory, and developmental signaling. HOTAIR is known to associate with cancer cell proliferation, motility, tumor invasion, and metastasis. The present mini-review focuses on the regulatory architecture and mechanistic complexity of HOTAIR transcriptional regulation, with emphasis on three organizing principles. First, we consider the impact of promoter choice between a canonical proximal promoter (P1), which supports the 2.2-2.4 kb transcript, and an alternative upstream promoter/TSS (P2), which contributes to context-dependent transcription initiation. Second, we examine the long-distance enhancer-promoter communication between HOTAIR distal enhancer and P1/P2. Third, we summarize the recent epigenetic and epi-transcriptomic mechanisms involved in HOTAIR transcript initiation and elongation. A combination of these events determines isoform-specific transcription to govern cell-type-, context-, and cancer specific modulation of HOTAIR expression that promotes tumor formation and cancer progression. Finally, the review proposes how large-scale RNA datasets, long-read sequencing, and isoform-specific studies can refine our understanding of this versatile lincRNA's regulation.
    Keywords:  Cancer; eukaryotic gene expression; long intervening non-coding RNA
    DOI:  https://doi.org/10.1042/BST20260099
  45. Hum Cell. 2026 Sep 03. pii: 134. [Epub ahead of print]39(9):
    HNRNPC contributes to ccRCC progression by stabilizing AURKB mRNA in an m6A-dependent manner.
    Zhengang Luo, Xiangrong Ying, Chong Shen, Ke Gao, Yu Ren, Yimn Chen, Gangfeng Wu.
      This study aimed to investigate the expression, biological functions, and underlying mechanisms of HNRNPC in clear cell renal cell carcinoma (ccRCC). The expression of HNRNPC in ccRCC tissues and cell lines was detected. The effects of HNRNPC knockdown and overexpression on ccRCC cell proliferation, migration, and invasion were analyzed using cellular models. The role of HNRNPC in recognizing m6A modifications and regulating AURKB mRNA stability was validated through treatment with the methylation inhibitor STM-245, an actinomycin D stability assay, a dual-luciferase reporter assay, and RNA immunoprecipitation. A nude mouse xenograft model was established for in vivo functional validation. The results showed that HNRNPC was significantly overexpressed in ccRCC tissues and cell lines. Knockdown of HNRNPC suppressed cell proliferation, sphere formation, migration, and invasion, while overexpression promoted these malignant phenotypes. Mechanistically, HNRNPC enhanced the stability and expression of AURKB mRNA by recognizing and binding to m6A modification sites on AURKB mRNA. HNRNPC overexpression reversed the suppression of cellular phenotypes induced by AURKB knockdown. In vivo experiments demonstrated that knockdown of either HNRNPC or AURKB significantly inhibited tumor growth and downregulated Ki-67 expression. In conclusion, HNRNPC contributes malignant progression of ccRCC, at least in part, by recognizing m6A modifications on AURKB mRNA and enhancing its stability, suggesting that the HNRNPC/AURKB axis may serve as a potential therapeutic target for ccRCC.
    Keywords:  AURKB; CcRCC; HNRNPC; M6A
    DOI:  https://doi.org/10.1007/s13577-026-01445-6
  46. Front Immunol. 2026 ;17 1865051
    Oxidative stress-driven epigenetic reprogramming of immune cells in COPD: from epitranscriptomic and metabolic crosstalk to treatable traits.
    Chun Feng Pan, Qiong Wan, Feng-Xian Ni, Pan Xu, Dong-Hui Huang, Ze-Bo Jiang.
      Chronic obstructive pulmonary disease (COPD) is a heterogeneous syndrome characterized by persistent oxidative stress and maladaptive immune responses, rather than a single disease entity. Oxidative stress not only damages lung tissue but also reprograms immune cells through both classical epigenetic mechanisms (DNA methylation, histone modifications) and epitranscriptomic regulation (m6A RNA methylation), shaping disease endotypes and treatment resistance. This review presents an integrated framework in which redox signals dynamically reshape the epigenetic and epitranscriptomic landscape, thereby locking immune cells into pathogenic states. Metabolic intermediates (S-adenosylmethionine, α-ketoglutarate, succinate, NAD+) serve as critical nodes that connect immunometabolism to both classical epigenetic enzymes and the m6A machinery, thereby linking redox status to RNA fate. Using NETosis as a paradigm, we illustrate how oxidative-epigenetic-metabolic loops sustain neutrophilic inflammation and resolution failure. Finally, we outline a treatable traits framework that integrates these mechanistic insights into precision combination therapies. This conceptual roadmap aims to shift COPD management from symptom control toward durable, mechanism-driven disease modification.
    Keywords:  COPD; NETosis; epigenetic reprogramming; immunometabolism; m6A modification; oxidative stress; treatable traits
    DOI:  https://doi.org/10.3389/fimmu.2026.1865051
  47. Int J Biol Sci. 2026 ;22(13): 7447-7470
    RNA Triple Helices: From Structures and Mechanisms to Therapeutic Targets.
    Yiqi Ding, Zhechao Wang, Zimo Wu, Benyuan Cao, Haiyang Dong, Yongfeng Jin.
      Major-groove RNA triple helices are conserved tertiary structures formed when a third strand inserts into the major groove of a classic double helix either via Hoogsteen base pairing or reverse Hoogsteen base pairing. These structures are widely distributed in eukaryotic, prokaryotic, and viral RNAs. This paper systematically summarizes the structural classification, stability-influencing factors, and identification methods of RNA triple helices. A growing body of evidence indicates that RNA triple helices are extensively involved in diverse biological processes, including RNA stability regulation, translation regulation, riboswitch ligand recognition, transposition regulation, telomerase activity, and the assembly of the spliceosome catalytic core, as well as serving as scaffolds for molecular recruitment. Notably, dysregulation of RNA triple helices is closely associated with tumorigenesis, viral infections, and genetic diseases. Based on their structural and functional characteristics, multiple therapeutic strategies targeting RNA triple helices have been explored, such as small molecules and antisense oligonucleotides. Collectively, RNA triple helices represent a pivotal link between RNA structural biology and precision medicine, with promising potential as an important candidate target for future RNA structural drug development.
