bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–04–12
forty-nine papers selected by
Cédric Chaveroux, CNRS
  1. 5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions.
  2. RNA G-Quadruplex-protein interactions: from nuclear RNA processing to cytoplasmic stress response and neurodegeneration.
  3. The integrated stress response suppresses PINK1-dependent mitophagy by preserving mitochondrial import efficiency.
  4. N6-methyladenosine modification of MRP7 mRNA modulates its expression and paclitaxel sensitivity in lung cancer-derived A549 cells.
  5. Detection technologies for RNA modifications and their applications in plants.
  6. SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response.
  7. RNA modifications and epigenetic regulation in plants.
  8. tRNA modifications in viral replication.
  9. ATF4-dependent upregulation of Bruno 1 remodels P-bodies to selectively protect mRNAs during ER stress throughout Drosophila melanogaster oogenesis.
  10. Novel insights into the assembly of the yeast translation initiation multifactor complex: The critical role of eIF5.
  11. Rei1 and Reh1 facilitate the loading of eL24.
  12. RNA export through the nuclear pore complex: pathways, mechanisms, and imaging strategies.
  13. Key enzymes in N6-methyladenosine modification regulate plant stress tolerance by modulating mRNA stability.
  14. Neuronal Subtype-Specific Ribosomal Protein mRNA Expression.
  15. Recent advances in m6A RNA modification in hepatocellular carcinoma: from mechanisms to therapeutic potential.
  16. RNA binding proteins: Post-transcriptional regulation in craniofacial bone, tooth, and periodontium.
  17. Overcoming immunotherapy resistance in breast cancer: a novel strategy by targeting the integrated stress response.
  18. Cytoplasmic circular dsDNA is a key constituent of stress granules.
  19. The role of mTOR signaling in regulating the quality of mammalian oocytes.
  20. Mechanisms of human mitochondrial leaderless mRNA translation initiation.
  21. Translating the blueprint of cell fate: eIF5A-mediated translation regulates cellular identity in the pancreas.
  22. PARP16 is a Druggable Regulator of Ribosome MARylation and Protein Homeostasis in Ovarian Cancer Cells.
  23. The rice DEAD-box RNA helicase OseIF4AIIa associates with the CCR4-NOT complex and exhibits stress-responsive expression.
  24. Maternal regulation of translation capacity across generations.
  25. Integrated analysis of the redoxome and zinc proteome links ribosomal protein oxidation to zinc homeostasis.
  26. Omega stabilizes RNA polymerase condensates and contributes to cellular fitness during acid stress.
  27. Many paths to destruction: Family-specific turnover and stress responses for tRNA introns.
  28. RNA modifications in cancer stem cells: molecular mechanisms and targeted therapeutic strategies.
  29. Translation control by altered start codon usage as a means of modulating the general stress response and virulence in Listeria monocytogenes.
  30. Rad6-mediated ubiquitination regulates the formation of Sam1-containing stress granules during nutrient stress in budding yeast.
  31. Enhanced Intracellular Stability and Translation Efficiency of mRNA Drugs by a 2-arm mRNA Platform.
  32. The m7G modification: An emerging player in neurological diseases.
  33. Multivalent weak contacts shape chaperone-nascent protein interactions.
  34. Engineering Bisubstrates to Target m6Am RNA Methyltransferases: Synthesis and Computational Studies.
  35. Identification of ribosomal protein eL21 as a novel externalized protein and a target in triple-negative breast cancer.
  36. Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.
  37. FTO-mediated m6A demethylation inhibits bladder cancer progression via decreasing EMG1 and reducing ribosome biosynthesis.
  38. Regulation of the Growth-Inhibitory Activity of Fhl1 via Interaction With Ifh1 and Crf1 at the Ribosomal Protein Gene Promoters in Saccharomyces cerevisiae.
  39. Dietary restriction shapes intergenerational ribosome abundance and early growth of Caenorhabditis elegans offspring.
  40. GL-V9 disrupts the mitochondrial homeostasis and triggers the integrated stress response by promoting the binding of cytosolic MDM2 with NDUFS1 in colorectal cancer.
  41. Identification of biomarkers associated with integrated stress response in pituitary adenomas based on bioinformatics.
  42. Systematic profiling of cytosolic membraneless organelles reveals enrichment of oncogenic mRNA upon oxidative stress.
  43. Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.
  44. STI1 domains coordinate partitioning of UBQLN2 into stress-induced condensates.
  45. Ribosome Heterogeneity Revealed by Complex-Up Native Mass Spectrometry and Top-Down Proteomics.
  46. Disrupting PQBP1-eEF2 protein-protein interaction: From synaptic translation to immunity and cancer.
  47. Mechanism by which SAHA regulates HLA-E expression via the endoplasmic reticulum stress-related PERK/ATF4/CHOP pathway in neuroblastoma.
  48. Viral effector suppresses MTA/MTB-mediated m6A modification of genomic RNAs of a plant virus to facilitate infection.
  49. mtHsp70 chaperone converts mitochondrial proteostasis stress into impaired protein import.
  1. bioRxiv. 2026 Mar 31. pii: 2026.03.30.714548. [Epub ahead of print]
    5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions.
    Alexis B Roberson, James Marks, Ruby Pitts, Bavavarshini Tamilselvam, Brian Grieb, William P Tansey, Sezen Meydan.
      5-Azacytidine (5-AzaC) is a cytidine analog and is widely used to treat myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Although its therapeutic activity is primarily attributed to hypomethylation resulting from DNA incorporation, the majority of 5-AzaC is incorporated into RNA. However, the functional consequences of 5-AzaC incorporation into RNA have been unknown. Here, we show that 5-AzaC treatment of cells leads to inhibition of protein synthesis. Ribo-seq, Disome-seq, and RNA-seq in cells treated with 5-AzaC exhibit a time-dependent C-to-G transversion signature in mRNAs within 2 h of treatment. These transversion events are enriched within footprint positions corresponding to the A-site of monosomes or leading stalled ribosome in a disome complex. Consistently, ribosome and disome footprints are accumulated at sites with C-rich codons in the A-site, specifically with the codons containing a C in the second position. 5-AzaC activates the integrated stress response (ISR) and the ribotoxic stress response (RSR) in a GCN2- and ZAK-dependent manner, consistent with disome-mediated signaling. Furthermore, loss of the Ribosome Quality Control (RQC) factor, ZNF598, sensitizes cells to 5-AzaC. Collectively, our results support a model where 5-AzaC is rapidly incorporated into mRNAs, disrupts decoding, and triggers disome-mediated signaling pathways, which contribute to its cytotoxicity. These findings suggest that translation disruption represents an additional layer of 5-AzaC's mechanism of action, alongside its known DNA-mediated effects.
    DOI:  https://doi.org/10.64898/2026.03.30.714548
  2. RNA Biol. 2026 Apr 10.
    RNA G-Quadruplex-protein interactions: from nuclear RNA processing to cytoplasmic stress response and neurodegeneration.
    Dimitrios G Anastasakis, Markus Hafner.
      RNA G-quadruplexes (rG4s) are stable secondary structures formed by non-canonical Hoogsteen base-pairing of guanine-rich sequences in precursor and mature messenger and non-coding RNAs. We review evidence that rG4s exist in two functionally distinct worlds. In the nucleus, rG4s fold co-transcriptionally to regulate gene expression and RNA processing and organizing membraneless organelles through liquid-liquid phase separation. Splicing regulation by rG4s is restricted to vertebrates and co-evolved with transcriptome complexity. In the cytoplasm, rG4s are actively maintained in an unfolded state by dedicated helicases and RNA-binding proteins, but fold upon stress to nucleate stress granules, that sequester mRNAs and sustain cell survival. When compartmentalization of rG4-protein interactions fails, cells lose both nuclear RNA processing control as well as cytoplasmic translational regulation and proper stress response. The same biophysical properties that make rG4s effective scaffolds for reversible phase separation in RNA processing, proteostasis, and acute stress become liabilities under chronic conditions: in ageing neurons, failure of rG4-protein homoeostasis transforms protective condensates into irreversible aggregates associated with α-synuclein, tau, TDP-43, and FUS pathology. We discuss the implications of a dynamic equilibrium of folded and unfolded rG4s in health and disease, with particular focus on their emerging roles in neurodegeneration.
    Keywords:  ALS; RNA G-quadruplex; RNA-binding proteins; co-transcriptional splicing; liquid-liquid phase separation; neurodegeneration; rG4 homoeostasis; stress granules
    DOI:  https://doi.org/10.1080/15476286.2026.2658922
  3. Nat Commun. 2026 Apr 09.
    The integrated stress response suppresses PINK1-dependent mitophagy by preserving mitochondrial import efficiency.
    Mingchong Yang, Zengshuo Mo, Kelly Walsh, Wen Liu, Imane Nait Irahal, Damien Arnoult, Xiaoyan Guo.
      Mitophagy is crucial for maintaining mitochondrial health, but how its levels adjust to different stress conditions remains unclear. In this study, we investigated the role of the DELE1-HRI axis of the integrated stress response (ISR) in regulating mitophagy, a key mitochondrial quality control mechanism. Our findings show that the ISR suppresses PINK1-dependent mitophagy under many mitochondrial stress conditions by maintaining mitochondrial presequence protein import, independent of ATF4 activation. Mitochondrial presequence protein import efficiency is tightly linked to the rate of protein synthesis. Without the ISR, increased protein synthesis overwhelms the mitochondrial import machineries, reducing import efficiency. This impairment can be mitigated by pharmacological attenuation of protein synthesis, such as with mTOR or general translation inhibitors. Under severe depolarizing stress, mitochondrial import is heavily impaired even with an active ISR, leading to significant PINK1 accumulation. In contrast, mild mitochondrial stress allows more efficient protein import in the presence of the ISR, resulting in lower mitophagy. Without the ISR, mitochondrial protein import becomes significantly compromised, causing PINK1 accumulation to reach the threshold level necessary to trigger mitophagy. These findings reveal a link between ISR-regulated protein synthesis, mitochondrial protein import, and mitophagy, offering potential therapeutic targets for diseases associated with mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s41467-026-71630-6
  4. Drug Metab Pharmacokinet. 2026 Jan 14. pii: S1347-4367(26)00005-4. [Epub ahead of print]68 101519
    N6-methyladenosine modification of MRP7 mRNA modulates its expression and paclitaxel sensitivity in lung cancer-derived A549 cells.
    Takuto Inamoto, Masataka Nakano, Tatsuki Fukami, Miki Nakajima.
