bims-ribost 2026-02-22 papers

bims-ribost

Biomed News

on Ribostasis and translation stress

Issue of 2026–02–22
39 papers selected by
Cédric Chaveroux, CNRS

Domain architecture of plant eukaryotic translation initiation factor 3 subunit E governs interaction with translational cis-elements to regulatepollen tube growth.
RNA sample preparation strategies for mass spectrometry sequencing of the epitranscriptome and therapeutic RNAs: A review.
Seven wonders of RNA modification biology.
Functional Divergence of bL36m Protein in Yeast and Human Mitochondrial Ribosomes.
NSUN5 and RNA m5C epitranscriptomic regulation in tumor progression.
eIF3 musketeers: loyal in health, rogue in disease, and redeemed by therapeutic targeting.
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes.
Extracellular Small RNAs in Human Milk: Molecular Profiles, Stability and Fragment-Specific Responses in Cell-Based Assays.
Rewriting the RNA code: an m6a-centric framework to classify tumors and guide combination therapies.
Engineering a human-based translational activator for targeted protein expression restoration.
Recent advances in understanding the roles of PPR proteins in plant responses to biotic and abiotic stresses.
Effect of Seed Length and Binding Motifs on Hfq-Mediated sRNA-mRNA Annealing Analyzed Using Single-Molecule FRET.
Ribosome demand links transcriptional bursts to protein expression noise.
Structural and mechanistic basis of ADAR1-mediated RNA editing and immune regulation.
The methyltransferase METTL16 in digestive system cancers: functions and mechanisms.
Biogenesis, features, and functions of coding transcripts-derived siRNAs in plants.
The DExD-box RNA helicase Dbp7 unwinds short double-stranded RNAs.
Incorporation of a Human-Derived CU-Rich Element in the 3' UTR Improves Synthetic mRNA Stability and Expression In Vivo.
Bulk and single-cell transcriptomics for identification of potential diagnostic biomarkers associated with pulmonary arterial hypertension and integrated stress response and experimental validation.
Cas10 residues lining the target RNA binding channel regulate interference by distinguishing cognate target RNA from mismatched targets.
Development of an immobilized system for RNA modification analysis.
A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions.
Mechanisms at the Intersection of lncRNA and m6A Biology.
Vitamin D Reprograms Non-Coding RNA Networks to Block Zika Virus in Human Macrophages.
Human messenger RNA harbors widespread noncoding splice isoforms.
Bridging technical innovation and computational advances in studies of RNA-protein assemblies.
Two codes of RNA editing by deamination in human diseases.
Xinfeng capsule improves hyperinflammation-associated hypercoagulability and self-perception in osteoarthritis by regulating KLF4 through METTL14-mediated m6A modification of lncRNA MEG3.
Identification and comparison of RNA structures in 5'- and 3'-terminal genomic regions across four coronavirus genera by SHAPE analysis.
NAT10 and ac4C modification in cancer immunity and metabolism: emerging mechanisms and therapeutic potential.
Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.
Intestinal stem cell damage caused by specific amino acid deprivation is linked to a potent integrated stress response triggered by the direct sensing of stem cells.
Mechanistic insights into non-coding RNAs regulate autophagy in chondrocytes and their contribution to osteoarthritis.
Composite SMG5-SMG6 PIN domain formation is essential for NMD.
Fluorescence Amplification Tags for Single-Molecule Imaging and Tracking of Proteins, RNA, and DNA in Live Cells.
METTL18 Ensures Pancreatic Function by Maintaining Proper Translation and Proteostasis.
A reprogrammed genetic code consisting of 32 distinct amino acids.
De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response.
5'UTR Editing of the Ribosomal Protein UL3Z Gene Unveils Its Critical Roles in Pre-rRNA Processing and Global mRNA Translation Dynamics.

Plant Cell. 2026 Feb 16. pii: koag005. [Epub ahead of print]38(2):

Domain architecture of plant eukaryotic translation initiation factor 3 subunit E governs interaction with translational cis-elements to regulatepollen tube growth.

Vinod Kumar, Rémy Merret, Marie C Carpentier, David Honys, Said Hafidh.

An octameric eukaryotic translation initiation factor 3 subunit E (eIF3E) preserves translational homeostasis through selective messenger RNA (mRNA) recognition and ribosome assembly. Yet, the mechanisms by which eIF3E maintains translational equilibriumremain poorly understood. We show here that eIF3E domain architecture and phosphorylation sites (Thr417, Ser421) are conserved across eukaryotes. Deleting the Proteasome-COP9 signalosome-Initiation factor 3 domain (PCI domain) abolished nuclear localization, disrupted eIF3E-eIF3L interaction, and impaired eIF3E dissociation from the polysomes. Affnity RNA immunoprecipitation sequencing of eIF3E::YFP in tobacco pollen tubes identified mRNAs bearing coding-sequence motifs (MC1 to MC3) that co-immunoprecipitate with eIF3E.Using mRNA reporter assay, we reveal that these motifs act in tandem as eIF3E-dependent translational repressors and enhancers. AlphaFold3 structural modeling and Förster resonance energy transfer verification indicate that PCI domain deletion or PCI-phosphosite mutagenesis weaken eIF3E-eIF3L interactions and block translational activation of MC2 RNA reporter. We further show thatloss of the PCI domain or PCI-phosphosite mutagenesis misregulate pollen tube growth and membrane organization. Together, our findings underscore eIF3E as a selective regulator of mRNA translation that couplescis-motifrecognition to membrane integrityand pollen tube growth, thereby ensuringplant fertility.

DOI: https://doi.org/10.1093/plcell/koag005
Anal Chim Acta. 2026 Apr 01. pii: S0003-2670(26)00104-2. [Epub ahead of print]1393 345154

RNA sample preparation strategies for mass spectrometry sequencing of the epitranscriptome and therapeutic RNAs: A review.

Nina J Fitzgerald, Weichen Huang, Kevin D Clark.

   BACKGROUND: More than 170 post-transcriptional modifications of RNA have been discovered to date that are increasingly recognized as key contributors to all aspects of RNA function, including RNA metabolism, trafficking, and translation properties. These modifications range in complexity from simple methylations to glycosylations and altogether constitute what is known as the epitranscriptome. Chemical modifications are also strategically incorporated into RNA therapeutics to enhance RNA stability, reduce immunogenicity, and improve translational efficiency. As a result of their critical importance to the function of both endogenous and therapeutic RNAs, there is intense demand for methods that enable sequencing and quantification of RNA modifications.
RESULTS: Here, we provide a critical review of state-of-the-art sample preparation strategies for mass spectrometry (MS)-based sequencing of RNA modifications. We offer guidance on selecting methods for extraction, purification, preconcentration, and RNA labeling that are tailor-made for specific sample matrices and RNA types.
SIGNIFICANCE: Mass spectrometry has emerged as an indispensable technique for sequencing modifications of RNA with single-nucleotide resolution and providing quantitative measurements of modification stoichiometry. However, MS analysis of RNA is complicated by myriad sample matrix components that are incompatible with MS, contributing to RNA signal suppression or creating substantial data analysis challenges. The judicious selection of an appropriate sample preparation method is therefore an essential, yet often overlooked, step prior to MS characterization of RNA.