    Keywords:  RNA stability; RNA triple helix; RNA-targeted therapeutics; gene expression regulation
    DOI:  https://doi.org/10.7150/ijbs.132736
  48. mSystems. 2026 Sep 03. e0000926
    Chloramphenicol stress triggers oxidative adaptation in Acinetobacter baumannii ATCC19606 devoid of RND efflux pumps AdeAB or AdeIJ.
    Wuen Ee Foong, Xinxin Xiang, Wenjun He, Xuan Yan, Jiabin Huang, Klaas M Pos, Heng-Keat Tam.
      Efflux pumps play a key role in both intrinsic and acquired antibiotic resistance in Acinetobacter baumannii, yet their broader physiological roles remain unclear. Here, we investigated the transcriptomic and phenotypic responses of A. baumannii ATCC19606 mutants lacking the efflux pumps AdeAB, AdeIJ, or CraA under chloramphenicol stress. The deletion of craA resulted in a 32-fold reduction in chloramphenicol MIC, while ΔadeIJ showed a modest 4-fold decrease, and ΔadeAB had no effect on chloramphenicol susceptibility. Transcriptomic profiling revealed minimal alterations in ΔcraA, but notable transcriptional reprogramming in ΔadeAB and ΔadeIJ, including upregulation of ribosomal genes, iron-sulfur cluster biogenesis, aromatic compound catabolism, and amino acid transport systems. Under chloramphenicol stress, ΔadeAB exhibited metabolic remodeling, activating oxidative stress defenses and protein quality control pathways while repressing type VI secretion. Both ΔadeIJ and wild-type strains upregulated arginine and glutamate metabolism, likely contributing to redox balance. Phenotypically, the ΔadeIJ strain showed elevated basal and H₂O₂-induced ROS levels, as well as heightened sensitivity to nitrosative stress and Cu2+, which may suggest a role for AdeIJ in oxidative and metal stress responses. Despite increased adeAB and craA expression under chloramphenicol stress, only craA deletion significantly impaired resistance, highlighting its dominant role in chloramphenicol efflux. Collectively, our findings reveal efflux pump-specific and strain-specific adaptations to antibiotic stress, positioning CraA as a major determinant of chloramphenicol resistance, while RND transporters such as AdeABC and AdeIJK may also be associated with broader stress adaptation processes, including redox and metal homeostasis, in A. baumannii.IMPORTANCEEfflux pumps are key drivers of multidrug resistance in Acinetobacter baumannii, yet their broader roles in stress adaptation remain insufficiently understood. Here, we show that the loss of major efflux systems reshapes the transcriptomic and metabolic landscape under chloramphenicol stress, a condition that also imposes oxidative stress. In particular, the RND efflux pump AdeIJK may be linked to alterations in cellular responses to oxidative, nitrosative, and metal stress, although the mechanistic basis of this interplay remains to be further investigated. Overall, these findings suggest that efflux pumps may contribute to bacterial resilience beyond drug resistance, providing additional insight into efflux system hierarchy and functional redundancy in A. baumannii, and may inform future studies aimed at understanding persistence and efflux-mediated multidrug resistance mechanisms.
    Keywords:  Acinetobacter baumannii; CraA; RND; antibiotic resistance; stress adaptation
    DOI:  https://doi.org/10.1128/msystems.00009-26
  49. Front Oncol. 2026 ;16 1906093
    Isoform-resolved 14-3-3/YWHA networks in colorectal cancer: phospho-adaptor mechanisms, biomarker contexts and therapeutic opportunities.
    Qian Liu, Rudong Li, Wei Ye, Zhipeng Zhao.
      YWHA/14-3-3 proteins are conserved phosphoserine/phosphothreonine-binding adaptors that coordinate signaling-complex assembly, subcellular localization, stress responses and cell-state transitions. Although often discussed as a single adaptor family, colorectal cancer (CRC) studies suggest that individual YWHA isoforms act through distinct clients, RNA-associated layers and tumor-state contexts. In this narrative and mechanistic review, we synthesized PubMed-indexed CRC literature through 18 May 2026 and appraised CRC-relevant mechanistic modules using an explicit evidence-maturity rubric developed by the authors distinct from formal GRADE assessment. We propose an isoform-client-context framework for interpreting 14-3-3 biology in CRC. YWHAG has been linked to CTTN-dependent Wnt/β-catenin activation, whereas YWHAE/14-3-3ϵ protein has been associated with extracellular-vesicle secretion and EV-associated β-catenin/Wnt outputs. Separately, the YWHAE-encoded lncRNA, hereafter referred to as YWHAE lncRNA, has been proposed to activate KRAS/ERK and PI3K/AKT signaling through a competing endogenous RNA mechanism. YWHAZ participates in epithelial-mesenchymal and G2/M transitions through miR-1-3p- and TRIP13-associated mechanisms. YWHAB supports PIK3R2-dependent PI3K/AKT signaling, whereas YWHAH connects NAT10/ac4C regulation, CD8+ T-cell exhaustion and MAPK/ERK-dependent autophagy-associated invasion. SFN illustrates context-dependent tumor-suppressive or stress-adaptive functions. Overall, total 14-3-3 abundance is insufficient for mechanistic or translational interpretation. Interactomics, phosphoproteomics, spatial profiling, extracellular-vesicle analysis and patient-derived models should be used to prioritize YWHA-dependent candidate mechanisms for functional validation. These modules should currently be regarded as testable biomarker and therapeutic hypotheses, not as clinically validated CRC biomarkers or targets.
    Keywords:  14-3-3 proteins; YWHA; colorectal cancer; extracellular vesicles; immune exhaustion; patient-derived organoids; phosphorylation-dependent adaptor proteins
    DOI:  https://doi.org/10.3389/fonc.2026.1906093
  50. Nat Commun. 2026 Aug 07. pii: 9488. [Epub ahead of print]17(1):
    DNTTIP2 coordinates RNA exosome activities to ensure fidelity of human ribosome assembly.