      Methylation of adenosine at the N6 position (m6A modification) is the most prevalent epitranscriptomic modification in mammals, regulating RNA stability, splicing, translation, and decay. Growing evidence has revealed that m6A modification is intricately linked to cancer progression. This study aimed to investigate the effects of m6A modification on the sensitivity of lung cancer-derived A549 cells to paclitaxel (PTX). Knockdown of methyltransferase like (METTL) 3/14, the m6A writer complex, increased A549 cell viability under PTX, indicating m6A modification enhances PTX sensitivity. METTL3/14 knockdown increased the expression of multidrug resistance-associated protein (MRP) 7, but not multiple drug resistance (MDR) 1 or MRP1, promoting PTX efflux. RNA immunoprecipitation showed that MRP7 mRNA is highly methylated at the 5'-untranslated region (UTR), coding region, and 3'-UTR. METTL3/14 knockdown stabilized MRP7 mRNA, while depletion of m6A readers YTHDC2 or YTHDF2 also elevated MRP7 mRNA, suggesting these readers mediate its degradation. Moreover, knockdown of the erasers fat mass and obesity-associated protein (FTO) or AlkB homolog 5 as well as treatment with entacapone, an FTO inhibitor, increased PTX sensitivity in PTX-resistant A549 cells. These results suggest that the m6A-dependent regulation of MRP7 expression contributes to PTX resistance, highlighting a potential therapeutic avenue in lung cancer.
    Keywords:  Drug resistance; Drug transporter; Post-transcriptional regulation; RNA methylation; RNA modification
    DOI:  https://doi.org/10.1016/j.dmpk.2026.101519
  5. aBIOTECH. 2026 Mar;7(1): 100002
    Detection technologies for RNA modifications and their applications in plants.
    Jiayin Du, WingTing Cheung, Lixing Zhang, Pingxian Zhang, Guanqun Wang.
      Chemical modifications of RNA molecules play diverse regulatory roles in gene expression by influencing RNA biogenesis, stability, and translation. Emerging evidence indicates that RNA modifications in plants have functional significance for enhancing crop performance, stress resistance, and agricultural productivity. Recent advances in quantitative mapping of RNA modifications at the single-base level have highlighted the critical roles of RNA modifications in regulating RNA metabolism and translation in mammals. However, our understanding of the regulatory roles of these chemical modifications at the single-base level remains limited in plants, hindering deeper insights into their biological significance. This gap can be attributed to the limited use of advanced base-resolution detection technologies in plant research. Here, we systematically review both conventional and base-resolution methods that have been used to detect RNA modifications in mammals and plants. We highlight the implications of RNA modifications at the single-base level, and discuss how modification levels could be manipulated during crop improvement and breeding to regulate RNA metabolism and translation without altering amino acid sequences.
    Keywords:  Direct RNA sequencing; Epitranscriptomics; Plants; RNA modifications
    DOI:  https://doi.org/10.1016/j.abiote.2025.100002
  6. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2536296123
    SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response.
    Nicholas A Parenti, Renee Cusic, David M Renner, Nathaniel Jackson, Chengjin Ye, Li Hui Tan, Jessica J Pfannenstiel, Anthony R Fehr, Noam A Cohen, Luis Martinez-Sobrido, James M Burke, Susan R Weiss.
      Coronaviruses pose a serious threat to public health, driving the need for antiviral therapeutics and vaccines. Therefore, it is paramount to understand how this family of viruses evades cellular antiviral responses and establishes productive infection. The conserved coronavirus nonstructural protein 1 (nsp1) has been shown to inhibit host protein synthesis and, in some coronaviruses, promote host messenger RNA (mRNA) degradation while viral mRNAs are protected. We showed previously that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) induces activation of host integrated stress response (ISR) kinases protein kinase R (PKR) and PKR-like endoplasmic reticulum kinase (PERK), which promote phosphorylation of eukaryotic initiation factor 2 (eIF2α) and consequent inhibition of host protein synthesis. In contrast, eIF2α remains unphosphorylated during Middle East respiratory syndrome coronavirus (MERS-CoV) infection. To investigate the interactions of nsp1 and the ISR kinases, we utilized recombinant SARS-CoV-2 and MERS-CoV expressing nsp1 with mutations in each of two conserved domains. Upon infection with SARS-CoV-2 nsp1 mutants, translation was shut down in wildtype (WT) and PKR knockout (KO) cells but rescued in PERK KO cells, likely due to reduced p-eIF2α. In contrast, translation was rescued during infection with the analogous MERS-CoV nsp1 mutants even in WT cells. Moreover, SARS-CoV-2 WT suppressed expression of GADD34, a negative regulator of eIF2α phosphorylation, while SARS-CoV-2 nsp1 mutants induced GADD34. In contrast, MERS-CoV WT induced GADD34. Utilizing single-molecule fluorescence in situ hybridization, we found that SARS-CoV-2 and MERS-CoV nsp1 promote host mRNA degradation during WT, but not nsp1 mutant, infection. Thus, SARS-CoV-2 and MERS-CoV differ in interactions with the ISR and nsp1 control of host protein synthesis.
    Keywords:  coronavirus; integrated stress response; mRNA degradation; mRNA translation; nonstructural protein 1
    DOI:  https://doi.org/10.1073/pnas.2536296123
  7. aBIOTECH. 2026 Jun;7(2): 100020
    RNA modifications and epigenetic regulation in plants.
    Xinran Zhang, Jiangbo Wei.
      Chemical modifications of RNA, such as N 6-methyladenosine (m6A), have emerged as critical regulators of gene expression and chromatin dynamics in eukaryotes. Research on RNA modifications in plants has primarily focused on mRNAs and their post-transcriptional roles. Recent studies in mammals have shown that various chromatin-associated RNAs (caRNAs) regulate chromatin structure and transcription, but the presence and functions of plant caRNAs remain largely unexplored. This review systematically introduces the current mechanisms and detection methods of RNA modifications and their roles in epigenetic regulation, with a specific focus on caRNAs in plants. Finally, we offer future perspectives, emphasizing that a deeper understanding of the epitranscriptomic regulation of caRNAs will be essential for decoding plant chromatin dynamics and may open new avenues for crop improvement.
    Keywords:  Chromatin-associated RNAs; Epitranscriptome; N6-methyladenosine; Plant chromatin regulation
    DOI:  https://doi.org/10.1016/j.abiote.2026.100020
  8. J Biol Chem. 2026 Apr 07. pii: S0021-9258(26)00300-5. [Epub ahead of print] 111430
    tRNA modifications in viral replication.
    Chathuri Pathirage, Kristin S Koutmou, Karin Musier-Forsyth.
      tRNA modifications are key players in post-transcriptional gene expression regulation under external and cellular stresses. Viral infection is a common external stress that hijacks cellular processes for replication. Host cell tRNA pools and modification profiles are often reshaped during viral infection, eliciting both pro- and anti-viral effects. Changes in the host tRNA modifications, particularly in the anticodon sequence, have the capability to reprogram host and viral proteomes. For example, anticodon loop modifications contribute to programmed ribosomal frameshifting essential for producing certain viral proteins. However, the roles of tRNA modifications are not limited to translation during viral infection. Retroviruses use select host cell tRNAs as reverse transcription primers and modifications modulate steps in reverse transcription. Furthermore, some non-primer modified tRNAs are selectively packaged into virion particles, though their functions remain unknown. Virally-encoded tRNAs harbor modifications that expand the anticodon pool, as host tRNAs are depleted. Expression and activity of several tRNA-modifying enzymes are regulated upon viral infection, the functional implications of which remain to be elucidated. tRNA modifications are involved in anti-viral defense, particularly in tRNA cleavage at the anticodon loop following viral infection, leading to tRNA-derived fragments. While the tRNA modification landscape is likely significantly altered following most viral infections, current evidence is limited to a few specific examples. A global tRNAome analysis during viral infection will shed light on the regulation of these and other processes. Emerging technologies including advances in direct tRNA sequencing and modification detection via mass spectrometry are making this possible.
    Keywords:  RNA modification; anti-viral immune response; codon usage; reverse transcription; tRNA-derived RNA (tDR); tRNA-like structures (TLS); tRNA-modifying enzymes; transfer RNA (tRNA); translation regulation; viral replication
    DOI:  https://doi.org/10.1016/j.jbc.2026.111430
  9. bioRxiv. 2026 Apr 05. pii: 2026.04.01.715972. [Epub ahead of print]
    ATF4-dependent upregulation of Bruno 1 remodels P-bodies to selectively protect mRNAs during ER stress throughout Drosophila melanogaster oogenesis.
    Samantha N Milano, Livia V Bayer, Julie J Ko, Gwendolyn S Posner, Albina H Granovsky, Diana P Bratu.
      P-bodies are cytoplasmic membraneless organelles involved in mRNA storage, yet their role in cellular stress responses remains poorly understood. Here, we demonstrate that P-bodies are rapidly and selectively remodeled during the early response to endoplasmic reticulum (ER) stress in D. melanogaster oogenesis, positioning them as key early stress responders. Notably, this remodeling occurs within minutes of stress induction and precedes stress granule formation. This early remodeling is characterized by changes in P-body morphology and internal organization and promotes selective mRNA regulation. Specifically, ER stress leads to the recruitment and stabilization of maternal mRNAs and those encoding P-body components, while transcripts not associated with P-bodies are degraded. These observations indicate that P-body remodeling is not merely structural but functionally linked to the selective preservation of mRNA populations during stress. Mechanistically, we find that this process is driven by transcriptional upregulation of the RNA-binding protein, Bruno 1, downstream of ATF4-dependent stress signaling, thereby establishing a direct connection between the unfolded protein response and condensate regulation. Consistent with this model, loss of Bruno 1 abolishes, whereas its overexpression enhances P-body remodeling, demonstrating that stress-induced changes in RNA binding protein levels can actively reprogram condensate properties. Together, our findings reveal that P-bodies function as dynamic, stress-responsive hubs that integrate transcriptional signaling with post-transcriptional control, enabling the selective preservation of essential mRNAs during ER stress. More broadly, this work uncovers a previously unrecognized mechanism by which stress signaling pathways reorganize cytoplasmic architecture to shape mRNA fate.
    DOI:  https://doi.org/10.64898/2026.04.01.715972
  10. Protein Sci. 2026 May;35(5): e70550
    Novel insights into the assembly of the yeast translation initiation multifactor complex: The critical role of eIF5.
    Borja Sáez de la Fuente, Laura Villamayor-Belinchón, José Rafael Ciges-Tomas, Marisa López-Redondo, Carolina Espinosa, Elisabetta Boeri Erba, José L Llácer.
      The eukaryotic translation initiation is a biological process in which at least a dozen eukaryotic initiation factors (eIFs) are involved. Specifically, eIF3, eIF1, eIF5, and eIF2 as a ternary complex (eIF2-TC) bound to GTP and methionyl initiator tRNA (Met-tRNAi Met). They interact to form a large complex called the multifactor complex (MFC). This complex binds cooperatively to the ribosomal pre-initiation complex (PIC), promoting the loading of the Met-tRNAi Met into the peptidyl (P) site of the 40S ribosomal subunit. While some interactions between eIFs have been described in the context of the PIC, the interactions within the MFC remain poorly understood. Here, we combine biophysical and biochemical approaches, including mass photometry and native mass spectrometry, with structural biology methods such as electron microscopy, to gain deeper insights into the MFC architecture. Our findings provide novel insights into the critical role of eIF5 during MFC assembly. Notably, two copies of eIF5 are involved in the formation of the MFC. We propose that one eIF5 molecule engages eIF2β and eIF2γ, whereas a second eIF5 molecule interacts with eIF1 together with eIF3c.