Keywords:  Epitranscriptome; Mass spectrometry; Nucleic acids; RNA modification; Sample preparation

DOI:  https://doi.org/10.1016/j.aca.2026.345154
RNA. 2026 Feb 17. 32(3): 269-275

Seven wonders of RNA modification biology.

Jordan L Meier.

This Perspective discusses seven frontiers in RNA modification research. The examples cited highlight technological advances, regulatory principles both unique and broad-spanning, and questions about how biological information is post-transcriptionally encoded in chemical marks comprising just a few atoms.

DOI: https://doi.org/10.1261/rna.080887.125
Biochemistry (Mosc). 2026 Jan;91(1): 178-187

Functional Divergence of bL36m Protein in Yeast and Human Mitochondrial Ribosomes.

Uliana E Piunova, Mariia V Baleva, Margarita S Lantsova, Ivan V Chicherin, Ruslan A Vasilev, Anastasia M Moysenovich, Sergey A Levitskii, Piotr A Kamenski.

  L36 is a structural protein of the large ribosomal subunit of bacterial, mitochondrial, and chloroplast ribosomes. L36 stabilizes the peptidyl transferase center and the L7/L12 stalk, which is a binding site for the elongation factors during the translation cycle. According to the cryoelectron microscopy data, L36 incorporates into the large ribosomal subunit in both bacteria and mitochondria at the final assembly step. Bacterial L36 is not an essential protein, since deletion of its gene in bacteria did not impair the colony growth or reduce the mRNA translation levels. Deletion of the RTC6 gene coding for the mitochondrial homologue of L36 (bL36m) in Saccharomyces cerevisiae, impeded yeast growth on the media with non-fermentable carbon sources. Our findings indicate that the mitochondrial dysfunction associated with the absence of bL36m was caused by a decreased activity of cytochrome c oxidase complex that resulted from the selective disruption of synthesis of its subunits encoded in the mitochondrial genome. Furthermore, selective inhibition of mitochondrial protein synthesis did not induce critical structural abnormalities of mitochondrial ribosomes or reduce their ability to bind mRNA. Furthermore, we demonstrated that in contrast to S. cerevisiae, the absence of bL36m protein in human cells had no substantial impact on the synthesis of mitochondrially encoded proteins or mitochondrial ribosome assembly. However, the observed reduction in the mitochondrial respiration in the bL36m-deficient cells may be indicative of disturbances in the respiratory chain organization not associated with the mitochondrial translation.

Keywords:  mitochondria; mitochondrial translation; regulation of translation

DOI:  https://doi.org/10.1134/S000629792560348X
Front Cell Dev Biol. 2026 ;14 1771110

NSUN5 and RNA m5C epitranscriptomic regulation in tumor progression.

Qiao Zhou, Chunhong Li, Xiulin Jiang, Yixiao Yuan, Qiang Zhou, Qiang Wang, Lili Jiang.

  NSUN5 is a pivotal RNA 5-methylcytosine (m5C) methyltransferase that predominantly catalyzes site-specific m5C modifications in ribosomal RNA (rRNA), thereby regulating ribosome assembly, selective translation, and cellular stress adaptation. Recent studies have demonstrated that NSUN5 is aberrantly expressed in multiple cancer types, and its upregulation is often associated with advanced tumor stage, poor prognosis, and immune evasion. Mechanistically, NSUN5 modulates the m5C modification of rRNA or specific mRNAs, reshaping the cellular proteome and influencing tumor cell proliferation, migration, invasion, and stemness maintenance. Moreover, NSUN5 participates in tumor metabolic reprogramming, including glycolysis and lipid biosynthesis, as well as in cellular stress responses and resistance to chemotherapy and radiotherapy. NSUN5 can also mediate tumor microenvironmental regulation through RNA modifications, such as modulating macrophage polarization, enhancing antioxidative capacity, and facilitating immune escape. Functional crosstalk exists between NSUN5 and other RNA epigenetic regulators, forming a complex regulatory network. Given its central role and structural features, NSUN5 represents a potential therapeutic target and biomarker. Direct strategies include small-molecule inhibitors that block its methyltransferase activity, whereas indirect approaches focus on interfering with downstream signaling pathways or synergizing with other RNA modifications to inhibit tumor progression. Additionally, NSUN5 expression may serve as a stratification marker for patient classification and treatment response prediction, supporting precision oncology. Future research should focus on genome-wide target identification, integration of single-cell and spatial transcriptomics, and mechanism-driven drug development to advance the clinical translation of NSUN5-targeted interventions.

Keywords:  NSUN5; RNA m5C methylation; biomarker; chemoresistance; epitranscriptomic crosstalk; metabolic reprogramming; therapeutic target; tumor microenvironment

DOI:  https://doi.org/10.3389/fcell.2026.1771110
EMBO J. 2026 Feb 18.

eIF3 musketeers: loyal in health, rogue in disease, and redeemed by therapeutic targeting.

Reza Mohammadinejad, Dan Su, Fanglin Luo, Mengyu Li, Haoran Duan, Jing Wang, Fajin Li, Michal Shapira, Dieter A Wolf.

  The eukaryotic translation initiation factor 3 (eIF3) is the largest and most complex initiation factor in eukaryotes, functioning as a central hub that integrates signals from cellular stress, metabolism, and developmental pathways to regulate mRNA translation. Recent advances have uncovered subunit-specific roles of eIF3 that extend beyond canonical cap-dependent translation to include specialized mechanisms such as selective mRNA recruitment, noncanonical cap recognition, and translation elongation. This review summarizes the current mechanistic understanding of the contribution of aberrant eIF3 activity to diverse disease processes, including oncogenesis, neurodevelopmental and neurodegenerative disorders, muscle pathology, and infectious disease. We evaluate therapeutic strategies aimed at modulating eIF3 function, including subunit-selective small molecules, RNA-based therapeutics, and CRISPR-based interventions. We discuss the therapeutic promise of both inhibitory approaches-targeting oncogenic or pathogen-hijacked eIF3-and restorative strategies to correct genetic loss-of-function in neurological disease. Finally, we outline key challenges and opportunities for clinical translation, including tissue-specific delivery, subunit selectivity, and the identification of predictive biomarkers. eIF3 emerges as a versatile and druggable node in translational control with broad relevance across human disease.