    Agnese Pisano, Jessie Bourdeaux, Jarosław Mazur, Florine Roses, Yves Romeo, Elisabeth Petfalski, Tobias von Arx, Daniela Portugal-Calisto, Michaela Oborská-Oplová, Cohue Peña, Clément Chapat, David Tollervey, Anthony K Henras, Vikram Govind Panse.
      The RNA exosome-associated helicase Mtr4/MTR4 (yeast/human) is recruited by adaptor proteins bearing Arch-Interacting Motifs (AIMs) to selectively degrade RNA substrates. Although the exosome targets diverse RNAs, only a few adaptors have been identified. Here, we extend the inventory of human adaptors to include a pre-tRNA splicing-ligase complex component, a spliceosome-associated factor, and DNTTIP2, a constituent of the small ribosomal subunit (40S) precursor, the 90S pre-ribosome. Structure-guided studies reveal how the DNTTIP2AIM-docked processive exosome core and its associated distributive exonuclease EXOSC10, which contact distant sites on the 90S pre-ribosome, cooperate to degrade part of the 5'-external transcribed spacer (5'-ETS), a key RNA scaffold that coordinates early 40S assembly. By contrast, productive pre-ribosomal RNA trimming within the 90S pre-ribosome necessitates EXOSC10, which safeguards against uncontrolled processive degradation by the DNTTIP2AIM-docked exosome core. We propose that multivalent contacts provide a mechanistic framework by which the RNA exosome coordinates its distinct enzymatic activities, ensuring selective processing and surveillance during ribonucleoprotein particle maturation.
    DOI:  https://doi.org/10.1038/s41467-026-76536-x
  51. J Assist Reprod Genet. 2026 Sep 03.
    RNA m⁶A modification and its regulatory factors are altered in granulosa cells from women with PMOS.
    Snehal Bhingardeve, Pooja Sagvekar, Sadhana Desai, Vijay Mangoli, Richa Jagtap, Srabani Mukherjee.
       PURPOSE: Polyendocrine metabolic ovarian syndrome (PMOS), an endocrine disorder with unknown aetiology is the leading cause of anovulatory infertility. N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA, regulates multiple aspects of RNA metabolism and reproductive function. However, the contributions of m6A modification and its regulatory factors including microRNAs to the pathophysiology of PMOS remain poorly understood. We therefore investigated global m6A abundance, expression of key m6A regulatory genes, and selected experimentally validated m6A-associated microRNAs in granulosa cells (GCs) from women with PMOS.
    METHODS: GCs were collected from 23 women with PMOS and 23 age- and BMI- matched controls undergoing in vitro fertilization. Global m6A modification was quantified by ELISA, whereas the m6A writer, reader, eraser (WRE) protein-coding genes and selected microRNAs were assessed by RT-qPCR.
    RESULTS: The total m6A levels were significantly increased in GCs from women with PMOS. Transcript encoding the core writer complex (METTL3, METTL14, WTAP, RBM15, VIRMA) and reader proteins (YTHDF1, YTHDF3, YTHDC1) were upregulated, whereas transcripts encoding the eraser proteins (FTO, ALKBH5) were downregulated. Elevated m6A, METTL3, METTL14 and YTHDF1 levels positively correlated with androgen excess, anti-Müllerian hormone and reduced oocyte fertilization rates. Among the experimentally validated m6A-associated microRNAs, miR-20b, whose maturation is regulated by METTL3, was downregulated, whereas miR-607, a validated regulator of FTO, was upregulated in PMOS.
    CONCLUSION: Coordinated alterations in global m6A abundance, m6A regulatory genes and the selected microRNAs indicate widespread epitranscriptomic dysregulation in GCs from women with PMOS, providing a foundation for future mechanistic and therapeutic studies.
    Keywords:  Epigenetics; Epitranscriptomics; IVF; PMOS; m6A; miRNA
    DOI:  https://doi.org/10.1007/s10815-026-04016-8
  52. eNeuro. 2026 Aug 31. pii: ENEURO.0196-26.2026. [Epub ahead of print]
    Local synthesis of CaMKII does not contribute to activity-dependent generation of ghost boutons.
    Kelsey J Clements, Leslie C Griffith.
      Activity-dependent structural plasticity is essential for the growth and remodeling of synaptic connections. At the Drosophila melanogaster larval neuromuscular junction (NMJ), spaced stimulation induces the translation-dependent formation of ghost boutons (GBs), which are immature boutons that lack a corresponding postsynaptic structure. Calcium/calmodulin-dependent protein kinase II (CaMKII) has previously been implicated in GB formation and is locally translated at synapses, raising the possibility that activity-dependent CaMKII synthesis contributes to GB formation. We examined activity-induced synaptic outgrowth in female larvae using a spaced depolarization paradigm combined with genetic manipulations of the endogenous CaMKII locus. While whole-animal CaMKII null mutants exhibited fewer GBs after spaced depolarization, selective disruption of activity-dependent CaMKII synthesis by deletion of the CaMKII 3' untranslated region (3'UTR) in either presynaptic motor neurons or postsynaptic muscle cells had no effect on GB formation. Consistent with this, inhibition of the signaling pathways upstream of CaMKII synthesis also did not impair bouton outgrowth. Cell-specific deletion of the CaMKII coding region in presynaptic neurons also did not alter GB formation, but postsynaptic deletion significantly reduced it. These findings demonstrate that local synthesis of CaMKII is dispensable for activity-dependent ghost bouton formation. Instead, our results indicate that only steady-state CaMKII protein is necessary for this specific type of structural plasticity and identifies a new trans-synaptic function for postsynaptic CaMKII in GB formation. These findings distinguish the role of CaMKII protein from CaMKII synthesis and suggest that other locally translated proteins underlie the protein synthesis dependence of GB formation.Significance Statement Local protein synthesis is thought to support long-lasting forms of synaptic plasticity. At the Drosophila neuromuscular junction, CaMKII is synthesized during patterned stimulation, which also triggers CaMKII-dependent ghost bouton formation, suggesting CaMKII local synthesis might be involved in this form of structural plasticity. In contrast to this hypothesis, disrupting activity-dependent CaMKII translation in either presynaptic or postsynaptic cells had no effect on ghost bouton formation. Instead, loss of CaMKII protein in the whole animal blocked synaptic outgrowth, and loss of postsynaptic CaMKII protein reduced it. Our findings indicate that CaMKII protein function, but not local CaMKII synthesis, is involved in activity-dependent ghost bouton formation. Identifying the precise molecular players driving local translation-dependent remodeling remains a task for future research.