    Keywords:  eIF5; eukaryotic initiation factors; multifactor complex; translation initiation
    DOI:  https://doi.org/10.1002/pro.70550
  11. bioRxiv. 2026 Apr 02. pii: 2026.03.31.715693. [Epub ahead of print]
    Rei1 and Reh1 facilitate the loading of eL24.
    Ran Lin, Madison J Reynolds, Nila R Shankar, Arlen W Johnson.
      The correct assembly of ribosomes is essential for viability and faithful gene expression. In eukaryotic cells, the pre-40S and pre-60S ribosomal subunits are largely pre-assembled in the nucleolus before they are exported to the cytoplasm for final maturation. Although most ribosomal proteins of the large subunit are loaded onto pre-60S particles in the early nucleolar steps, a few, including eL24, are loaded in the cytoplasm. eL24 is thought to recruit the zinc-finger protein Rei1 (ZNF622 in humans). In yeast, Rei1 has a paralog, Reh1. While we and others have previously shown that Rei1 facilitates the removal of Arx1, Rei1 and Reh1 appear to have an additional unknown function. To identify this function, we first examined the protein composition of pre-60S subunits isolated from rei1Δ reh1Δ mutant cells and found that these subunits were specifically defective for eL24. However, the absence of eL24 did not impair Rei1 binding to pre-60S. Moreover, overexpression of eL24 suppressed the growth defect of the double mutant. As an alternative approach to understanding the function of Rei1 and Reh1, we screened for bypass suppressors of the growth defect of rei1Δ reh1Δ cells. We identified mutations in the genes coding for ribosomal protein uL3, the GTPase Lsg1 and the protein phosphatase Ppq1. Importantly, these suppressors all partially reversed the eL24 loading defect of rei1Δ reh1Δ cells. Based on these results, we propose a revised order of cytoplasmic assembly events where Rei1 and Reh1 facilitate the recruitment of eL24 to the pre-60S particle.
    DOI:  https://doi.org/10.64898/2026.03.31.715693
  12. RNA Biol. 2026 Apr 06.
    RNA export through the nuclear pore complex: pathways, mechanisms, and imaging strategies.
    Donghong Fu, Wenlan Yu, Fanghemei Zhang, Coby Rush, Mark Tingey, Weidong Yang.
      Understanding how RNA molecules traverse the nuclear pore complex (NPC) is central to regulated gene expression because the NPC serves as the selective gateway for RNA export from the nucleus. Distinct RNA classes, including tRNAs, snRNAs, miRNAs, lncRNAs, piRNAs, rRNAs, mRNAs, and circRNAs, follow biogenesis-coupled pathways and engage specific transport receptors and accessory factors to cross this barrier. Recent advances in single-molecule and super-resolution microscopy now enable direct, NPC-resolved visualization of transport for selected RNA species, allowing quantitative measurements of export kinetics, 3D trajectories through the pore, and interaction dynamics with NPC substructures. Here, we review and compare what has been learned from NPC-resolved imaging across RNA classes studied to date, highlighting both shared organizing principles and cargo-specific behaviours. We then describe an experimental and analytical toolbox for NPC-resolved studies of mRNA and pre-ribosomal particle export, including RNA-labelling strategies, major single-molecule and super-resolution modalities, and quantitative metrics used to extract transport parameters. Finally, we discuss key technical and conceptual barriers that currently limit extension to other RNA classes, particularly small and/or low-abundance RNAs, and outline practical strategies to overcome these constraints. Together, this review provides a unified framework for the next generation of single-molecule dissection of RNA dynamics at the nuclear pore.
    Keywords:  RNA classes; RNA nuclear export; nuclear pore complex; nucleocytoplasmic transport; single molecule fluorescence microscopy; super-resolution microscopes
    DOI:  https://doi.org/10.1080/15476286.2026.2656571
  13. Plant Cell Rep. 2026 Apr 07. pii: 116. [Epub ahead of print]45(5):
    Key enzymes in N6-methyladenosine modification regulate plant stress tolerance by modulating mRNA stability.
    Zishuo Han, Hongxiang Zheng, Yinping Gao, Simin Li, Zengting Chen, Fangning Zhang, Fenghui Wu, Zhiying Zhao, Lei Yan, Na Sui.
       KEY MESSAGE: m6A writer and eraser mutants exhibit contrasting stress-dependent responses, highlighting that m6A-mediated regulation modulates plant stress responses in a stress-type-specific manner. N6-methyladenosine (m⁶A) is the most prevalent internal RNA modification in eukaryotic mRNAs and plays important roles in plant development and abiotic stress responses. However, how distinct m⁶A regulatory components contribute to stress adaptation under a unified experimental framework remains incompletely understood. Here, we performed a comparative analysis of Arabidopsis thaliana loss-of-function mutants of core m⁶A regulators, including m6A methyltransferase (writer) mutants (atfip37-2 and atmtb) and m6A demethylase (eraser) mutants (atalkbh9b-1 and atalkbh10b), using parallel phenotypic, physiological, molecular, and transcriptomic approaches under matched conditions. Under normal growth conditions, all mutants exhibited reduced primary root length, lower fresh weight, and delayed flowering compared with wild-type plants. Under stress treatments, all mutants were more growth-compromised than the wild type, but the magnitude of inhibition differed among regulatory classes in a stress-type-dependent manner: writer mutants exhibited comparatively less overall growth inhibition than eraser mutants under mannitol-based osmotic stress, whereas eraser mutants showed comparatively milder growth inhibition than writer mutants under NaCl treatment. Transcript stability assays further suggested that disruption of m⁶A regulatory components is associated with altered stability of selected stress-responsive transcripts, including genes involved in ABA biosynthesis and signaling. Together, these results provide a comparative genetic framework linking m⁶A regulatory perturbation to drought- and salt-related responses and support a context-dependent role for post-transcriptional regulation in plant stress adaptation.
    Keywords:   Arabidopsis thaliana ; Abiotic stress; Post-transcriptional regulation; m6A
    DOI:  https://doi.org/10.1007/s00299-026-03801-0
  14. RNA. 2026 Apr 09. pii: rna.080954.126. [Epub ahead of print]
    Neuronal Subtype-Specific Ribosomal Protein mRNA Expression.
    Joaquin Garat, Sofia Niño-Rivero, Patricia Lagos, Andres Di Paolo, Pablo Smircich, Jose Sotelo-Silveira.
      Current understanding recognizes that ribosomal proteins (RPs) have regulatory roles beyond their canonical structural functions in translation, raising the question of how their expression is organized across cell types. Given the diversity of neuronal cell types, understanding RP gene expression at the neuronal subtype level is an important and previously inaccessible question. Here, leveraging advances in single-cell transcriptomics, we analyzed single-cell RNA-seq datasets from the mouse cerebral cortex and hippocampus to examine RP mRNA expression across neuronal subtypes. We observed distinct RP mRNA expression profiles between excitatory and inhibitory neurons and found that higher Rps27 transcript levels in inhibitory neurons corresponded to increased Rps27 protein abundance. Beyond excitatory-inhibitory differences, RP mRNA expression further segregated across well-defined neuronal subclasses, with 59 of 84 RP genes differentially expressed, including enrichment of Rpl21 in Lamp5 and Rps27 in Vip interneurons. These patterns were consistent across cortical regions and reproducible across two independent single-cell technologies (Smart-seq2 and 10x Genomics). Analysis of aging- and stress-associated datasets revealed stable RP expression signatures, with limited phenotype-linked changes. Together, we present a comprehensive atlas of ribosomal protein gene expression at neuronal subclass resolution, revealing robust subclass-specific transcriptional signatures suggesting an underestimated regulatory layer.
    Keywords:  Neurons; Ribosome; Single cell RNAseq; Transcriptomics
    DOI:  https://doi.org/10.1261/rna.080954.126
  15. Front Mol Biosci. 2026 ;13 1772310
    Recent advances in m6A RNA modification in hepatocellular carcinoma: from mechanisms to therapeutic potential.
    Qingmiao Shi, Yingru Liu, Mengjuan Xuan, Leiya Fu, Na Lou, Chi Lv, Chen Xue.
      Hepatocellular carcinoma (HCC) remains a major global health burden due to its high incidence and mortality, underscoring the urgent need to elucidate the molecular mechanisms of HCC and to improve diagnosis and therapeutic approaches. As the most prevalent form of mRNA modification, N6-methyladenosine (m6A) plays a central role in regulating diverse cellular processes in both physiological and pathological conditions, particularly in cancer initiation, development, and progression. This comprehensive review systematically outlines the biological function of three primary classes of m6A regulator proteins, "writers", "erasers", and "readers". It further examines the dysregulated expression patterns of m6A regulators in HCC, analyzes their clinical associations with tumor grade, clinical stage, and survival outcomes, and evaluates their functional contributions to key oncogenic processes, including cell proliferation, apoptosis, and metastasis. Moreover, this review highlights the critical involvement of m6A RNA modification in orchestrating major molecular mechanisms in HCC, offering an in-depth analysis of its regulatory effects on glycolysis, lipid metabolism, ferroptosis, cancer stemness, tumor immunity, cell cycle progression, and resistance to therapy. Finally, the review synthesizes current progress in emerging therapeutic strategies that target the m6A RNA modification for the treatment of HCC. In conclusion, this review presents a systematic summary of recent advances in m6A RNA modification in HCC, delivering valuable insights for future basic and translational studies. Ongoing research into m6A-mediated regulatory mechanisms hold promise for transforming diagnostic paradigms and enabling the development of innovative therapeutic strategies for patients with HCC.
    Keywords:  N6-methyladenosine; RNA methylation; gene expression regulation; hepatocellular carcinoma; molecular targeted therapy
    DOI:  https://doi.org/10.3389/fmolb.2026.1772310
  16. Arch Oral Biol. 2026 Mar 31. pii: S0003-9969(26)00087-7. [Epub ahead of print]187 106581
    RNA binding proteins: Post-transcriptional regulation in craniofacial bone, tooth, and periodontium.
    Kebing Zhou, Yuanyuan Xu, Liwei Zheng, Xin Zhou.
       OBJECTIVES: This review aims to summarize the roles of RNA binding proteins (RBPs) in post-transcriptional regulation in craniofacial bone, tooth, and periodontal tissues.
    DESIGN: PubMed and Web of Science were searched from inception to November 2025 for original research, reviews, and clinical studies. Key terms combined RBP concepts ("RNA binding protein" or RBP) with craniofacial/dental terms (craniofacial or maxillofacial or tooth or dental or enamel or dentin or odontogenesis or periodontal or periodontium or alveolar bone) and process terms (splicing or "RNA modification" or m6A or "mRNA stability" or translation or microRNA or miRNA or "noncoding RNA").
    INCLUSION CRITERIA: studies linking RBPs to craniofacial bone, tooth, or periodontal tissues with mechanistic, functional, or clinical evidence.