Keywords:  Cancer; Infectious Disease; Neurodevelopmental Disorders; Targeted Therapy; Translation initiation factor eIF3

DOI:  https://doi.org/10.1038/s44318-026-00721-3
Science. 2026 Feb 19. 391(6787): eadr4287

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes.

Andre Schwarz, Mara Mueller, Helene Will, Lea Dietrich, Stefano L Giandomenico, Georgi Tushev, Ina Bartnik, Iskander Khusainov, Claudia M Fusco, Erin M Schuman.

Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formation of inactive ribosome-ribosome clusters (disomes). We used cryo-electron tomography (cryo-ET) to visualize ribosomes in situ and observed that this ribosome dimerization was mediated by a homotypic interaction of the ribosomal RNA (rRNA) expansion segment ES31Lb. ES31Lb interactions were both necessary and sufficient for disome formation and conferred a growth advantage and stress resistance to brain cells. ES31Lb is predicted to homodimerize in ~20% of chordates, including variants in both chicken and human. Cryo-ET analysis of chicken tetrasomes revealed an interaction between ES31Lb and ES9La. Thus, in animal cells, translation regulation can use a flexible component of the protein synthesis machinery-rRNA expansion segments.

DOI: https://doi.org/10.1126/science.adr4287
Noncoding RNA. 2026 Feb 09. pii: 5. [Epub ahead of print]12(1):

Extracellular Small RNAs in Human Milk: Molecular Profiles, Stability and Fragment-Specific Responses in Cell-Based Assays.

Clara Claus, Carla Borini Etichetti, Bruno Costa, Julieta B Grosso, Juan Pablo Tosar, Uciel Chorostecki, Silvana V Spinelli.

  Background/Objectives: Human milk is a complex biological fluid containing not only macro- and micronutrients but also diverse bioactive molecules, including extracellular RNAs. Although RNA has been detected in milk for decades, only a subset of RNA species has been characterized in detail, and abundant families such as tRNA-, yRNA-, and rRNA-derived fragments remain underexplored. This study aimed to define the composition, fragmentation patterns, stability, and exploratory functional activity of these highly abundant RNAs in human milk. Methods: We performed small RNA sequencing on skim milk samples and analyzed the resulting profiles in comparison with publicly available milk and biofluid datasets. RNA stability assays, Northern blotting, and RT-qPCR were conducted to validate RNA abundance and degradation kinetics. Extracellular vesicles (EVs) and non-vesicular fractions were analyzed to determine the subcellular distribution of RNA species. Exploratory functional assays using synthetic RNA fragments were carried out to assess their ability to modulate cellular responses in vitro. Results: Human milk was found to be highly enriched in small RNA fragments derived from tRNA, yRNA, and rRNA, dominated by a limited set of discrete sequences. These profiles were highly reproducible across independent datasets and distinct biofluids. Orthologal validation assays confirmed their abundance and stability, with RNA levels exceeding those of serum by over two orders of magnitude. Full-length transcripts were enriched in EVs, whereas shorter fragments predominated in the non-vesicular fraction. Synthetic milk-derived exRNAs showed detectable pro-survival activity under stress conditions in vitro. Conclusions: This study reveals that human milk carries a limited set of highly abundant stable sRNA molecules, primarily derived from tRNAs, yRNAs, and rRNAs. These findings provide new insights into the RNA cargo of human milk and offer preliminary evidence that selected sRNA fragments can modulate cellular stress responses in in vitro models.

Keywords:  RNA stability; cell survival; exRNA; extracellular vesicles; human milk; non-vesicular RNA; sRNA-seq; tRNA fragments

DOI:  https://doi.org/10.3390/ncrna12010005
Front Immunol. 2026 ;17 1749911

Rewriting the RNA code: an m6a-centric framework to classify tumors and guide combination therapies.

Yi Sun, Jinliang Wu, Guanhao Chen, Haojun Ma, Wenshuya Li, Hongyu Tan, Kerong Yang.

   Background: The epitranscriptome, particularly N6-methyladenosine (m6A), represents a dynamic layer of post-transcriptional regulation fundamentally implicated in cancer. However, the clinical translation of this knowledge is hampered by profound context-dependency, where the same m6A regulator can exert opposing roles in different tumors. To overcome this barrier, we propose a novel, clinically actionable taxonomic framework that classifies tumors based on their dominant dysregulated m6A component.
Methods: We synthesized current evidence through systematic reviews of primary research and high-impact papers from PubMed and Google Scholar, focusing on the mechanistic role of m6A modifications in cancer biology, therapy resistance, and therapeutic targeting. This synthesis was used to integrate pan-cancer molecular data including regulator expression, genetic dependency scores, and modification landscapes to define and characterize m6A-driven molecular subtypes.
Results: We classify tumors into Writer-Dominant (METTL3/14-high, Eraser-High (FTO/ALKBH5-high), Reader-Amplified (IGF2BP/YTHDF-high), and Immune-Modulatory subtypes, each with distinct oncogenic programs, therapy resistance mechanisms, and, crucially, actionable therapeutic vulnerabilities. We provide explicit, evidence-based molecular and functional inclusion criteria for each subtype and acknowledge that tumors can exhibit hybrid features, which directly inform rational combination strategies. Furthermore, we detail a diagnostic-therapeutic roadmap that integrates liquid biopsy-based m6A biomarker detection with subtype-specific treatment assignment.
Conclusion: Targeting the m6A epitranscriptome represents a paradigm shift in oncology; our framework provides the essential strategic approach needed to overcome context-dependency, offering a logical structure for tumor classification, vulnerability prediction, and the translation of epitranscriptomic insights into patient benefit through personalized, biomarker-guided combination therapies.

Keywords:  N6-methylAdenosine (m6A); RNA modification; cancer immunotherapy; epitranscriptome; targeted therapy; therapeutic resistance

DOI:  https://doi.org/10.3389/fimmu.2026.1749911
Nucleic Acids Res. 2026 Feb 05. pii: gkag113. [Epub ahead of print]54(4):

Engineering a human-based translational activator for targeted protein expression restoration.

Riley W Sinnott, Ani Solanki, Anitha P Govind, William N Green, Bryan C Dickinson.