    DOI:  https://doi.org/10.1523/ENEURO.0196-26.2026
  53. PLoS Comput Biol. 2026 Sep 02. 22(9): e1014729
    Synergies and trade-offs in the heat shock response mechanism.
    Rupal Chauhan, Biswajit Das, Ajeet K Sharma.
      E. coli relies on the heat shock response (HSR) to preserve protein homeostasis under stress, through three feedback modules: feedforward translational control, chaperone-mediated sequestration and targeted degradation. Although previous studies have highlighted how this layered architecture ensures rapid and robust protection compared to simpler designs, not much attention is paid to how these modules interact. Moreover, how do interactions among the three modules balance performance trade-offs, where gains in one module may come at the expense of another, yet together yield an optimal overall response? We address this using a mathematical model that integrates protein folding with σ32 regulation. We show that the feedback modules both cooperate and compete, giving rise to nonmonotonic dynamics that govern HSR performance. Specifically, increasing feedforward strength does accelerate response, but beyond a threshold, despite increasing chaperone levels, it paradoxically slows recovery. Similarly, while sequestration enhances relative chaperone production and per-chaperone efficiency, when excessive, it traps σ32 in inactive complexes, prolonging recovery and delaying shutdown. Mapping the parameter space reveals regimes of synergy as well as trade-offs between speed and efficiency, with wild-type parameters lying near the optimal region. These results reveal design principles that produces a robust and efficient heat shock response.
    DOI:  https://doi.org/10.1371/journal.pcbi.1014729
  54. Clin Exp Pharmacol Physiol. 2026 Sep;53(9): e70153
    ANGII Initiated HSF2 Trans-Activating HIF-1α Through Induction of ER Stress to Promote Cardiac Hypertrophy.
    Renchuang Cao, Qingying Meng, Gengyuan Li, Shumei Yuan, Chunmei Li, Xin Zhao, Dongmei Zhang.
      Heat shock factor 2 (HSF2) and hypoxia-inducible factor 1α are activated by angiotensin II (ANGII) in cardiomyocytes. The endoplasmic reticulum (ER) stress plays a critical role in cardiac hypertrophy. Moreover, HIF-1α is known to be regulated by HSF2 in tumour cells. In this study, we hypothesised and clarified whether HSF2 trans-activated HIF-1α through initiation of ER stress in hypertrophic cardiomyocytes. Myocardial hypertrophy was induced by the treatment of ANGII. Expression of the gene or protein was assessed by applying RT-PCR, WB, ICC and IHC. Luciferase and CHIP were applied to detect the transcription of HIF-1α by HSF2. Both in vitro and in vivo, the expression of HIF-1α, ER stress markers and HSF2 was increased in ANGII-treated hypertrophic cardiomyocytes. Blocking ER stress suppressed the expression of HSF2 and HIF-1α in ANGII-treated cardiomyocytes. Silencing HSF2 inhibited HIF-1α, thereby reducing hypertrophy but had no effect on ER stress. Similarly, silencing HIF-1α reduced hypertrophy without affecting ER stress or HSF2 expression. HSF2 transcriptionally activated HIF-1α. We concluded that ER stress induced by ANGII activates HSF2, which then trans-activates HIF-1α, promoting cardiac hypertrophy.
    Keywords:  ER stress; HSF2‐HIF‐1α signalling; hypertrophic cardiomyocyte
    DOI:  https://doi.org/10.1111/1440-1681.70153
  55. Methods Mol Biol. 2026 ;3037 59-73
    Functional Prediction of Epitranscriptome.
    Yuxin Zhang, Bowen Song, Kunqi Chen.
      N6-methyladenosine (m6A) is one of the most prevalent and well-studied RNA modifications, playing a pivotal role in many biological processes. With the recent advances in high-throughput sequencing technologies, tens of thousands of m6A sites have been reported. However, not all m6A sites are important or functionally significant, highlighting the need to distinguish biologically relevant m6As from non-functional or technically artefactual ones. Here, we describe ConsRM, which is a web-based resource that was designed to evaluate the importance of m6As from an evolutionary perspective. It introduced a novel scoring framework for quantifying the conservation degree of m6As in humans. Its web interface includes a database of 177998 distinct human m6A sites along with their calculated conservation score, and allows users to analyze their own data via the web server. ConsRM is freely accessible at: http://180.208.58.19/conservation/browser.html .
    Keywords:  Conservation analysis; Evolutionary; Genome analysis; Machine learning; N6-methyladenosine (m6A); Scoring framework
    DOI:  https://doi.org/10.1007/978-1-0716-5284-8_4
  56. Methods Mol Biol. 2026 ;3056 279-292
    How to Validate miRNA Targeting: Western Blot Analysis.
    Roma Karna, Federica Calore.