    EXCLUSION CRITERIA: non-relevant tissues, non-RBP regulators, or studies lacking interpretable post-transcriptional evidence. Duplicates were removed; titles/abstracts were screened followed by full-text assessment, and reference lists were checked.
    RESULTS: RBP mechanisms were summarized across alternative splicing, RNA modification and mRNA stability regulation, translation control, and noncoding RNA regulation. Reported outcomes were tissue- and cell-type dependent, spanning osteogenesis/osteoclastogenesis, enamel/odontoblast lineage programs, and periodontal homeostasis and regeneration.
    CONCLUSIONS: RBPs coordinate multiple post-transcriptional steps that shape craniofacial bone remodeling, tooth development, and periodontal repair. Evidence remains uneven across tissues and models, supporting the need for more cell-resolved and in vivo validation.
    Keywords:  Bone remodeling; Craniofacial; Periodontal homeostasis; RNA binding proteins; Tooth development
    DOI:  https://doi.org/10.1016/j.archoralbio.2026.106581
  17. Front Cell Dev Biol. 2026 ;14 1720480
    Overcoming immunotherapy resistance in breast cancer: a novel strategy by targeting the integrated stress response.
    Jian Yue, Tianyi Pu, Dele He, Yangyong Luo, Simin Ruan, Huahan Li, Jianwei Zhan, Guosen Su, Jianyuan Su, Sheng Chen, Guoxing Huang.
      Immunotherapy resistance remains a major obstacle in treating breast cancer, particularly aggressive subtypes like triple-negative breast cancer (TNBC). This review delineates the pivotal role of the Integrated Stress Response (ISR) as a central metabolic-immune regulator driving this resistance. The ISR is activated in the tumor microenvironment (TME) by diverse stressors-including hypoxia, nutrient scarcity, and ER stress-via four upstream kinases (PERK (PKR-like ER kinase), GCN2, PKR, HRI). These kinases converge to phosphorylate eukaryotic initiation factor 2α (eIF2α), leading to the selective translation and robust activation of the transcription factor ATF4. The ensuing ATF4-driven program fosters an immunosuppressive TME through multifaceted mechanisms: tumor-intrinsic upregulation of PD-L1, secretion of immunosuppressive exosomes, metabolic reprogramming that depletes critical amino acids, and direct impairment of T cell function and antigen presentation. Concurrently, ISR activation in immune cells-such as myeloid-derived suppressor cells (MDSCs) and dendritic cells-further dampens antitumor immunity. Targeting the ISR with small-molecule inhibitors (PERK or GCN2 inhibitors, ISRIB) or repurposed agents (metformin) demonstrates compelling preclinical efficacy in reversing immunosuppression and synergizing with immune checkpoint inhibitors. Biomarker-driven strategies, including ISR gene signatures and p-eIF2α immunohistochemistry, offer promising avenues for patient stratification. Thus, pharmacological targeting of the ISR represents a strategically viable approach to reprogram the immunosuppressive TME and overcome immunotherapy resistance in breast cancer, warranting urgent clinical investigation.
    Keywords:  breast cancer; eIF2α-ATF4 axis; immune checkpoint inhibitors; immunotherapy resistance; integrated stress response (ISR); tumor microenvironment
    DOI:  https://doi.org/10.3389/fcell.2026.1720480
  18. bioRxiv. 2026 Mar 15. pii: 2026.03.12.711345. [Epub ahead of print]
    Cytoplasmic circular dsDNA is a key constituent of stress granules.
    Natalia A Demeshkina, Adrian R Ferré-D'Amaré.
      Stress granules are large cytoplasmic bodies formed in response to environmental insults by eukaryotic cells. Stress granule formation is key for post-stress recovery, and many diseases and infections are characterized by dysregulation of these membraneless organelles. How specific and non-specific macromolecular interactions drive formation of stress granules and other large assemblies is an area of active research. Stress granules are comprised of dense, ∼200 nm cores, and these are known to contain numerous RNAs and proteins. Now, we have discovered that more than half of the nucleic acid content of stress granule cores is circular, double-stranded DNA. We demonstrate cytologically that these extrachromosomal circular DNAs (eccDNAs) colocalize cytoplasmically with canonical stress granule marker proteins, and through CRISPR targeting in yeast, that they are required for stress granule formation upon stress. This discovery thus reveals a key function for eccDNA in the eukaryotic stress response.
    DOI:  https://doi.org/10.64898/2026.03.12.711345
  19. J Assist Reprod Genet. 2026 Apr 08.
    The role of mTOR signaling in regulating the quality of mammalian oocytes.
    Xin Bai, Pengfei Zhu, Xueqing Wu.
       BACKGROUND: mTOR (mammalian target of rapamycin) is a central sensor of cellular nutrient and energy status. It regulates key biological processes, including metabolism, protein synthesis, and autophagy. Increasing evidence shows that mTOR signaling plays an important role in maintaining oocyte quality.
    OBJECTIVE: This review aims to provide a systematic overview of how mTOR signaling regulates oocyte quality in mammals.
    CONTENT: We summarize current knowledge on the role of mTOR in key cellular processes related to oocyte competence. These processes include metabolic regulation, translational control, autophagy, and mitochondrial function. We also discuss evidence from experimental and clinical studies. These studies link dysregulated mTOR activity to impaired oocyte maturation and reduced fertility.
    KEY FINDINGS: Current evidence shows that precise control of mTOR activity is essential for maintaining oocyte developmental potential. In contrast, the dysregulation of mTOR impairs oocyte quality and negatively affects reproductive outcomes.
    CONCLUSION: A better understanding of mTOR-related regulatory mechanisms may help identify new therapeutic strategies. These strategies may improve oocyte quality and female fertility.
    Keywords:  Clinical translation; IVF-ET; MTOR; Oocyte quality
    DOI:  https://doi.org/10.1007/s10815-026-03863-9
  20. Nat Commun. 2026 Apr 04.
    Mechanisms of human mitochondrial leaderless mRNA translation initiation.
    Shuangjie Shen, Yinghua Xu, Daniel L Kober, Jinfan Wang.
      Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ribosomes initiate translation remain poorly understood, particularly because mitochondrial mRNAs generally lack the 5' untranslated regions that guide translation initiation in bacterial and cytoplasmic systems. Using real-time single-molecule fluorescence measurements, biochemical assays, and cryo-EM analysis, we show that human mitochondrial translation initiation occurs through two parallel pathways. In one pathway, leaderless mRNA first loads onto the 28S small subunit, followed by recruitment of the 39S large subunit to form the 55S initiation complex. In the second pathway, a preassembled 55S monosome directly loads onto leaderless mRNA. Both pathways require recruitment of mtIF2 and fMet-tRNAMet before mRNA binding. However, the monosome-loading pathway tolerates non-formylated Met-tRNAMet and is suppressed by mtIF3. Together, these findings define the heterogeneous pathways of human mitochondrial translation initiation on leaderless mRNAs.
    DOI:  https://doi.org/10.1038/s41467-026-71535-4
  21. Mol Metab. 2026 Apr 02. pii: S2212-8778(26)00046-3. [Epub ahead of print] 102362
    Translating the blueprint of cell fate: eIF5A-mediated translation regulates cellular identity in the pancreas.
    Danielle L Overton, Catharina Bp Villaca, Dorian J Dale, Caleb D Rutan, Morgan A Robertson, Craig T Connors, Emily K Anderson-Baucum, Teresa L Mastracci.
      Cellular identity is fundamentally determined by the precise regulation of protein synthesis, which governs growth, differentiation, and function. In the pancreas, the balance between exocrine and endocrine cell types is critical for organ function, and the disruption of protein synthesis in these cells can lead to diseases such as exocrine insufficiency and diabetes. The specialized mRNA translation factor eukaryotic initiation factor 5A (eIF5A) has emerged as an essential regulator of on-demand protein synthesis in professional secretory cells. Here, we investigate the role of eIF5A-mediated mRNA translation in lineage specification during pancreas development. Using genetic mouse models, our studies reveal that loss of eIF5A results in a marked reduction of exocrine volume and a paradoxical expansion of the insulin-producing beta cell population. We reveal that these cellular changes are driven by impaired on-demand protein synthesis during the critical stage of pancreatic cell differentiation. Mechanistically, we show that eIF5A deficiency disrupts the synthesis of proteins critical for proper pathway signaling-most notably Notch-that instruct cell fate decisions. As a result, we observe impaired ductal branching and tip formation as well increased Ngn3+ endocrine progenitors within the ducts. These changes in lineage allocations directly contribute to decreased acinar cell and increased beta cell mass. Remarkably, eIF5A-deficient mice maintain elevated beta cell mass and exhibit preserved glucose tolerance despite severe exocrine deficiency. Collectively, our findings establish that eIF5A-mediated mRNA translation regulates critical developmental signaling pathways and reinforces the finding that disruptions in protein synthesis can reprogram cellular identity and drive disease pathogenesis.
    DOI:  https://doi.org/10.1016/j.molmet.2026.102362
  22. bioRxiv. 2026 Apr 02. pii: 2026.04.01.715986. [Epub ahead of print]
    PARP16 is a Druggable Regulator of Ribosome MARylation and Protein Homeostasis in Ovarian Cancer Cells.
    Sridevi Challa, Morgan Dasovich, Jonathan C Abshier, Komal Pekhale, Lu Yang, Cristel V Camacho, W Lee Kraus.
      Cytosolic NAD□ synthesis supports ovarian cancer growth by enabling PARP16-dependent mono(ADP-ribosyl)ation (MARylation) of ribosomal proteins, thereby fine-tuning translation and maintaining protein homeostasis. While genetic depletion of PARP16 disrupts ribosome MARylation and impairs tumor cell growth, the therapeutic potential of pharmacologic PARP16 inhibition in this pathway remains unexplored. Here, we characterized the effects of DB008, a tool compound that functions as a selective inhibitor of PARP16, in ovarian cancer cells. Biochemical analyses demonstrated that PARP16 undergoes NAD□-dependent auto-MARylation and that NMNAT-2 supplies NAD□ to support this activity. DB008 potently inhibited PARP16 auto-MARylation in vitro. In ovarian cancer cells, DB008 engaged PARP16, reduced its MARylation, and decreased ribosome-associated MARylation. Consistent with PARP16 depletion, DB008 enhanced global protein synthesis, increased protein aggregation, and suppressed cell growth and anchorage-independent colony formation. CRISPR-mediated deletion of the PARP16 gene in ovarian cancer cells abolished the effects of DB008 on translation, protein aggregation, and proliferation, demonstrating on-target activity. Moreover, cells expressing a PARP16 mutant resistant to DB008 were unaffected by inhibitor treatment, further confirming that the cellular effects of DB008 require on-target inhibition. Finally, DB008 significantly inhibited tumor growth in OVCAR3 xenografts, with on-target engagement of PARP16 in the xenograft tumors. Collectively, these findings establish PARP16 as a druggable regulator of ribosome MARylation and protein homeostasis in ovarian cancer and provide pharmacologic proof-of-concept that disrupting ribosomal MARylation impairs tumor growth.