Therapeutic modalities to programmably increase protein production are in critical need to address diseases caused by deficient gene expression via haploinsufficiency. Restoring physiological protein levels by increasing translation of their cognate messenger RNA (mRNA) would be an advantageous approach to correct gene expression but has not been evaluated in an in vivo disease model. Here, we investigated whether a translational activator could improve phenotype in a Dravet syndrome mouse model, a severe developmental and epileptic encephalopathy caused by SCN1a haploinsufficiency, by increasing translation of the SCN1a mRNA. We identify and engineer human proteins capable of increasing mRNA translation using the CRISPR-Cas-inspired RNA-targeting system (CIRTS) platform to enable programmable, guide RNA-directed translational activation with entirely engineered human proteins. We identify a compact (601 amino acid) CIRTS translational activator (CIRTS-4GT3) that can drive targeted, sustained translation increases up to 100% from three endogenous transcripts relevant to epilepsy and neurodevelopmental disorders. AAV-delivery of CIRTS-4GT3 targeting SCN1a mRNA to a Dravet syndrome mouse model led to increased SCN1a translation and improved survivability and seizure threshold-key phenotypic indicators of Dravet syndrome. This work validates a strategy to address SCN1a haploinsufficiency and emphasizes the preclinical potential of targeted translational activation to address neurological haploinsufficiency.

DOI: https://doi.org/10.1093/nar/gkag113
J Plant Physiol. 2026 Feb 12. pii: S0176-1617(26)00039-8. [Epub ahead of print]319 154726

Recent advances in understanding the roles of PPR proteins in plant responses to biotic and abiotic stresses.

Kwanuk Lee.

  Pentatricopeptide repeat (PPR) proteins, one of the largest families of RNA-binding proteins in higher plants, play essential roles in the post-transcriptional regulation of RNA metabolism in organelles. PPR proteins are predominantly localized in mitochondria and/or chloroplasts, and participate in various post-transcriptional processes, including RNA editing (C-to-U conversion), intron splicing, RNA stabilization, cleavage, and translation. Although the importance of PPR proteins in organellar biogenesis and plant development are well established, recent studies have revealed their critical roles in plant's response to biotic and abiotic stresses. In this review, recent advances in understanding how distinct subclasses of P- and PLS-class PPR proteins mediate organellar RNA metabolism and influence stress signaling networks in plant's response to biotic and abiotic stresses are summarized. In particular, this review focuses on their functional relevance in responses to drought, salinity, extreme temperatures, heavy metal stress response, as well as pathogen infection, with emphasis on mechanisms involving reactive oxygen species homeostasis and organelle-to-nucleus retrograde signaling. Furthermore, recent progress in the synthetic redesign of PPR motifs, which enables programmable RNA recognition, is discussed. These advances provide valuable insights into the regulatory roles of PPR proteins and highlight the potential applications of synthetic PPR systems as tools to improve plant performance and resilience to environmental stress in changing climate conditions.

Keywords:  Chloroplasts; Mitochondria; Organellar RNA metabolism; Pentatricopeptide repeat proteins; Stress response; Synthetic biology

DOI:  https://doi.org/10.1016/j.jplph.2026.154726
J Vis Exp. 2026 Jan 30.

Effect of Seed Length and Binding Motifs on Hfq-Mediated sRNA-mRNA Annealing Analyzed Using Single-Molecule FRET.

Maciej Dylewski, Ewelina M Małecka.

Defining the rules that govern annealing between bacterial small RNAs (sRNAs) and their mRNA targets is challenging because these RNAs are highly heterogeneous in sequence and structure. To disentangle the contribution of individual features, we systematically varied key determinants, including seed strength, Hfq-binding motifs, and the spacing between them. The effects of these features on sRNA-mRNA duplex stability were tested using single-molecule Förster resonance energy transfer (smFRET), which enables monitoring of individual RNA molecules on the millisecond timescale and provides access to dynamic events often obscured in ensemble assays. We demonstrate that short seed regions (4-5 bp) form unstable, short-lived complexes, whereas longer seeds (8-10 bp) produce stable duplexes. Extending Hfq-binding motifs or introducing a spacer between the binding sites on mRNA further increased interaction lifetimes, highlighting the importance of motif strength and spatial arrangement in Hfq-mediated annealing efficiency. Moreover, this approach provides a robust and reproducible framework for dissecting RNA-RNA interaction dynamics at single-molecule resolution and for probing RNA chaperone mechanisms.

DOI: https://doi.org/10.3791/69981
Elife. 2026 Feb 18. pii: RP99322. [Epub ahead of print]13

Ribosome demand links transcriptional bursts to protein expression noise.

Sampriti Pal, Upasana Ray, Riddhiman Dhar.

  Stochastic variation in protein expression generates phenotypic heterogeneity in a cell population and has an important role in antibiotic persistence, mutation penetrance, tumor growth, and therapy resistance. Studies investigating molecular origins of noise have predominantly focused on the transcription process. However, the noise generated in the transcription process is further modulated by translation. This influences the expression noise at the protein level which eventually determines the extent of phenotypic heterogeneity in a cell population. Studies across different organisms have revealed a positive association between translational efficiency and protein noise. However, the molecular basis of this association has remained unknown. In this work, through stochastic modeling of translation in single mRNA molecules and empirical measurements of protein noise, we show that ribosome demand associated with high translational efficiency in a gene drives the correlation between translational efficiency and protein noise. We also show that this correlation is present only in genes with bursty transcription. Thus, our work reveals the molecular basis of how coding sequence of genes, along with their promoters, can regulate noise. These findings have important implications for investigating protein noise and phenotypic heterogeneity across biological systems.

Keywords:  S. cerevisiae; computational biology; protein expression noise; ribosome demand; systems biology; transcriptional bursts; translational bursts; translational efficiency

DOI:  https://doi.org/10.7554/eLife.99322
Cell Insight. 2026 Apr;5(2): 100299

Structural and mechanistic basis of ADAR1-mediated RNA editing and immune regulation.

Xiangyu Deng, Mariam Elsharkawy, Yang Gao.

  Adenosine deaminase acting on RNA 1 (ADAR1) is a central regulator of innate immunity. By binding to and catalyzing adenosine-to-inosine deamination within double-stranded RNAs, ADAR1 mitigates the immunogenicity of self-derived RNAs and preserves cellular homeostasis. In this review, we summarize recent structural and mechanistic advances that illuminate key features of ADAR1 architecture, including how its multi-domains engage dsRNA substrates and contribute to substrate selectivity. Integrated with decades of biochemical and genetic studies, these insights refine our understanding of ADAR1's catalytic mechanism, domain-specific activities, and roles in suppressing immune signaling. We further highlight emerging knowledge on ADAR1's RNA substrate landscape, its interactions with protein partners, and the mechanistic principles that underlie its broad RNA editing and immune regulatory functions, with implications for disease pathogenesis and therapeutic RNA editing.

Keywords:  ADAR1; Innate immune regulation; RNA editing; dsRNA recognition

DOI:  https://doi.org/10.1016/j.cellin.2026.100299
Front Oncol. 2026 ;16 1744928

The methyltransferase METTL16 in digestive system cancers: functions and mechanisms.

Jia Li, Yueyuan Bao, Fei Yao, Qingming Wu.