      MicroRNAs (miRNAs) are non-coding RNA molecules, usually 19-22 nucleotides long, that modulate gene expression by binding to specific mRNA targets. This interaction involves both the translation process and the stability of the mRNAs, thereby affecting gene expression after transcription. Their regulatory activity is carried out by binding to complementary sequences on target mRNAs, usually at their 3' UTR level, and resulting in their degradation or inhibition of translation. Given their ability to modulate the expression of targeted molecules, miRNAs can act either as oncogenes or tumor suppressor genes in cancer cells. Aberrant miRNA expression can lead to irregular gene expression, contributing to cancer development. Changes in miRNA expression profiles have been documented across multiple cancer types and are linked to clinical factors, such as tumor progression, metastasis, and patient survival rates. Certain miRNAs have potential as diagnostic biomarkers for early cancer detection and can serve as prognostic markers to predict patient outcomes and response to treatments. This chapter outlines the experimental procedures for validating microRNA targets through Western blotting. Western blotting, a "gold-standard" technique for protein analysis, offers a reliable approach for validating the impact of miRNAs on their target genes by assessing protein expression levels [1]. This validation is essential for understanding the roles miRNAs play in health and disease.
    Keywords:  Post-transcriptional regulation; Protein expression analysis; Western blotting; microRNA (miRNA)
    DOI:  https://doi.org/10.1007/978-1-0716-5392-0_15
  57. Methods Enzymol. 2026 ;pii: S0076-6879(26)00175-8. [Epub ahead of print]734 199-216
    Mass spectrometry-based mapping of the ubiquitin chaperone code.
    Ayush Nigam, Prasun Kumar Bhunia, Trayambak Basak, Prasad Kasturi.
      Maintenance of proteome integrity is essential for cellular homeostasis and organismal health. This integrity depends on proteostasis, a coordinated network of protein quality control systems that regulate protein folding, stabilization, and degradation. Molecular chaperones, together with proteolytic pathways such as the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway, prevent the accumulation of misfolded and aggregation-prone proteins. Perturbations, including genetic mutations, environmental stress, and aging challenge protein folding fidelity, leading to proteotoxic stress and contributing to the pathogenesis of neurodegenerative disorders. Among the chaperone machinery, the HSP70 and HSP90 families play central roles in maintaining protein conformational homeostasis and directing damaged or misfolded substrates toward refolding or degradation pathways. Recent studies show that chaperone activity is dynamically regulated by diverse post-translational modifications (PTMs), including phosphorylation, acetylation, and ubiquitination, collectively termed the "chaperone code." These modifications modulate chaperone-client interactions, enzymatic activity, localization, and coordination with protein degradation systems. Mass spectrometry (MS)-based proteomics has emerged as a powerful approach for mapping ubiquitination sites and quantifying ubiquitin signaling dynamics. This chapter outlines experimental and computational strategies for MS-based analysis of the ubiquitin chaperone code, including di-glycine peptide enrichment, site identification, quantitative analysis, and validation.
    Keywords:  Chaperone code; Chaperones; PTMs; Proteomics; Proteostasis; Ubiquitination
    DOI:  https://doi.org/10.1016/bs.mie.2026.05.047
  58. Methods Enzymol. 2026 ;pii: S0076-6879(26)00172-2. [Epub ahead of print]734 1-28
    Lysine methylation is an endogenous post-translational modifications of tau protein in human brain and a modulator of aggregation propensity.
    Marisel Sanchez, Jeff Kuret.
      Tau protein undergoes a broad range of post-translational modifications in the brain, influencing its structure, solubility, and propensity to aggregate. This chapter presents an integrated methodological framework for characterizing tau methylation and evaluating its impact on tau biology. We describe procedures for isolating soluble and filamentous tau from post-mortem human brain tissue while preserving modifications for proteomic analysis. These approaches support precise mapping of methylation sites alongside other co-occurring modifications. To model methylation under controlled conditions, we outline protocols for recombinant tau expression, purification, and chemical reductive methylation, including radiolabeled assays for determining modification stoichiometry. We then detail biophysical assays used to assess how methylation alters tau conformation and aggregation propensity. This methodological framework supports experimentation seeking insight into mechanisms relevant to Alzheimer's disease and related tauopathies.
    Keywords:  Alzheimer’s disease; Lysine methylation; Mass spectrometry; Post-translational modification; Protein aggregation; Reductive methylation; Tau protein; Tauopathies
    DOI:  https://doi.org/10.1016/bs.mie.2026.05.044
  59. Methods Mol Biol. 2026 ;3051 117-137
    Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La.
    Gunhild Sommer, Jemima Riess, Christian Weinzettl, Marie Matthes, Tilman Heise.
      It is well established that the RNA-binding protein La has RNA chaperone activity. Recent work suggests that the La protein has two distinct RNA chaperone domains (RCD-A and RCD-B), assisting structural changes in diverse groups of RNA molecules such as RNA Polymerase III transcripts (e.g., pre-tRNA, U6 snRNA), cellular messenger, and viral RNAs. In this protocol, we focus on the RNA chaperone domain RCD-B, which is located in the carboxy-terminal domain of La. It has been shown that this RNA chaperone domain assists structural changes in predicted RNA hairpins folded in the 5'-untranslated regions of cyclin D1 and Bcl2 mRNAs. Besides RNA helicases, which are implicated in melting RNA hairpin structures in an ATP-dependent manner, RNA chaperones fulfill a similar function in an ATP-independent manner. Aiming to study the RNA chaperon activity of La, we established a La-dependent Molecular Beacon-based RNA chaperone assay and systematically tested the various salt conditions. Herein we describe the assay format and design to study the salt dependency of RNA chaperones. This protocol can be easily adapted to test the RNA chaperone activity of other RNA-binding proteins and to optimize assay conditions.
    Keywords:  Intrinsic disordered region; RNA binding; RNA chaperone; RNA structure; SSB
    DOI:  https://doi.org/10.1007/978-1-0716-5372-2_7
  60. Biosci Rep. 2026 Sep 16. pii: BSR20260051. [Epub ahead of print]46(9):
    Ribosomal protein S3: a critical regulator of human disease mechanisms.
    Joeline Dreik, Marwa Al Ali, Jalil Daher, Zeina Nasr.