    DOI:  https://doi.org/10.64898/2026.04.01.715986
  23. Mol Biol Rep. 2026 Apr 07. pii: 597. [Epub ahead of print]53(1):
    The rice DEAD-box RNA helicase OseIF4AIIa associates with the CCR4-NOT complex and exhibits stress-responsive expression.
    Vu Bao Nguyen, Thi Hien Nguyen, Thi Mai Nguyen, Hoang Mau Chu.
       BACKGROUND: The CCR4-NOT complex is a major regulator of mRNA metabolism in eukaryotes, yet the contribution of plant DEAD-box RNA helicases to this complex remains insufficiently defined. Rice contains two closely related eIF4AII-like helicases, OseIF4AIIa and OseIF4AIIb, whose evolutionary origins, expression characteristics, subcellular distribution, and molecular interactions have not been comprehensively analyzed.
    METHODS AND RESULTS: OseIF4AIIa and OseIF4AIIb were characterized through phylogenetic analyses, expression analyses, fluorescence-based subcellular localization assays, and protein-protein interaction studies. Phylogenetic reconstruction and sequence conservation analyses indicate that the two paralogs likely arose from a recent duplication event within the grasses. Expression analysis showed that OseIF4AIIa is widely expressed in both vegetative and reproductive tissues, with the highest accumulation in nodes, internodes, and leaf sheaths. OseIF4AIIa transcript abundance was strongly induced by salinity and cold, moderately altered by drought, and suppressed by heat. Fluorescent protein fusions demonstrated that both paralogs are restricted to the cytoplasm. BiFC assays further revealed that OseIF4AIIa associates with multiple CCR4-associated factor 1 (CAF1) proteins and interacts with the MIF4G domain of OsNOT1, mirroring the interaction profile of OseIF4AIIb. In addition, CRISPR/Cas9-edited OseIF4AIIa mutant lines exhibited reduced early seedling growth, supporting a role for OseIF4AIIa in vegetative development.
    CONCLUSIONS: These findings demonstrate that OseIF4AIIa is a cytoplasmic, stress-responsive RNA helicase that engages core components of the CCR4-NOT complex. The close evolutionary relationship and shared interaction partners of OseIF4AIIa and OseIF4AIIb support the possibility of overlapping functions within the eIF4AII-like helicase family in rice. This study advances understanding of helicase-associated mechanisms involved in mRNA regulation under abiotic stress conditions.
    Keywords:   Oryza sativa ; CCR4-NOT complex; DEAD-box RNA helicase; OseIF4AIIa; Stress response
    DOI:  https://doi.org/10.1007/s11033-026-11779-x
  24. PLoS Biol. 2026 Apr;24(4): e3003727
    Maternal regulation of translation capacity across generations.
    Elif Sarinay Cenik.
      How animals allocate resources between growth, maintenance, and reproduction is a fundamental question. In this issue of PLOS Biology, Pradhan and colleagues show that maternal nutrient sensing regulates ribosome deposition into embryos, shaping the early growth dynamics in the next generation.
    DOI:  https://doi.org/10.1371/journal.pbio.3003727
  25. Redox Biol. 2026 Apr 02. pii: S2213-2317(26)00150-3. [Epub ahead of print]93 104152
    Integrated analysis of the redoxome and zinc proteome links ribosomal protein oxidation to zinc homeostasis.
    Katarzyna Jonak, Ulrike Topf.
      Zinc is an essential trace mineral for human health. However, consuming large amounts of zinc can be toxic. Therefore, zinc homeostasis must be actively regulated. Within cells, zinc mostly exists in a form bound with proteins. We show that the existence of zinc-binding proteins is a conserved feature of kingdoms of life, emphasizing the fundamental importance of zinc in biological systems. Cysteine residues chemically coordinate zinc binding within proteins and are highly sensitive to oxidative modifications under conditions of oxidative stress and aging. This study uses available datasets that analyzed the redoxome and combines this information with zinc-binding annotations. Our analysis reveals that zinc-binding cysteine residues are significant targets of reversible protein oxidation. In particular, we identified proteins of the cytosolic ribosome as zinc-binding oxidation targets during aging. We integrated our findings with data on changes in protein abundance under conditions of low zinc bioavailability. These analyses revealed that ribosomal proteins that bind zinc and are targets of oxidative modifications tend to be less abundant under zinc-depletion conditions. Additionally, the molecular dynamics simulations allowed us to link reversible oxidation of ribosomal proteins to zinc removal from these proteins and their following unfolding in zinc-deficient conditions. Thus, these findings open new possibilities for regulating zinc homeostasis during aging.
    Keywords:  Aging; Oxidative stress; Ribosomal proteins; Thiol oxidation; Zinc
    DOI:  https://doi.org/10.1016/j.redox.2026.104152
  26. bioRxiv. 2026 Apr 03. pii: 2026.04.03.716306. [Epub ahead of print]
    Omega stabilizes RNA polymerase condensates and contributes to cellular fitness during acid stress.
    Stefan Biedzinski, Cyril Haller, Shadi Rajab, Stephanie C Weber.
      In eukaryotes, organization of the nucleolus is tightly linked to ribosomal RNA (rRNA) synthesis. External stresses, such as heat shock and acidosis, induce a transition of the nucleolus from a liquid- to solid-like state. Bacterial RNA polymerase (RNAP) condensates share similarities with the nucleolus as they colocalize with pre-rRNA synthesis and their assembly correlates with high rRNA synthesis. In addition, their organization is growth dependent, highlighted by dissolution upon nutritional stress. However, their behavior and biophysical properties during other stresses remain unknown. Here, we find that RNAP condensates persist during acid stress despite an arrest in cell growth. In contrast to fast-growth RNAP condensates, acid-stabilized RNAP condensates become insensitive to drug treatments, suggesting a change in their dynamics. We identify both passive and active mechanisms that contribute to the maintenance of RNAP condensates during acid stress: a drop in intracellular pH and the stringent response. Specifically, the omega subunit of RNAP, which contributes to (p)ppGpp binding site 1, is critical for condensate maintenance during acid stress. In contrast, we show that DksA, a major stress regulator that binds to RNAP, does not contribute to RNAP condensate stabilization. Interestingly, we find that maintenance of RNAP condensates correlates with survival during recovery from acid stress. Our work sheds light on a new aspect of bacterial stress tolerance through regulation of RNAP codensates and a new role for the omega subunit. Our data bring RNAP condensates conceptually one step closer to nucleoli.
    DOI:  https://doi.org/10.64898/2026.04.03.716306
  27. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2537315123
    Many paths to destruction: Family-specific turnover and stress responses for tRNA introns.
    Sara Metcalf, Regina T Nostramo, Alicia Bao, Katherine Clark, Paolo L Sinopoli, Anita K Hopper.
      In organisms ranging from Archaea to humans, a subset of genes encoding tRNAs contain introns. Upon splicing, the tRNA exons are joined and the released free introns are rapidly degraded. Although tRNAs introns were previously considered to be "junk" sequences, we recently reported that free tRNA introns (fitRNAs) of Saccharomyces cerevisiae serve as negative regulators of the cellular levels of mRNAs that bear long stretches of open reading frame sequence complementarity to tRNA introns. We also reported that 2 of the 10 families of tRNA introns accumulate to elevated levels when cells suffer oxidative stress. The results led to the current investigations of the regulation of tRNA intron cellular levels. We document that tRNA intron turnover occurs by combinations of 5' RNA kinases, 5' to 3' and 3' to 5' exonucleases as well as by at least three endonucleases and, generally, the levels of each tRNA intron family are regulated by a unique combination of nucleases/kinases. Similarly, one family of excised intron forms circles whereas the other free tRNA intron families do not. Further, levels of individual tRNA introns differ in response to environmental conditions including type of media, stage in growth curves, and exposure to elevated temperature. Together, the findings highlight the many cellular pathways utilized to regulate tRNA intron levels and the specificity of these pathways for different tRNA families and varying cellular conditions. The results underscore the likely important roles of the discovered individual fitRNAs in regulation of cell biology and responses to environmental conditions.
    Keywords:  RNA turnover; environmental conditions; stress; tRNA introns
    DOI:  https://doi.org/10.1073/pnas.2537315123
  28. Front Cell Dev Biol. 2026 ;14 1818554
    RNA modifications in cancer stem cells: molecular mechanisms and targeted therapeutic strategies.
    Jiankun Zhang, Yixiao Yuan, Chongxin Li, Xiulin Jiang, Weiqiang Song.
      Cancer stem cells (CSCs) are a key subpopulation within tumors, characterized by their self-renewal and differentiation potential, and they drive tumor initiation, progression, metastasis, and recurrence. Recent epitranscriptomic studies have revealed that RNA modifications, including m6A, m5C, ac4C, m7G, and m1A, play critical roles in maintaining CSC stemness, determining cell fate, reprogramming metabolism, and promoting therapy resistance. This review systematically summarizes the functions of different RNA modifications and their associated enzymes in CSCs. We also discuss how RNA modifications regulate core CSC signaling pathways, such as Wnt/β-catenin, Notch, Hedgehog, PI3K-AKT-mTOR, JAK/STAT, Hippo/YAP, and TGF-β/SMAD, and we highlight strategies targeting RNA modifications for CSC intervention along with their potential challenges. These findings suggest that RNA modifications and their regulators represent promising therapeutic targets in CSCs, providing a rationale for developing highly selective or combination treatment strategies.
    Keywords:  AC4C; M6A; RNA modifications; cancer stem cells; m1A; m5C; m7G; self-renewal
    DOI:  https://doi.org/10.3389/fcell.2026.1818554
  29. PLoS Genet. 2026 Apr;22(4): e1011851
    Translation control by altered start codon usage as a means of modulating the general stress response and virulence in Listeria monocytogenes.
    Jialun Wu, Claire Kelly, Duarte N Guerreiro, Brenda Chanza, Ashley Reade, Catherine M Burgess, Conor O'Byrne.
      In the food-borne pathogen Listeria monocytogenes, SigB is the central regulator of general stress response (GSR) and it mediates host entry by promoting acid resistance and epithelial cell attachment. However, mutations can readily arise to disable regulators of SigB (Rsb proteins), which suggests a considerable genetic plasticity in the GSR. To further investigate this, we defined the complete genome sequence of a clinical isolate and elucidated how sequential mutations within sigB operon (rsbX N77K and rsbU Q317*) impacted fitness through modulation of SigB activity. To investigate the plasticity of the GSR, we followed its genetic adaptation to lethal acidic challenge (mimicking the selective pressure encountered during entry into the host). Acid resistance developed rapidly and all 6 acid resistant derivatives (ARDs) selected for analysis had acquired mutations in rsbW, which encodes an antagonist of SigB that suppresses SigB activity during non-stress conditions. These mutations resulted in non-canonical start codons (rsbWATG to rsbWATA or rsbWATT) or premature translation termination (rsbW-) and all were found to result in increased SigB activity. A translational reporter assay demonstrated distinct differences in translation efficiency between three start codons: ATG > ATA > ATT, suggesting that a perturbation of RsbW:SigB stoichiometry alters SigB activity. We then analysed start codon usage for all conserved genes in 60,692 L. monocytogenes genomes. This analysis revealed flexible usage of start codons associated with genetic clades in 39 conserved genes, 13 of which are involved in virulence and stress response. Further, we show that flexible use of canonical start codons (ATG and GTG) can also mediate different levels of expression of virulence and stress response genes. Taken together, we show the genetic plasticity of GSR regulation in a model pathogen, and highlight the importance of translational control as a means of fine-tuning gene expression during short-term adaptation and long-term evolution for optimal fitness.