  N6-methyladenosine (m6A) methylation, the most prevalent mRNA modification, affects RNA transcription, splicing, and stability. Methyltransferase-like 16 (METTL16), a novel m6A methyltransferase, regulates the expression of target mRNAs via m6A-mediated modifications. The methyltransferase domain of METTL16 is essential for its catalytic activity. In addition to acting as a methyltransferase, METTL16 can also facilitate mRNA translation in an m6A-independent manner, thus regulating cancer development and progression. Accumulating evidence has indicated that METTL16 plays a pivotal role in the progression of various cancers by regulating cell proliferation, apoptosis, metastasis, and resistance to chemotherapy. In this review, we provide a narrative review of the functions of METTL16 and summarize its oncogenic and tumor-suppressive functions as well as its underlying mechanisms in human digestive system cancers. However, further in-depth studies are required to validate these findings. By comprehensively summarizing the current literature on METTL16, we provide a theoretical basis for its application as a diagnostic and prognostic marker as well as a potential therapeutic target for digestive system cancers.

Keywords:  M6A; METTL16; RNA modification; digestive system cancers; methyltransferase

DOI:  https://doi.org/10.3389/fonc.2026.1744928
J Genet Genomics. 2026 Feb 16. pii: S1673-8527(26)00059-7. [Epub ahead of print]

Biogenesis, features, and functions of coding transcripts-derived siRNAs in plants.

Yan Yan, Yuelin Liu, Hongwei Guo.

  Plant small RNAs (sRNAs) are pivotal regulators of development, genome stability, and environmental adaptation. In plants, endogenous sRNAs are broadly grouped into microRNAs (miRNAs) and small interfering RNAs (siRNAs). siRNAs can be further subdivided into those derived from noncoding transcripts, such as transposable elements and long noncoding RNAs, and those generated from protein-coding transcripts. Among these, coding transcript-derived siRNAs (ct-siRNAs) represent a critical link between RNA quality control (RQC) and post-transcriptional gene silencing. When RNA decay and RQC pathways are genetically impaired or attenuated by environmental and biotic stresses, aberrant protein-coding mRNAs can be converted into ct-siRNAs, with 22-nt species efficiently triggering secondary siRNA amplification. ct-siRNA production is highly selective, concentrating at hotspot loci whose transcripts are shaped by characteristic RNA features, translational status, and contributes to enhanced stress resistance by modulating defense- and metabolism-related gene networks. ct-siRNAs bridge mRNA surveillance and growth defense trade-offs, acting as endogenous danger signals to expand post-transcriptional regulation and improve crop resilience. This review summarizes recent advances in endogenous sRNA biology with a particular focus on ct-siRNAs, detailing their biogenesis, regulatory properties, and biological functions. We further discuss their physiological significance and highlight key open questions and future directions in this emerging field.

Keywords:  Growth–defense trade-off; PTGS; RNA decay; Silencing storm; ct-siRNA

DOI:  https://doi.org/10.1016/j.jgg.2026.02.015
Biochimie. 2026 Feb 12. pii: S0300-9084(26)00046-5. [Epub ahead of print]244 102-105

The DExD-box RNA helicase Dbp7 unwinds short double-stranded RNAs.

Julia Contreras, Régine Capeyrou, Yves Henry, Anthony K Henras, Odile Humbert, Jesús de la Cruz, Eduardo Villalobo.

  DExD-box proteins are ATP-dependent enzymes that unwind double-stranded RNAs in a non-processive manner, often initiating strand separation from 5'- or 3'-single-stranded overhangs. Dbp7, a member of this family, is required for yeast ribosome biogenesis and has been specifically implicated in the release of the small nucleolar RNA snR190 from early pre-60S particles. To gain mechanistic insight into its function, we have examined the in vitro helicase activity of recombinant Dbp7. We show that it efficiently unwinds short double-stranded RNA substrates in an ATP-dependent manner, irrespective of overhang polarity, thereby establishing it as a bona fide DExD-box RNA helicase.

Keywords:  DEAD-box protein; Dbp7; RNA binding; RNA helicase; Ribosome biogenesis; Saccharomyces cerevisiae

DOI:  https://doi.org/10.1016/j.biochi.2026.02.010
ACS Synth Biol. 2026 Feb 18.

Incorporation of a Human-Derived CU-Rich Element in the 3' UTR Improves Synthetic mRNA Stability and Expression In Vivo.

Jia Tang, Meng Li, Baiyao Liu, Chuantao Wu, Fangmeng Dai, Hanzhi Kang, Ke He, Wenxue Zhao.

  Synthetic mRNA provides a powerful platform to transfer genetic information encoding therapeutic proteins in vivo. However, their applications are limited by their intrinsic instability and insufficient protein yield. Here we report a 40-nt RNA sequence (ARF6.40) that markedly improves mRNA stability and protein bioavailability of synthetic mRNA. ARF6.40, identified from the 3' UTR of the human ARF6 mRNA, contains a novel CU-rich element that interacts with the protein U2AF2. Compared with the broadly used globin 3' UTR, fusing ARF6.40 to the 3' UTR of EGFP mRNA results in markedly increased mRNA half-life and protein level; transfection of cells with SARS-CoV-2 RBD-encoding mRNA or administration of mice with LNP-encapsulated firefly luciferase mRNA fused with ARF6.40 leads to significantly higher and more sustained RBD secretion or luciferase expression in vivo. Together, our study demonstrates the potential of ARF6.40 in mRNA therapeutics and provides new insights into how the expression of ARF6 is regulated.

Keywords:  3′ UTR; RNA; RNA element; RNA therapy; Synthetic mRNA; mRNA stability

DOI:  https://doi.org/10.1021/acssynbio.5c00824
Clin Exp Hypertens. 2026 Dec 31. 48(1): 2629926

Bulk and single-cell transcriptomics for identification of potential diagnostic biomarkers associated with pulmonary arterial hypertension and integrated stress response and experimental validation.

Haoran Li, Meiling Li, Chenming Qiu, Yongjian Yang, Cong Lan.