      Ribosomal protein S3 (RPS3) is an essential structural component of the 40S ribosomal subunit, yet growing evidence highlights crucial extraribosomal roles in genome maintenance, cell-cycle control, and immune signaling. Dysregulation of RPS3 contributes to diverse human disorders, including cancer, inflammatory diseases, neurodegeneration, and resistance to antimicrobial and anticancer therapies. As a cofactor of NF-κB and a participant in DNA damage responses, RPS3 occupies a node that integrates stress signaling with transcriptional reprogramming, enabling both protective and pathological outcomes. The present review critically evaluates mechanistic insights into RPS3 biology, emphasizing recent findings that delineate its context-dependent effects, discrepancies across models, and remaining gaps that restrict translational applications. Understanding these complexities is essential to assess RPS3's potential as a biomarker and therapeutic target.
    Keywords:  DNA damage response; NF-κB signaling; RPS3; cancer; inflammation; ribosomal stress
    DOI:  https://doi.org/10.1042/BSR20260051
  61. Malays J Pathol. 2026 Aug;48(2): 257-266
    Autophagy in testicular physiology and male fertility: Mechanisms, dysregulation, and translational opportunities.
    M F A Al Salman, S O Ekeuku, K Y Chin.
      Autophagy is a highly conserved intracellular degradation pathway that plays a central role in maintaining testicular homeostasis and male reproductive function. This review summarises recent advances in the understanding of autophagy in the testis, with particular emphasis on its roles in Sertoli cells, Leydig cells, and germ cells, as well as its regulatory mechanisms and implications for male infertility. Autophagy contributes to key processes, including spermatogenesis, spermiogenesis, blood-testis barrier integrity, and steroidogenesis, through coordinated organelle turnover and cellular remodelling. Core regulatory pathways such as mTOR, AMPK, PI3K/Akt, and oxidative stress-responsive signalling dynamically controls autophagic flux in response to metabolic and environmental cues. Emerging evidence highlights extensive molecular crosstalk between autophagy, apoptosis, ferroptosis, and ubiquitin-mediated proteostasis, with oxidative stress serving as a central upstream regulator. Dysregulation of autophagy, whether through impaired flux or excessive activation, is strongly associated with male infertility phenotypes, including azoospermia, oligozoospermia, and asthenozoospermia. These effects are driven by defects in germ cell development, mitochondrial function, and hormonal balance, and are further exacerbated by environmental toxicants, lifestyle factors, and ageing. Although autophagy-related proteins such as microtubule-associated protein 1 light-chain 3, p62, and Beclin-1 show promise as biomarkers, their clinical application remains limited by challenges in accurately measuring autophagic flux and context-dependent interpretation. Therapeutic modulation of autophagy using pharmacological agents and antioxidants represents a promising but complex strategy that requires precise, context-specific application. Overall, this review underscores the dual role of autophagy in male fertility and highlights the need for improved biomarkers and translational approaches.
  62. Front Oncol. 2026 ;16 1917106
    SPRTN preserves RNA polymerase I transcription under genotoxic drug stress in lung adenocarcinoma.
    Mansi Sharma, Srikanth Karnati, Süleyman Ergün, Srivatsava Naidu.
       Background: Hyperactivated RNA polymerase I (Pol I)-driven ribosomal DNA (rDNA) transcription sustains malignant growth and chemotherapy tolerance in lung adenocarcinoma (LUAD). Genotoxic chemotherapeutics such as doxorubicin and cisplatin preferentially damage rDNA by inducing DNA-protein crosslinks (DPCs), yet how tumor cells preserve Pol I transcriptional output under this damage remains poorly understood.
    Methods: We investigated SPRTN function in LUAD using complementary approaches spanning molecular, cellular, and in vivo levels, including DNA-protein crosslink isolation, chromatin immunoprecipitation, nascent RNA synthesis assays, apoptosis and invasion assays in SPRTN loss- and gain-of-function cell models, mouse xenograft studies, and transcriptomic analysis of clinical LUAD datasets.
    Results: SPRTN was enriched at the rDNA promoter, limited basal DPC accumulation, sustained Pol I transcriptional output, suppressed the p53-p21 nucleolar stress checkpoint, and promoted Pol I-dependent proliferation. Under doxorubicin or cisplatin treatment, SPRTN was recruited to G-quadruplex-rich rDNA promoters, a process associated with PARP-1 co-recruitment, and facilitated DPC resolution and transcriptional recovery. Catalytically inactive SPRTN failed to resolve rDNA-DPCs and restore Pol I output under both basal and drug-treated conditions. Doxorubicin- and cisplatin-resistant LUAD cells exhibited elevated SPRTN expression and enhanced rRNA synthesis relative to parental cells. SPRTN knockdown increased apoptotic response to doxorubicin and cisplatin, and co-inhibition of SPRTN and Pol I additively induced apoptosis in both parental and resistant cells. SPRTN further promoted Pol I-dependent migration and invasion. Transcriptomically, SPRTN was upregulated in LUAD, correlated with advanced disease stage and reduced overall survival, and was transcriptionally activated by ZEB1 and post-transcriptionally repressed by miR-195-5p. In vivo, SPRTN silencing reduced tumor burden and suppressed Pol I transcription, with further reduction upon doxorubicin treatment.
    Conclusion: These findings establish SPRTN as an rDNA-associated repair factor that couples genotoxic damage resolution to Pol I transcriptional resilience, defining the SPRTN-Pol I axis as a determinant of nucleolar homeostasis and therapeutic vulnerability in lung adenocarcinoma.
    Keywords:  DNA-protein crosslinks; RNA polymerase I (Pol I); SPRTN; chemoresistance; cisplatin; doxorubicin; genotoxic chemotherapy; lung adenocarcinoma
    DOI:  https://doi.org/10.3389/fonc.2026.1917106
  63. J Clin Invest. 2026 Sep 01. pii: e199847. [Epub ahead of print]136(17):
    Mitophagy in neuronal health and disease: from mechanisms to neurodegeneration.
    Bishal Basak, Julia F Riley, Neha M Nataraj, Erika Lf Holzbaur.