    DOI:  https://doi.org/10.1371/journal.pgen.1011851
  30. Biochem Biophys Res Commun. 2026 Mar 31. pii: S0006-291X(26)00465-1. [Epub ahead of print]816 153701
    Rad6-mediated ubiquitination regulates the formation of Sam1-containing stress granules during nutrient stress in budding yeast.
    Atsuki Kitajima, Kazuha Bessho, Yuki Takano, Kunio Nakatsukasa.
      Stress granules (SGs) are dynamic cytoplasmic structures that form in response to environmental stress and contribute to cellular adaptation. Recent studies have shown that metabolic enzymes localize to SGs under nutrient stress; however, the molecular mechanisms regulating the assembly and organization of metabolic enzyme-containing SGs remain poorly understood. In this study, we examined the role of ubiquitination in the regulation of SGs containing the S-adenosylmethionine synthase Sam1 in budding yeast. We demonstrate that Sam1 is stable but undergoes non-proteolytic ubiquitination in vivo. We identified Rad6 as one of the major ubiquitin-conjugating enzymes that catalyze Sam1 ubiquitination. Deletion of RAD6 caused pronounced alterations in Sam1-containing SGs during nutrient stress. Specifically, rad6Δ cells exhibited increases in both the proportion of cells forming Sam1-positive SGs and the number of SGs per cell. These results demonstrate that Rad6-mediated ubiquitination restricts the number and organization of Sam1-containing stress granules under nutrient stress. Our findings reveal a non-proteolytic role for ubiquitination in regulating stress granule architecture and provide new insight into the regulation of metabolic enzyme assemblies during nutrient stress.
    Keywords:  Rad6; S-adenosylmethionine synthase; Saccharomyces cerevisiae; Stress granule; Ubiquitin
    DOI:  https://doi.org/10.1016/j.bbrc.2026.153701
  31. Adv Sci (Weinh). 2026 Apr 09. e75244
    Enhanced Intracellular Stability and Translation Efficiency of mRNA Drugs by a 2-arm mRNA Platform.
    Xucong Teng, Jiahao Lin, Qiushuang Zhang, Xiangdong Zhang, Yicong Dai, Jinghong Li.
      The poly(A) tail deadenylation and transient protein expression of messenger RNA (mRNA) extremely hinder its therapeutic potential in genetic diseases, from which it follows that improving RNA stability and translation efficiency has emerged as a critical priority. In this study, we construct a 2-arm mRNA via a streamlined modular assembly approach, characterized by a unique topology formed through the dimerization of two mRNA 3' poly(A) tails. This distinctive architecture exhibits the capacity for efficiently recruiting poly(A)-binding proteins (PABPs) to activate the eIF3-eIF4F complex and promote highly efficient cap-dependent translation, markedly improving 3' tail stability and resistance to nuclease degradation, with an intracellular half-life of up to 65 h. Furthermore, the 2-arm mRNA sustains higher-level protein expression for over two weeks in protein replacement therapy of hemophilic mice compared to linear mRNA. In conclusion, this work presents a novel 2-arm mRNA platform that substantially enhances the translation capacity of mRNA, broadening its potential applications in mRNA-based therapeutics, particularly for the treatment of genetic disorders.
    Keywords:  2‐arm mRNA; dendritic mRNA; mRNA stability​; prolonged protein expression; ​mRNA therapy
    DOI:  https://doi.org/10.1002/advs.75244
  32. Pathol Res Pract. 2026 Apr 04. pii: S0344-0338(26)00118-4. [Epub ahead of print]282 156465
    The m7G modification: An emerging player in neurological diseases.
    Yuting Song, Zitong Zhao, Yuxin Dai, Chenchen Li, XiangJun He, Yongjun Wang, Zhi-Qing David Xu, Yutao Yang.
      With the growing researches on RNA epigenetics, the importance of 7-methylguanosine (m7G) modification is increasingly recognized. The m7G modification is known as a kind of post-transcriptional modifications of RNA and present in many types of RNAs, including mRNAs, microRNAs, ribosomal RNA, and transfer RNAs. Increasing evidence indicates that m7G modifications are involved in a variety of critical biological processes through affecting the stability of RNA, nucleoplasmic transfer and translation efficiency. In the central nervous system (CNS), m7G modification is catalyzed by three major methyltransferase complexes: METTL1/WDR4, RNMT/RAM, and WBSCR22/TRMT112. Dysregulation of this modification is tightly associated with the pathogenesis of various neurological diseases, such as Alzheimer's disease (AD), Amyotrophic lateral sclerosis (ALS), epilepsy, glioblastoma, ischemic stroke (IS), etc. Here, we review the current knowledge regarding the latest findings on the distribution, regulatory factors, detection techniques and prediction methods of m7G. We further highlight critical knowledge gaps, especially the limited understanding of m7G "readers," the absence of validated "erasers," and the scarcity of cell-type-resolved profiling in the brain. In addition, we also discuss the translational opportunities and challenges, including biomarker discovery, therapeutic targeting of m7G regulators, and specificity concerns in precision neurological medicine.
    Keywords:  N7-methylguanosine (m7G); Neurological diseases; RNA epigenetics; RNA modification
    DOI:  https://doi.org/10.1016/j.prp.2026.156465
  33. bioRxiv. 2026 Mar 10. pii: 2026.03.09.709851. [Epub ahead of print]
    Multivalent weak contacts shape chaperone-nascent protein interactions.
    Nandakumar Rajasekaran, Dmitri Toptygin, Ting-Wei Liao, Vincent J Hilser, Taekjip Ha, Christian M Kaiser.
      Molecular chaperones interact with non-native proteins, playing crucial roles in preventing misfolding and enable efficient folding in the cellular environment. Trigger factor is a bacterial chaperone that binds to ribosomes, interacting with nascent polypeptides emerging from the ribosome and guiding their early folding steps. In contrast to the central role of the chaperone in promoting folding of newly synthesized proteins, its dynamic interactions with nascent chains emerging from the ribosome remain poorly understood. Here, we use single-molecule fluorescence and optical tweezers approaches to directly observe and characterize trigger factor interactions with a ribosome-bound client protein at increasing chain lengths. We find that trigger factor binding to nascent proteins is best described by a combination of multiple weak, dynamic interactions that are established after the chaperone docks onto the ribosome and evolve during polypeptide elongation. Application of mechanical force perturbs trigger factor binding, supporting a multivalent interaction model. This binding mode may help to stabilize nascent proteins against misfolding while allowing them to dynamically sample conformational space in search of their native structures.
    DOI:  https://doi.org/10.64898/2026.03.09.709851
  34. Chemistry. 2026 Apr 09. e03378
    Engineering Bisubstrates to Target m6Am RNA Methyltransferases: Synthesis and Computational Studies.
    Yoann Colas, Laurent Le Corre, Mélanie Ethève-Quelquejeu, Emmanuelle Braud.
      Phosphorylated CTD-interacting factor 1 (PCIF1) has been recently discovered to introduce a methyl group at the N6 position of the first transcribed Am-adenosine in nascent capped mRNA (m6Am modification), modulating mRNA stability, transcription, and translation. In addition, the activity of PCIF1 is involved in various diseases, making PCIF1 a potential therapeutic target. In the absence of complete crystal structures of PCIF1 with an RNA substrate and/or cofactor and with the aim of accessing potent inhibitors, the bisubstrate strategy was employed to synthesize a series of bisubstrate analogs of PCIF1 that contain an analog of the cofactor S-adenosyl-L-methionine (SAM) covalently linked to an Am-modified RNA substrate. The versatility of the synthesis was exploited to increase structural diversity at the amino acid chain of SAM, and a cap analog was introduced by click chemistry. Also, AlphaFold 3 was used to generate a complete structure of PCIF1 with an RNA substrate. Docking studies carried out with the bisubstrates indicate that the SAM analog occupies the cofactor binding site while the Am-RNA substrate interacts with the putative RNA pocket. We think that these results could be a valuable starting point for the design of potent inhibitors of PCIF1.
    Keywords:  RNA cap methyltransferase PCIF1; bisubstrate; cofactor SAM analogs; convertible nucleoside; molecular modeling
    DOI:  https://doi.org/10.1002/chem.202503378
  35. Cancer Gene Ther. 2026 Apr 09.
    Identification of ribosomal protein eL21 as a novel externalized protein and a target in triple-negative breast cancer.
    Lucie Arnould, Nina Radosevic-Robin, Laura Duranton, Jérémy Néri, Frédérique Penault-Llorca, Jean-Jacques Diaz, Marie Alexandra Albaret, Frédéric Catez.
      Proteins normally localized in the intracellular compartments of healthy cells have been observed at the surface of cancer cells, despite lacking a transmembrane domain or secretion signals. This unexpected localization likely reflects yet-unknown functions and presents a unique opportunity to develop cancer cell-specific antibody- or peptide-based therapeutic strategies. While ribosomal proteins (RPs) are primarily involved in translation, several display moonlighting functions in the cytoplasm and nucleus. In this study, we uncover an extracellular form of the ribosomal protein L21 (eL21) in triple-negative breast cancer (TNBC) cells. Using complementary approaches and a broad set of antibodies, we demonstrate that eL21 localizes to the surface of cancer cells. Remarkably, we show that anti-eL21 antibodies trigger a potent, rapid and dose-dependent anti-proliferative effect, including TNBC cell cycle arrest and apoptosis. These findings identify eL21 as a novel ribosomal protein with extra-ribosomal functions at the cancer cell surface and highlight its potential as a therapeutic target in TNBC.
    DOI:  https://doi.org/10.1038/s41417-026-01026-7
  36. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2527693123
    Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.
    George Wanes, Udayan Mohanty, Paul C Whitford.
      While it is well known that ion binding can stabilize RNA structure, little is known about how transient/probabilistic ionic interactions facilitate biologically relevant conformational rearrangements. To address this, we developed a theoretical model that employs all-atom resolution with a simplified representation of biomolecular energetics (i.e., a structure-based "SMOG" model), explicit electrostatics, and ions (K+, Cl-, Mg2+). For well-studied RNA systems, the model accurately describes the concentration-dependent ionic environment, which includes chelated and hydrated/diffuse ions. With this foundation, we applied the model to simulate the yeast ribosome and quantified the ion-dependent energy landscape of intersubunit rotation. These calculations show how millimolar increases in [MgCl2] shift the energetics to favor the unrotated state. The free-energy barrier is also increased, leading to an order-of-magnitude reduction in kinetics that is correlated with formation of ion-mediated interactions between the subunits. This provides a physical description for how transient ionic interactions can contribute to large-scale biomolecular dynamics.