   BACKGROUND: Pulmonary arterial hypertension (PAH) is a lethal vascular disorder characterized by irreversible remodeling of the pulmonary arteries, but the systematic role of the integrated stress response (ISR)-related genes (ISR-RGs) in its pathogenesis remains unexplored.
OBJECTIVE: This study aimed to identify and validate ISR-associated potential biomarkers for PAH using integrative bioinformatics, single-cell transcriptomics, and experimental approaches.
METHODS: We analyzed bulk RNA-seq datasets (GSE38267, GSE131793) and a single-cell RNA sequencing (scRNA-seq) dataset (GSE210248) from PAH patients and controls. A total of 529 ISR-RGs were integrated. Differential expression analysis, machine learning, and functional enrichment analyses were employed to identify potential biomarkers. A diagnostic nomogram was constructed and validated. Immune infiltration, regulatory networks, drug-gene interactions, and molecular docking were further investigated. Key cellular mechanisms were elucidated via scRNA-seq, and biomarker expression was validated using Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) and Enzyme-linked immunosorbent assay (ELISA) in clinical whole blood samples.
RESULTS: We identified four ISR-related diagnostic biomarkers: ABCC4, ATM, SERPINH1, and ZBTB40. These genes showed consistent dysregulation in PAH across multiple datasets and were integrated into a nomogram with good predictive performance (hosmer-lemeshow (HL) test P = 0.432). Gene set enrichment analysis (GSEA) revealed their involvement in translation, neutrophil degranulation, and glucocorticoid pathways. The scRNA-seq highlighted their cell-type-specific expression in T cells and monocytes. Molecular docking identified CAMONSERTIB as a potent ATM-targeting drug (binding energy: -10.2 kcal/mol), and its therapeutic effects on pulmonary arterial hypertension were validated through both animal and cellular models. RT-qPCR and Elisa confirmed upregulation of ABCC4 and downregulation of ATM, SERPINH1 and ZBTB40 in PAH patients.
CONCLUSIONS: This study identified four novel ISR-related biomarkers for PAH and elucidated their roles in immune infiltration and cellular remodeling. The findings provided new insights into PAH pathogenesis and offered potential tools for diagnosis and targeted therapy.

Keywords:  ABCC4; ATM; Pulmonary arterial hypertension; SERPINH1; ZBTB40; bioinformatics; diagnostic biomarkers; integrated stress response; single-cell RNA sequencing

DOI:  https://doi.org/10.1080/10641963.2026.2629926
RNA Biol. 2026 Feb 18.

Cas10 residues lining the target RNA binding channel regulate interference by distinguishing cognate target RNA from mismatched targets.

Sarah Khweis, Mason Blackburn, Calvin Perdigao, Megan Pierce, Colby Lewis, Jack Dunkle.

  Type III CRISPR systems are defined by the presence of the Cas10 protein and are among the most abundant CRISPR systems in nature. Cas10 forms a complex with crRNA and several Cas proteins that surveils prokaryotic cells for foreign RNA molecules and when they are detected it activates a cascade of interference activities. The synthesis of the cyclic oligoadenylate signalling molecule by Cas10 is a key aspect of the interference cascade. Despite structures of the Cas10 complex bound to target RNAs, the molecular mechanism by which Cas10 senses the bound state to licence interference is lacking. We identified five residues in S. epidermidis Cas10, two in the Cas10 Palm2 domain and three in domain 4, that line the target RNA binding channel. We assessed the contribution of these residues to interference in the context of a cognate or mismatched target RNA. We found that the residues regulate whether a mismatched crRNA-target RNA duplex is able to activate interference in vivo. We purified two site-directed mutants of Cas10-Csm and show with in vitro cOA synthesis assays that they demonstrate enhanced discrimination of cognate versus mismatched target RNAs.

Keywords:  CRISPR-Cas; Cas10; cyclic oligoadenylate; interference; type III

DOI:  https://doi.org/10.1080/15476286.2026.2633385
Mol Omics. 2026 Jan 10. pii: aaiaf005. [Epub ahead of print]22(1):

Development of an immobilized system for RNA modification analysis.

Zhiyan Li, Luyao Yu, Xingyu Liu, Liangle Deng, Zongtao Lin, Zhuocheng Liu, Benjamin A Garcia, Yixuan Xie.

Characterizing RNA modifications is crucial for understanding fundamental biological processes, such as RNA folding, stability, translation, and splicing. However, current systems for ribonucleoside sample preparation are limited to the solution phase. In this study, we employed the click reaction between methyltetrazine and trans-cyclooctene to immobilize RNases, including nuclease P1, phosphodiesterase I, and shrimp alkaline phosphatase, on agarose beads. Using this digestion method, RNA was fully converted to ribonucleosides within 30 min. Importantly, integrating these immobilized RNases with a microspin tube modified with porous graphitic carbon enabled direct downstream MS analysis, constituting a streamlined system. We applied this system to monitor RNA modification dynamics during transforming growth factor-β (TGF-β)-induced epithelial-mesenchymal transition in lung cancer cells and observed significant changes in several RNA modifications (e.g. m6A and m5U), which is consistent with the indispensable role of RNA modifications in tumour metastasis. Overall, our results demonstrate the efficiency and robustness of our method and highlight a promising direction for RNA modification analysis, supporting the development of automated, high-throughput workflows for future large-cohort studies.

DOI: https://doi.org/10.1093/momics/aaiaf005
RNA. 2026 Feb 19. pii: rna.080892.125. [Epub ahead of print]

A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions.

Shaimae I Elhajjajy, Zhiping Weng.

  RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions of most RBPs are not well-characterized. Previous studies have shown that motif context is an important contributor to RBP binding specificity, but its precise role remains unclear. Despite recent computational advances to predict RBP binding, existing methods are challenging to interpret and largely lack a categorical focus on RBP motif contexts and RBP-RBP interactions. There remains a need for interpretable predictive models to disambiguate the contextual determinants of RBP binding specificity in vivo. Here, we present a novel and comprehensive pipeline to address these knowledge gaps. We devise a Natural Language Processing-based method to deconstruct sequences into entities comprising a target k-mer and its flanking regions, then use this representation to formulate RBP binding prediction as a weakly supervised Multiple Instance Learning problem. To interpret our predictions, we introduce a deterministic motif discovery algorithm to leverage our data structure, recapitulating the established motifs of numerous RBPs as validation. Importantly, we characterize the binding motifs and binding contexts for 71 RBPs in HepG2 and 74 RBPs in K562, with many of them being novel. Finally, through feature integration, transitive inference, and a new cross-prediction approach, we propose novel cooperative and competitive RBP-RBP interaction partners and hypothesize their potential regulatory functions. In summary, we present a complete framework for investigating the contextual determinants of specific RBP binding, and we demonstrate the significance of our findings in delineating RBP binding patterns, interactions, and functions.

Keywords:  NLP; RBP interactions; RNA-binding proteins

DOI:  https://doi.org/10.1261/rna.080892.125
Noncoding RNA. 2026 Jan 31. pii: 4. [Epub ahead of print]12(1):

Mechanisms at the Intersection of lncRNA and m6A Biology.

Samuel J Gonzalez, Edgardo Linares, Allison M Porman Swain, Aaron M Johnson.