      Regulation of mitochondrial health is critical for maintaining cellular homeostasis in the nervous system. Damaged mitochondria can have detrimental effects on neuronal health and are thought to be key contributors to the progression of neurodegenerative disorders including Parkinson's disease and amyotrophic lateral sclerosis. To mitigate this damage, multiple quality control mechanisms have evolved to eliminate aged or damaged mitochondria. One such quality control process is autophagy, a process that involves turnover of mitochondria at presynaptic sites and the axon terminal under basal conditions. This highly conserved mechanism sequesters mitochondria from the cytosol within autophagosomes followed by degradation upon fusion with a lysosome. Acute mitochondrial damage activates a selective form of autophagy called mitophagy that involves receptor-mediated engulfment and degradation of the damaged organelle. Multiple mechanisms have been shown to drive efficient mitophagy in neurons and glia, including PTEN induced kinase 1 (PINK1)/Parkin-dependent mitophagy and receptor-mediated mitophagy. Genetic, pathological, and experimental evidence all implicate defects in the removal of damaged mitochondria in the onset or progression of neurodegenerative disease. Both the initiation of PINK1/Parkin-dependent mitophagy and deficits in the removal of damaged mitochondria are linked to activation of neuroinflammatory pathways, including NF-κB and cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling. In this Review, we discuss the molecular pathways governing mitophagy in neurons and glial cells and how deficits in these pathways may lead to neurodegeneration. We also highlight emerging therapeutic strategies aimed at restoring mitophagy to preserve neuronal homeostasis and function.
    DOI:  https://doi.org/10.1172/JCI199847
  64. Cell Death Dis. 2026 Aug 07. pii: 766. [Epub ahead of print]17(1):
    Fructose induces PERK-dependent ER stress and mitochondrial dysfunction via nucleotide depletion in clear cell renal cell carcinoma.
    Na Li, Yanhong Ding, Bowen Yu, Yongqiang Wang, Tongbin Gao, Huiyong Yin, Zhenhua Li, Shuzhen Liu, Guohua Yu, Ningning Wang.
      Clear cell renal cell carcinoma (ccRCC) exhibits a paradoxical fructose metabolism signature characterized by upregulation of the fructose transporter GLUT5 alongside downregulation of the catabolic enzymes (ketohexokinase, aldolase B, and triokinase), a pattern associated with poor prognosis. Functionally, unlike the pro-survival effect of fructose under glucose deprivation, in the presence of glucose, fructose co-treatment suppresses ccRCC cell proliferation, and induces profound mitochondrial dysfunction, including impaired oxidative phosphorylation, loss of membrane potential, excessive mitochondrial superoxide production, reduced mtDNA copy number, and downregulation of mitochondria-encoded electron transport chain subunits (notably ND2 and ND4 of complex I). Mechanistically, co-treatment with glucose and fructose creates a metabolic trap resulting in fructose-1-phosphate accumulation and ATP depletion. This energy crisis drives profound depletion of purine and pyrimidine nucleotide pools, which selectively triggers the PERK-eIF2S1-ATF4-CHOP axis of the integrated stress response, thereby mediating mitochondrial impairment and ultimately sensitizing ccRCC cells to intrinsic apoptosis via BID cleavage and caspase-3 activation under nutrient stress. Pharmacological treatment with the chemical chaperone 4-phenylbutyric acid (4-PBA) or nucleoside supplementation reverses mitochondrial dysfunction and fructose-induced cytotoxicity. The tumor-suppressive effect of fructose is validated in patient-derived organoids and xenograft mouse models, where fructose administration significantly attenuates tumor growth via ER stress. These findings reveal fructose-driven nucleotide depletion and PERK-dependent ER stress leading to mitochondrial dysfunction, which underlies the tumor-suppressive toxicity of fructose and exposes a targetable metabolic vulnerability in ccRCC.
    DOI:  https://doi.org/10.1038/s41419-026-09157-3
  65. Cell Rep. 2026 Aug 28. pii: S2211-1247(26)00892-2. [Epub ahead of print]45(9): 117814
    An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch.
    Yarden Dan, Beáta E Jády, Yudit Halperin, Yuval Nevo, Aliza Fedorenko, Anat Bashan, Maram Arafat, Pnina Glick, Ada Yonath, Tamás Kiss, Daphna Nachmani.
      Epstein-Barr virus (EBV) establishes life-long latency in human B cells yet the molecular strategies that balance its persistence with lytic replication remain incompletely understood. Here, we identify the EBV-encoded small nucleolar RNA, v-snoRNA1, as a bona fide 2'-O-methylation guide that directs methylation of host ribosomal RNAs at 18S-C621 and 28S-U1760, two conserved residues in the ribosomal A-site. V-snoRNA1-mediated hypermethylation impairs 18S rRNA maturation and compromises translational fidelity and output, resulting in slower cellular proliferation. Infection with a v-snoRNA1 deleted virus (Δv-snoRNA1) leads to enhanced protein synthesis and increased proliferation, together with extensive rewiring of host and viral gene expression. This rewiring includes suppression of immune and interferon pathways and alterations in transcription factor activities important for B cell differentiation. Importantly, we find that v-snoRNA1 is required to facilitate viral production. Our findings reveal a molecular strategy by which EBV directly controls translation to promote infection.
    Keywords:  2′-O-methylation; CP: immunology; CP: molecular biology; EBV; rRNA; ribosome; snoRNA; translation
    DOI:  https://doi.org/10.1016/j.celrep.2026.117814
  66. Methods Mol Biol. 2026 ;3049 123-139
    mRNA Microinjection for Gene Expression Studies in Xenopus laevis and Xenopus tropicalis.
    Sian A Martin, Anita Abu-Daya.
      Microinjection of in vitro-transcribed, capped mRNA into Xenopus laevis and Xenopus tropicalis embryos provides a rapid and powerful approach for gene expression studies in vertebrate development. Owing to the large size, external development, and manipulability of Xenopus embryos, mRNA injection allows precise temporal and spatial control of expression and the ability to test both wild-type and mutant variants in vivo. Classic experiments using synthetic mRNAs identified key regulators of embryonic patterning and signaling, and the approach continues to underpin modern functional genomics and disease modeling. Integration of mRNA injection with CRISPR/Cas9-mediated knockouts, fluorescent reporters, and human variant testing has further enhanced its versatility. This chapter details practical methods for mRNA synthesis, quality control, and embryo injection, providing a reliable framework for controlled gene expression analysis and validation in Xenopus embryos.