    Keywords:  RNA; conformational transition; elongation; ions; simulation
    DOI:  https://doi.org/10.1073/pnas.2527693123
  37. Biochim Biophys Acta Mol Cell Res. 2026 Apr 08. pii: S0167-4889(26)00044-3. [Epub ahead of print] 120147
    FTO-mediated m6A demethylation inhibits bladder cancer progression via decreasing EMG1 and reducing ribosome biosynthesis.
    Kun Yao, Long Wang, Jinrong Wang, Jianye Liu, Chao Li, Weibin Hou, Bingzhi Wang, Wei Xiong, Jing Tan.
      Bladder cancer (BLCA) is one of the most common urological malignancies, entailing significant morbidity and mortality rates. A comprehensive understanding of the mechanisms driving bladder cancer initiation and development is required to devise improved treatment regimens. N6-methyladenosine (m6A) is the most prevalent internal RNA modification reported to regulate cancer metastasis. Here, the function of fat mass and obesity-associated protein (FTO), an m6A demethylase, was studied in bladder cancer by overexpressing or knocking down FTO, and the underlying mechanism of FTO in BLCA was explored using machine learning analysis, in vitro, and in vivo experiments. The FTO expression has been proven to be downregulated within bladder cancer, and it could exert a tumor-suppressive effect. Moreover, Gain- and loss-of-function experiments showed that FTO downregulation enhanced the proliferation, migration, and invasion of bladder cancer cells. Mechanistic studies revealed that FTO decreased EMG1 expression by demethylating EMG1 and reducing ribosome biosynthesis, thereby promoting bladder cancer cell proliferation, migration, and invasion and repressing tumor growth in vivo. This study has demonstrated the anti-tumor effect of FTO on bladder cancer development, making it a promising therapeutic target.
    Keywords:  Bladder cancer; Cancer progression; Demethylation; EMG1; FTO; Ribosome biosynthesis
    DOI:  https://doi.org/10.1016/j.bbamcr.2026.120147
  38. Genes Cells. 2026 May;31(3): e70109
    Regulation of the Growth-Inhibitory Activity of Fhl1 via Interaction With Ifh1 and Crf1 at the Ribosomal Protein Gene Promoters in Saccharomyces cerevisiae.
    Naoki Shimamura, Koji Kasahara.
      The transcription factor Fhl1, which binds to the promoters of the ribosomal protein genes (RPGs) in Saccharomyces cerevisiae, promotes transcription by recruiting the transcription activator Ifh1 under nutrient-rich conditions. During starvation, Ifh1 dissociates from the RPG promoter, and the transcriptional repressor Crf1 binds to Fhl1 instead of Ifh1, thereby suppressing transcription. However, the lethality of the ifh1Δ strain was suppressed by deletion of FHL1, suggesting that Ifh1 has essential functions beyond transcriptional activation. Detailed analyses using various deletion mutants of Fhl1 and Ifh1 revealed that the lethality of the ifh1Δ strain is suppressed by mutation of the forkhead-associated (FHA) domain, which interacts with the forkhead-binding (FHB) domains of Ifh1 and Crf1. Inducing Fhl1-expression in ifh1Δfhl1Δ strain suppressed growth, indicating that promoter-bound Fhl1 inhibits RPG transcription via an unknown mechanism. The lethality of ifh1Δ strain was suppressed by expression of the Ifh1 FHB domain from its native promoter or by overexpression of the corresponding domain of Crf1. These findings suggest that, while Fhl1 promotes transcription by recruiting Ifh1, dissociation of Ifh1 exposes the FHA domain, which triggers growth inhibition via an unknown mechanism. Binding to the FHA domain and neutralizing its inhibitory activity may represent a key function of Ifh1.
    DOI:  https://doi.org/10.1111/gtc.70109
  39. PLoS Biol. 2026 Apr;24(4): e3003692
    Dietary restriction shapes intergenerational ribosome abundance and early growth of Caenorhabditis elegans offspring.
    Sigma Pradhan, Klement Stojanovski, Ferdinand Dellemann, Sacha Psalmon, Joel Tuomaala, Nicholas E Stroustrup, Benjamin D Towbin.
      Cells adjust their proteome to their environment. Most prominently, ribosome expression often scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically wasteful ribosomal excess. In microbes, such proteome adjustments can passively perpetuate through symmetric cell division. However, in animals, a passive propagation is hindered by the separation between soma and germline. This separation raises the question whether the proteome of animals is reset at every generation or can be propagated from parent to offspring across this barrier. We addressed this question for the intergenerational effects of dietary restriction in Caenorhabditis elegans, combining proteomics and live imaging. Under ad libitum feeding, the offspring of dietarily restricted mothers grew more slowly than progeny of well-fed mothers. However, this growth disparity was attenuated when mTORC1 signaling in the progeny was inhibited, creating conditions in which the protein-synthesis capacity at hatching is less limiting. Maternal inhibition of mTORC1 signaling, either ubiquitously or specifically in the pharynx, similarly reduced growth and ribosomal protein levels in offspring, whereas other growth-reducing perturbations, such as reduced insulin signaling or mTORC1 inhibition in the epidermis, did not reduce progeny ribosomal protein levels. We conclude that maternal physiology shapes ribosomal protein provisioning across the soma-germline boundary, thereby modulating early offspring growth in accordance with post-hatching ribosome demand.
    DOI:  https://doi.org/10.1371/journal.pbio.3003692
  40. J Adv Res. 2026 Apr 06. pii: S2090-1232(26)00302-4. [Epub ahead of print]
    GL-V9 disrupts the mitochondrial homeostasis and triggers the integrated stress response by promoting the binding of cytosolic MDM2 with NDUFS1 in colorectal cancer.
    Yibo Zhang, Chen Xun, Chenxiao Shi, Rui Wang, Yuan Gao, Di Pan, Yongjian Guo, Libin Wei.
       INTRODUCTION: The oncogenic role of mouse double minute 2 (MDM2) is primarily attributed to its regulation of p53-dependent signaling cascades. The colorectal cancer (CRC) remains in the top five most prevalent and lethal cancers. P53 mutations are detected in 45-50% of CRC, leading to the failure of such MDM2 inhibitors in clinical trials.
    OBJECTIVES: Small molecular compound GL-V9 targets MDM2 and leads a non-canonical function of MDM2 mediated anti-CRC effects.
    METHODS: Interaction of MDM2 with NDUFS1 as well as the mitochondrial location of NDUFS1 were assessed by a pull-down assay and immunofluorescence analysis. The binding of GL-V9 to MDM2, was analyzed by molecular docking, cellular thermal shift assay (CESTA), surface plasmon resonance (SPR), GST-pulldown and amino acid mutations. Mitochondrial homeostasis was evaluated by mitochondrial membrane potential, mitochondrial superoxide, ATP generation and oxygen consumption rate.
    RESULTS: Different from MDM2 inhibitors, GL-V9 binds to the MDM2 amino-terminal domain (amino acids 1-101) and facilitates the interaction of MDM2 with NDUFS1 in cytoplasm through a p53-independent manner, instead of disruption of p53-MDM2 binding or the promotion of MDM2 protein degradation. This process additionally inhibits the formation of electron transport chain complex I and disrupts the mitochondrial homeostasis, which finally activates OMA1-DELE1 signaling axis and induces the integrated stress response (ISR)-triggered apoptosis.
    CONCLUSION: This study provides a novel candidate for CRC therapy with favorable safety profile. Importantly, the novelty mode of action by GL-V9, working as molecular glue for MDM2/NDUFS1, provides a new insight for targeting MDM2 regardless of p53 status.
    Keywords:  Colorectal cancer; GL-V9; Integrated stress response; MDM2-NDUFS1 interaction; Mitochondrial homeostasis
    DOI:  https://doi.org/10.1016/j.jare.2026.04.019
  41. Discov Oncol. 2026 Apr 09.
    Identification of biomarkers associated with integrated stress response in pituitary adenomas based on bioinformatics.
    Yuan Sui, Zhiqian Yang, Wei Zhang.
      
    Keywords:  Biomarkers; Integrated stress response; Pituitary adenoma; Regulatory network
    DOI:  https://doi.org/10.1007/s12672-026-04697-8
  42. Cell Rep. 2026 Apr 04. pii: S2211-1247(26)00281-0. [Epub ahead of print]45(4): 117203
    Systematic profiling of cytosolic membraneless organelles reveals enrichment of oncogenic mRNA upon oxidative stress.
    Savannah O'Connell, Helen E King, Peter Kjer-Hansen, Karina Pazaky, Gabriela Santos Rodriguez, Daisy Kavanagh, Helaine Graziele S Vieira, Javier Fernandez-Chamorro, Robert J Weatheritt.
      Cytosolic mRNA regulation during and after stress is driven by distinct membraneless organelles. However, their compositional and functional dynamics throughout the stress response remain unclear. We combine APEX2-mediated proximity labeling, RNA sequencing, and high-content imaging to map the human P-body and stress granule transcriptomes during oxidative stress and recovery. Our findings reveal that P-bodies undergo extensive compositional remodeling during stress and that these changes persist during stress recovery. P-body-associated mRNAs during stress exhibit increased AU-rich elements and oncogenic content relative to the cytosol. In contrast, stress granule-associated mRNAs closely resemble the cytosol. These results uncover critical differences between P-bodies and stress granules, shedding light on their functional specialization. Our study provides a valuable resource of cytosolic membraneless organelle-associated transcripts and suggests a specialized role for P-bodies in stress adaptation and recovery.
    Keywords:  APEX-sequencing; CP: cell biology; CP: molecular biology; P-bodies; bioinformatics; membraneless organelles; stress granules; stress response
    DOI:  https://doi.org/10.1016/j.celrep.2026.117203
  43. Cell Death Dis. 2026 Apr 10.
    Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.
    Lili Li, Taekyu Ha, Jing-Xin Feng, Michael DiPrima, Dunrui Wang, Parthav Jailwala, Thomas Meyer, Justin Lack, Hidetaka Ohnuki, Giovanna Tosato.
      Despite therapeutic advances, metastatic colorectal cancer remains a therapeutic challenge as most patients will develop resistance to therapy and will progress. Epigenetic mechanisms are implicated in enabling the acquisition of new phenotypic traits as drivers of colorectal cancer progression, rather than new genetic mutations or expansion of existing mutant clones. It remains unclear, however, which epigenetic mechanisms sustain colorectal cancer plasticity, how they are induced, and how this plasticity generates subclonal diversity that drives the aggressive cancer phenotype. Here we identify the integrated stress response as an inducer of colorectal cancer cell plasticity, subclonal diversity, and tumor progression in the stress-surviving cells. Combined analysis of chromatin accessibility and gene transcription profiling in these cells found the emergence of an endogenous interferon response as a key phenotypic trait associated with subclonal colorectal cancer cell diversity, treatment resistance and heightened aggressiveness. We unveil a new experimental approach to successfully prevent treatment-resistant colorectal cancer progression by combining epigenetic modulators with a cereblon-dependent degrader of GSPT1, a regulator of protein synthesis, to normalize chromatin accessibility and induce colorectal cancer cell death. Collectively, our study identifies the integrated stress response as an inducer of epigenetic and transcriptional plasticity in colorectal cancer cells and highlights a successful approach to therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41419-026-08720-2
  44. bioRxiv. 2026 Apr 03. pii: 2026.04.01.715099. [Epub ahead of print]
    STI1 domains coordinate partitioning of UBQLN2 into stress-induced condensates.