  This review provides a thorough survey of long noncoding RNAs that bear the RNA modification N6-methyladenosine (m6A) and current work to understand the resulting mechanistic and biological consequences. We give an overview of lncRNA and m6A biology first, describing the writers, erasers, and readers of m6A and their targeting of lncRNAs. Next, we give an in-depth review of the field of nuclear lncRNAs that regulate chromatin and their regulation via m6A. We then describe the growing appreciation of liquid-liquid phase separation properties in lncRNA and m6A biology. Finally, we cover examples of cytoplasmic lncRNAs regulated by m6A. Overall, this review aims to emphasize how epitranscriptomics influences noncoding RNA mechanisms to provide additional layers of regulation, integrated into downstream biological processes.

Keywords:  N6-methyladenosine (m6A); epitranscriptomics; gene regulation; long noncoding RNA

DOI:  https://doi.org/10.3390/ncrna12010004
Pathophysiology. 2026 Feb 03. pii: 15. [Epub ahead of print]33(1):

Vitamin D Reprograms Non-Coding RNA Networks to Block Zika Virus in Human Macrophages.

Julieta M Ramírez-Mejía, Geysson Javier Fernandez, Silvio Urcuqui-Inchima.

  Background: Zika virus (ZIKV), a mosquito-borne flavivirus, is associated with congenital malformations and neuroinflammatory disorders, highlighting the need to identify host factors that shape infection outcomes. Macrophages, key targets and reservoirs of ZIKV, orchestrate both antiviral and inflammatory responses. Methods: Vitamin D (VitD) has emerged as a potent immunomodulator that enhances macrophage antimicrobial activity and regulates inflammation. To investigate how VitD shapes macrophage responses to ZIKV, we reanalyzed publicly available RNA-seq and miRNA-seq datasets from monocyte-derived macrophages (MDMs) of four donors, differentiated with or without VitD and subsequently infected with ZIKV. Results: Differential expression analysis identified long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs integrated into competing endogenous RNA (ceRNA) networks. In VitD-conditioned and ZIKV-infected MDMs, 65 lncRNAs and 23 miRNAs were significantly modulated. Notably, lncRNAs such as HSD11B1-AS1, Lnc-FOSL2, SPIRE-AS1, and PCAT7 were predicted to regulate immune and metabolic genes, including G0S2, FOSL2, PRELID3A, and FBP1. Among the miRNAs, let-7a and miR-494 were downregulated, while miR-146a, miR-708, and miR-378 were upregulated, all of which have been previously implicated in antiviral immunity. Functional enrichment analysis revealed pathways linked to metabolism, stress responses, and cell migration. ceRNA network analysis suggested that SOX2-OT and SLC9A3-AS1 may act as molecular sponges, modulating regulatory axes relevant to immune control and viral response. Conclusions: Despite limitations in sample size and experimental validation, this study provides an exploratory map of ncRNA-mRNA networks shaped by VitD during ZIKV infection, highlighting candidate molecules and pathways for further studies on host-virus interactions and VitD-mediated immune regulation.

Keywords:  antiviral response; bioinformatics; competing endogenous RNA; lncRNA; mRNA; miRNA; pro-inflammatory response; virus

DOI:  https://doi.org/10.3390/pathophysiology33010015
Brief Bioinform. 2026 Jan 07. pii: bbag068. [Epub ahead of print]27(1):

Human messenger RNA harbors widespread noncoding splice isoforms.

Qili Shi, Haochen Li, Junjiao Song, Hao Wu, Yu Zeng, Jiawen Jiang, Shengli Li, Zhiao Chen, Xianghuo He.

  Premessenger RNA transcribed from canonical protein-coding genes is frequently alternatively spliced into diverse mature mRNA isoforms, thus translating into various protein products. However, it remains unknown whether human mRNA from a protein-coding gene harbors noncoding splice isoforms in the genome. Herein, we discovered 15 836 mRNA noncoding isoforms across 7298 protein-coding genes in human. mRNA noncoding isoforms are mainly produced by alternative splicing and polyadenylation, which display tissue-specific distributions and involve in RNA processing pathways. Notably, mRNA noncoding isoforms are frequently upregulated in cancer. Differentially expressed mRNA noncoding isoforms are associated with the cancer hallmarks and can independently predict patient survival. These findings discovered human mRNA harbors widespread noncoding splice isoforms and highlight the dual characters of mRNA accommodating protein-translation isoforms and regulatory noncoding isoforms, providing a new dimension for deeper insights into the functional duality of human mRNA.

Keywords:  mRNA; mRNA translation–noncoding duality; noncoding splice isoform; protein-coding isoform

DOI:  https://doi.org/10.1093/bib/bbag068
Nat Rev Genet. 2026 Feb 16.

Bridging technical innovation and computational advances in studies of RNA-protein assemblies.

Luca Ducoli, Suhas Srinivasan, Eimon Amjadi, Paul A Khavari.

RNA-dependent protein assemblies - including the spliceosome, ribosome and RNA-dependent membraneless organelles - have crucial roles in diverse cellular processes through RNA scaffolding and hierarchical assembly. Various empirical techniques and artificial intelligence algorithms have been developed to help understand the architecture, dynamics and functional implications of RNA-protein complexes, and their further development is underway to comprehensively integrate this information. This Review explores how combining these diverse technologies will enhance our understanding of the biological functions of RNA-dependent protein assemblies. We first explore methodological frontiers, contrasting traditional approaches with new platforms, which enable the identification and tracking of RNA-protein assembly dynamics on the same RNA molecules. We then present avenues for integrating these new experimental techniques with machine-learning methods to improve both predictive models of RNA-protein assembly and functional RNA design. We discuss how the synergy between experimental and digital biology can drive new insights into disease mechanisms and therapeutic strategies, including targeted modulation of pathogenic RNA-protein assemblies. Finally, we examine roadmaps for future research, emphasizing the potential of closed-loop systems that iteratively refine our understanding of RNA-protein assemblies through cycles of hypothesis generation, prediction, experimentation and validation.

DOI: https://doi.org/10.1038/s41576-026-00931-9
Exp Mol Med. 2026 Feb 18.

Two codes of RNA editing by deamination in human diseases.

Dong Jun Min, Suyeon Lee, Young-Suk Lee, Jun Cho.

RNA editing is a post-transcriptional modification that expands transcriptomic and proteomic diversity. Advances in high-throughput sequencing across a broad range of biological and pathological contexts have enabled systematic identification of editing events driven by two major RNA deaminase families: ADAR and APOBEC, which catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) substitution, respectively. Genome-wide profiling of RNA editing has uncovered a substantial number of differentially edited loci in various conditions, implicating the post-transcriptional events in physiological and pathological regulation. Aberrant RNA editing alters the functional information of coding and noncoding transcripts, perturbing protein activity, RNA stability and other gene expression programs, which contributes to immune imbalance, viral infection, neurological impairment, metabolic disorders and tumorigenesis. The two codes of A-to-I and C-to-U RNA editing harbor common potential for single base conversion with varied expression of responsible enzymes across many physiological and pathological conditions. Here we provide a comprehensive and parallel overview on ADAR-mediated A-to-I and APOBEC-mediated C-to-U editing, with emphasis on their molecular mechanisms, physiological roles and pathological dysregulation in human health and disease.