    Keywords:  Developmental biology; Embryogenesis; Fluorescent reporters; Gain-of-function; Gene expression; In vitro transcription; Rescue experiment; Xenopus laevis; Xenopus tropicalis; mRNA microinjection
    DOI:  https://doi.org/10.1007/978-1-0716-5360-9_4
  67. J Agric Food Chem. 2026 Aug 26. 74(33): 26655-26669
    Endoplasmic Reticulum Stress Drives Copper-Induced Reticulophagy in Porcine Hepatocytes.
    Shanglong Yang, Wei Chen, Hao Xi, Wenyue Qiu, Hui Huang, Shaofeng Wang, Jianzhao Liao, Zhaoxin Tang.
      Copper (Cu) supplementation for growth promotion in agriculture poses toxicological risks to animals and humans. Although Cu overload is known to trigger endoplasmic reticulum (ER) stress, the downstream cellular mechanisms driven by this stress are not fully characterized. Here, we identify the ER stress response as the primary initiator of reticulophagy (ER-phagy) in porcine liver models. Using an in vivo weaned piglet model exposed to agriculturally relevant Cu doses and an in vitro hepatocyte system, we demonstrate that Cu exposure activates UPR branches, including PERK/eIF2α phosphorylation, IRE1 and ATF6 proteins, and promotes GRP78-FAM134B association. This activation precipitated ER-phagy, evidenced by autophagosome formation, receptor upregulation, and LC3-II conversion. Pharmacological inhibition of ER stress (4-PBA) attenuated this autophagic response, whereas induction (PR-619) potentiated it. These findings suggest that the ER stress-ER-phagy axis contributes to Cu-induced hepatocellular stress, providing a mechanistic framework for reassessing Cu safety thresholds in livestock feed.
    Keywords:  copper; endoplasmic reticulum stress; hepatocytes; reticulophagy
    DOI:  https://doi.org/10.1021/acs.jafc.5c16689
  68. Nat Commun. 2026 08 03. pii: 9320. [Epub ahead of print]17(1):
    Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.
    Yun Yang, Xiaojuan Fan, Yanwen Ye, Zhenzhen Zhang, Chuyun Chen, Sebastian E J Ludwig, Sirui Zhang, Qianyun Lu, Cindy L Will, Henning Urlaub, Jing Sun, Reinhard Lührmann, Zefeng Wang.
      Although most eukaryotic mRNAs require a 5'-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we develop a circRNA-based system and unbiasedly identify more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3'UTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5'UTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5'UTR structures and facilitate ribosome scanning. Functionally, we show that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5'UTR structure and a new 3'-CiTI in response to hypoxia. Consistently, deletion of 3'-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3'UTR actively participate in the translation initiation.
    DOI:  https://doi.org/10.1038/s41467-026-75574-9
  69. Front Biosci (Landmark Ed). 2026 Aug 25. 31(8): 54223
    E3 Ubiquitin Ligase RNF126 Promotes Ovarian Cancer Progression and Cisplatin Resistance Through Targeting Numb/Notch1 Axis.
    Tianjiao Zheng, Han Wu, Li Niu, Xiaodong Wang, Hailiang Liu, Xinyan Jiang.
       BACKGROUND: RING finger protein 126 (RNF126) is an E3 ubiquitin ligase that is overexpressed in various malignancies. However, its role in ovarian cancer remains poorly understood.
    METHODS: Ovarian cancer cell lines, including SKOV3, A2780, and cisplatin-resistant SKOV3/DDP, were utilized in this study. RNF126 expression was modulated via lentiviral transduction. Cell viability, colony formation, and migration were assessed by cell counting kit-8 (CCK-8), colony formation, and Transwell assays. Protein and mRNA levels were measured by Western blotting and real-time quantitative PCR (qPCR). Protein interaction was evaluated by co-immunoprecipitation and ubiquitination assays. In vivo tumor growth and cisplatin response were examined using a xenograft model.
    RESULTS: In SKOV3 and A2780 cells, RNF126 overexpression promoted proliferation, colony formation, and migration, while its knockdown produced the opposite effects. Notably, elevated RNF126 expression was observed in the cisplatin-resistant SKOV3/DDP line. Silencing RNF126 in these cells increased cisplatin sensitivity while concurrently reducing proliferative capacity, clonogenicity, and migratory potential. RNF126 depletion in SKOV3/DDP cells led to decreased mRNA and protein expression of Notch1 and its downstream targets Myc, Cyclin D3, and Hes1. Meanwhile, Numb mRNA levels remained unchanged, whereas its protein levels increased, indicating post-transcriptional regulation. Furthermore, Numb silencing increased cell viability, clonality, migration, and Notch signaling activation in RNF126 knockdown SKOV3/DDP cells. In vivo, silencing RNF126 markedly enhanced the sensitivity of cells to cisplatin, suppressed tumor growth, and inhibited Myc, Cyclin D3, Hes1, and Notch1 protein expression. Silencing Numb can reverse the inhibitory effects of RNF126 knockdown. Mechanistic studies showed that RNF126 directly binds to the Notch signaling inhibitor Numb and mediates its ubiquitination and proteasomal degradation, thereby activating the Notch1 signaling pathway and upregulating its downstream genes. In addition, analysis of the TCGA dataset revealed that elevated RNF126 expression is a significant prognostic factor associated with increased mortality risk in ovarian cancer.
    CONCLUSIONS: These findings establish RNF126 as a critical contributor to cisplatin resistance in ovarian cancer via regulation of the Numb/Notch1 pathway and highlight its potential as a therapeutic target to counteract chemoresistance.
    Keywords:  E3 ubiquitin ligase; Notch pathway; cisplatin; drug resistance; ovarian neoplasms
    DOI:  https://doi.org/10.31083/FBL54223
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