    Billy Haws, Thuy P Dao, Bridget Varner, Holly B Jones, Mallory P Brown, Carlos A Castañeda.
      UBQLN2 is a ubiquitin-binding shuttle protein that undergoes phase separation in vitro and localizes to stress-induced cellular condensates including stress granules. The central region of UBQLN2 contains two chaperone- and substrate-binding STI1 domains (STI1-I, STI1-II) and disordered linkers; the individual contributions of these domains and linkers to cellular condensate partitioning remain poorly characterized. Here we use live-cell imaging and immunofluorescence experiments to systematically examine domain requirements for UBQLN2 puncta formation in cultured human cells. We show that in vitro phase separation propensity largely correlates with puncta formation in transfected cells. Importantly, STI1-II and UBA domains are each required for baseline puncta formation in cells, but not STI1-I. In contrast, both STI1 domains are required for heat stress-induced puncta formation. Removal of STI1-II abrogates this stress response, and STI1-I deletion substantially attenuates it. Using N-terminal truncation constructs, we demonstrate that STI1-I strongly promotes both phase separation and puncta formation in the absence of the N-terminal region containing the UBL domain. Together, our findings demonstrate that the two STI1 domains of UBQLN2 have distinct roles in puncta formation and condensate partitioning, with STI1-II essential under all conditions.
    DOI:  https://doi.org/10.64898/2026.04.01.715099
  45. J Am Chem Soc. 2026 Apr 10.
    Ribosome Heterogeneity Revealed by Complex-Up Native Mass Spectrometry and Top-Down Proteomics.
    Sachin C Tennakoon, Sarah B Giese, Jared B Shaw.
      Characterization of large molecular machines, such as the ribosome, under a breadth of biological states to elucidate regulatory details remains challenging. Herein, a workflow combining complex-up native mass spectrometry (nMS) with infrared multiphoton dissociation (IRMPD) and top-down proteomics (TDP) was developed to enable the rapid and direct characterization of ribosome heterogeneity. Preferential unfolding and fragmentation of rRNA by IRMPD enabled proteoform-resolved characterization of E. coli ribosome heterogeneity across growth states revealing ribosomal protein (RP) heterogeneity in unprecedented detail. TDP characterization of isolated RPs enabled confident proteoform characterization and facile interpretation of the IRMPD spectra. Additionally, differences in proteoform relative abundances determined by complex-up nMS and TDP reveal proteoform specific changes in relative interaction strengths. This experimental framework paves the way to a more rapid understanding of the diverse regulatory mechanisms conferred by ribonucleoprotein heterogeneity, including the role of RP composition and post-translational modification (PTM) heterogeneity in modulation of translation efficiency and specificity.
    DOI:  https://doi.org/10.1021/jacs.5c21227
  46. Neurochem Int. 2026 Apr 02. pii: S0197-0186(26)00045-8. [Epub ahead of print]196 106154
    Disrupting PQBP1-eEF2 protein-protein interaction: From synaptic translation to immunity and cancer.
    Emadeldin M Kamel, Sally Mostafa Khadrawy, Mohamed A M Ali, Noha A Ahmed, Nour Y S Yassin, Saleh Alkhedhairi, Faris F Aba Alkhayl, Al Mokhtar Lamsabhi.
      Polyglutamine-binding protein 1 (PQBP1) has emerged as a multifaceted regulator of gene expression, acting not only in the nucleus to influence transcription and splicing but also in the cytoplasm to control protein synthesis. A recent discovery identified a direct interaction between PQBP1 and the translation elongation factor eEF2, unveiling a new checkpoint in the elongation phase of protein synthesis. PQBP1 binds preferentially to the non-phosphorylated form of eEF2 and protects it from phosphorylation at Thr56 by its kinase eEF2K. Through this mechanism, PQBP1 promotes continuous elongation under conditions where unchecked eEF2K activity would otherwise stall ribosomes. The PQBP1-eEF2 complex plays critical roles in maintaining global proteome homeostasis and enabling activity-dependent protein synthesis in neurons. Disruption of this protein-protein interaction (PPI), whether by genetic mutations in PQBP1 or by sequestration of PQBP1 in cellular aggregates, has been linked to pathological states ranging from intellectual disability and impaired synaptic plasticity to altered innate immune responses and possibly tumorigenesis. In this review, we summarize the current understanding of the PQBP1-eEF2 interaction, its structural basis and regulation, the physiological processes it governs, and the consequences of its disruption in disease. We also discuss therapeutic considerations - when stabilizing this interaction might be beneficial (e.g. to restore synaptic function in neurodegeneration) versus when inhibiting it could be advantageous (e.g. to dampen excessive translation in cancer). Finally, we highlight experimental strategies and open questions for future research on this newly recognized nexus of translation control.
    DOI:  https://doi.org/10.1016/j.neuint.2026.106154
  47. Front Immunol. 2026 ;17 1741513
    Mechanism by which SAHA regulates HLA-E expression via the endoplasmic reticulum stress-related PERK/ATF4/CHOP pathway in neuroblastoma.
    Zhuoran Li, Xi Zhen, Chenggong Zeng, Yan Mao, Zhiqing Wei, Zijun Zhen.
       Background: Human leukocyte antigen E (HLA-E) plays a role in tumor immune escape and is associated with poor prognosis in neuroblastoma (NB). This study aimed to investigate the regulatory effect of suberoylanilide hydroxamic acid (SAHA) on HLA-E expression via the PERK/ATF4/CHOP pathway in NB.
    Methods: A high HLA-E expression model in NB cells was established by stimulation with interferon-gamma (IFN-γ). The effects of SAHA on NB cell proliferation and migration were evaluated. In addition, the influence of SAHA on the PERK/ATF4/CHOP signaling pathway and HLA-E expression at the mRNA and protein levels was analyzed. Bioinformatics analysis was performed using data from the TARGET and Gene Expression Omnibus (GEO; GSE85047) databases to identify prognostic genes associated with NB.
    Results: Stimulation with IFN-γ successfully induced high HLA-E expression in NB cells. SAHA significantly suppressed NB cell proliferation and migration and downregulated HLA-E expression at both the mRNA and protein levels. Analysis of the TARGET database revealed that the prognosis of patients with NB was closely related to the expression levels of endoplasmic reticulum stress (ERS)-related proteins, particularly PERK and HLA-E. This association was validated using the GEO dataset GSE85047. Moreover, SAHA inhibited the expression of ERS pathway proteins, including PERK and CHOP, in NB cell lines.
    Conclusion: This study demonstrated that SAHA downregulates HLA-E expression by inhibiting the PERK/ATF4/CHOP pathway, offering new insights into the regulation of tumor proliferation, migration, and immune evasion in NB.
    Keywords:  endoplasmic reticulum stress (ERS); human leukocyte antigen E (HLA-E); immune evasion; neuroblastoma; suberoylanilide hydroxamic acid (SAHA)
    DOI:  https://doi.org/10.3389/fimmu.2026.1741513
  48. Cell Rep. 2026 Apr 07. pii: S2211-1247(26)00311-6. [Epub ahead of print]45(4): 117233
    Viral effector suppresses MTA/MTB-mediated m6A modification of genomic RNAs of a plant virus to facilitate infection.
    Mingfeng Feng, Tianyi Zhang, Jie Zhao, Yulong Yuan, Qinhai Liu, Xingwang Zhang, Jia Li, Min Zhu, Peter Palukaitis, Mingjia Chen, Xiaorong Tao.
      N6-methyladenosine (m6A) is a prevalent dynamic RNA epigenetic modification that plays a crucial role in plant defense against viral infection. However, whether viruses have evolved mechanisms to counteract the m6A-associated defense remains unknown. Here, we report that a viral pathogen effector, the 2b protein encoded by cucumber mosaic virus (CMV), disables the methyltransferase of the m6A modification complex to evade the m6A-mediated plant defense. The viral effector 2b interacts with methyltransferase B (MTB), and this interaction re-localizes the MTA, the core component of the m6A methyltransferase, from the cytoplasm to the nucleus. The 2b protein not only prompts the MTA/MTB complex to form condensates in the nucleus but also inhibits their enzymatic activity, thereby suppressing m6A modification on the genomic/subgenomic RNAs of CMV to promote viral infection. Collectively, our findings uncovered a viral effector that targets and suppresses the m6A methyltransferase complex, shedding light on the mechanism by which plant viruses counteract m6A-mediated antiviral defense.
    Keywords:  2b protein; CP: microbiology; CP: plants; MTA; MTB; cucumber mosaic virus; m(6)A; methyltransferase; viral effector
    DOI:  https://doi.org/10.1016/j.celrep.2026.117233
  49. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2526136123
    mtHsp70 chaperone converts mitochondrial proteostasis stress into impaired protein import.
    Rupa Banerjee, Vanessa Trauschke, Nils Bertram, Ina Aretz, Christof Osman, Don C Lamb, Dejana Mokranjac.
      Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a variety of cellular processes. The conformational cycles of several Hsp70 chaperones, driven by ATP binding and hydrolysis, and regulated by cochaperones and substrate proteins, were analyzed in vitro in great detail. In contrast, little is known about the conformation Hsp70s adopt in their natural environments. In mitochondria, mtHsp70 is distributed between the TIM23 complex at the inner membrane, where it is involved in import of proteins from the cytosol, and a matrix-pool that is primarily involved in folding of proteins and prevention of their aggregation. Here, we used fluorescence microscopy to analyze the conformation of mtHsp70 at the single molecule level within physiologically active mitochondria. Our results revealed that the majority of mtHsp70 molecules are present in a substrate-bound state, suggesting that the mtHsp70 network functions at the limits of its capacity. To understand the biological significance of this finding, we modulated the levels of unfolded proteins in the matrix. Unfolded proteins reduced the association of mtHsp70 with the TIM23 complex and specifically impaired mtHsp70-dependent import of proteins. Our data show that unfolded proteins lead to a redistribution of mtHsp70 within mitochondria revealing how mitochondrial proteostasis stress is signaled to the cell-unfolded proteins remove mtHsp70 from the import sites, reducing the efficiency of protein import and initiating cellular programs to rescue or remove dysfunctional mitochondria. Thus, mtHsp70 acts as a mitochondrial quality control sensor that converts proteostasis stress into impaired protein import.
    Keywords:  Hsp70 chaperones; mitochondria; protein homeostasis; protein import; single molecule FRET
    DOI:  https://doi.org/10.1073/pnas.2526136123
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