DOI: https://doi.org/10.1038/s12276-025-01633-8
Front Immunol. 2026 ;17 1749727

Xinfeng capsule improves hyperinflammation-associated hypercoagulability and self-perception in osteoarthritis by regulating KLF4 through METTL14-mediated m6A modification of lncRNA MEG3.

Mingyu He, Jian Liu, Yanqiu Sun, Yanyan Fang, Fanfan Wang.

   Background: Our previous studies have demonstrated that Xinfeng Capsule (XFC) exerts therapeutic effects on hyperinflammation-associated hypercoagulability and self-perception of patients (SPP) with osteoarthritis (OA). However, the underlying molecular mechanisms remain unclear.
Objective: This study aimed to explore the mechanism by which XFC improves hyperinflammation-associated hypercoagulability and SPP in OA.
Methods: A keyword co-occurrence network was constructed to identify key targets involved in hyperinflammation-associated hypercoagulability in OA patients. m6A prediction databases and RNA pull-down assays were used to identify potential m6A modification sites and key binding proteins of lncRNA MEG3. Peripheral blood mononuclear cells (PBMCs) were collected from OA patients and healthy controls, and global m6A levels were measured using a colorimetric assay. Methylated RNA immunoprecipitation quantitative polymerase chain reaction (MeRIP-qPCR) was used to detect m6A modification levels of lncRNA MEG3. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot (WB) were performed to determine the mRNA and protein expression levels of target genes. Enzyme-linked immunosorbent assay (ELISA) was used to measure inflammatory and coagulation-related factors. Finally, clinical data mining was conducted to clarify the clinical efficacy of XFC in improving hyperinflammation-associated hypercoagulability and SPP in OA patients, and in vitro experiments were performed to validate the underlying mechanisms.
Results: The keyword co-occurrence network analysis indicated that inflammatory factors [interleukin-6 (IL-6), IL-10, and tumor necrosis factor-α (TNF-α)] and coagulation-related factors [tissue factor (TF), plasminogen activator inhibitor-1 (PAI-1), and prostaglandin I2 (PGI2)] are involved in the regulation of hyperinflammation-associated hypercoagulability in OA patients. PBMC analysis further confirmed these findings. In addition, the expression levels of lncRNA MEG3 and its target gene KLF4 were significantly decreased in OA patients and were closely associated with clinical indicators of inflammation, coagulation, and SPP. Methyltransferase-like 14 (METTL14) expression was significantly increased in OA patients and was negatively correlated with lncRNA MEG3 expression. Clinical data mining revealed that XFC is a key therapeutic agent for improving hyperinflammation-associated hypercoagulability and SPP in OA patients. XFC treatment reduced the expression levels of METTL14, pro-inflammatory factors, and procoagulant factors, while increasing the levels of lncRNA MEG3, KLF4, anti-inflammatory factors, and anticoagulant factors. In vitro These findings were further validated by in vitro experiments.
Conclusion: This study indicates that XFC may upregulate the expression of lncRNA MEG3 and KLF4 by modulating METTL14-mediated m6A modification of lncRNA MEG3. Through this mechanism, XFC may regulate inflammatory responses and coagulation disorders, thereby improving SPP and exerting therapeutic effects on hyperinflammation-associated hypercoagulability in patients with OA.

Keywords:  METTL14; Xinfeng capsule; hyperinflammation- associated hypercoagulability; lncRNA MEG3; osteoarthritis

DOI:  https://doi.org/10.3389/fimmu.2026.1749727
Virol J. 2026 Feb 16.

Identification and comparison of RNA structures in 5'- and 3'-terminal genomic regions across four coronavirus genera by SHAPE analysis.

Hsuan-Wei Hsu, Pei-Chi Hsu, Yu Teng, Meilin Wang, Feng-Cheng Hsieh, Chun-Chun Yang, Hung-Yi Wu.

   BACKGROUND: Comprehensive determination of RNA structures in 5'- and 3'-terminal genomic regions across four genetically divergent coronavirus genera and thus their conservation are the first steps toward the identification of their function in coronavirus gene expression. Although these RNA structures have been experimentally analyzed for β coronaviruses, those for α coronaviruses have primarily been analyzed using bioinformatics methods. In addition, information concerning these RNA structures in γ and δ coronaviruses is limited.
METHODS: To experimentally identify the conserved RNA structures in 5'- and 3'-terminal genomic regions across four coronavirus genera, the chemical probing method selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) was used. Moreover, on the basis of the determined RNA structures, the potential long-range RNA‒RNA interactions and the predicted 3-dimensional (3D) RNA structures in these genomic regions were identified using RNAcanvas and RNAComposer, respectively.
RESULTS: The results obtained were as follows: (i) the overall RNA structures in the 5'- and 3'-terminal genomic regions varied across the four coronavirus genera, as did their 3D structures; (ii) the 3'-terminal RNA structures in the representative γ coronavirus were unique among the four coronavirus genera; (iii) the stem loops (SLs) 1, 2, 4 and 5 in the 5'-termini and the SL2 and potential pseudoknot (PK) structures in the 3'-termini were the conserved RNA structures across the four coronavirus genera; and (iv) potential long-range RNA‒RNA interactions within the 5'- and 3'-terminal genomic regions can be identified.
CONCLUSIONS: The 5' and 3' terminal RNA structures in the represented α, β, γ and δ coronaviruses are analyzed and compared by using the chemical probing method SHAPE. Although different degrees of variations are found in the 5'- and 3'-terminal genomic regions across the four coronavirus genera, conserved RNA structures are identified. The determined RNA structures, the potential long-range RNA‒RNA interactions and the predicted 3D RNA structures within these genomic regions may contribute to the identification of RNA elements important for coronavirus gene expression.

Keywords:   cis-acting RNA elements; Coronavirus; Gene expression; RNA structure; SHAPE

DOI:  https://doi.org/10.1186/s12985-026-03105-5
J Transl Med. 2026 Feb 16.

NAT10 and ac4C modification in cancer immunity and metabolism: emerging mechanisms and therapeutic potential.

Yanqi Yang, Changren Chen, Yanan Feng, Qiaoli Lv.

   BACKGROUND: Tumor immunity and metabolism are interconnected through the tumor microenvironment (TME), with RNA modifications playing pivotal epigenetic regulatory roles. N4- acetylcytidine (ac4C) is the first acetylated modification identified on eukaryotic RNAs, and N- acetyltransferase 10 (NAT10) is the key enzyme catalyzing this modification, depositing ac4C on transfer RNA(tRNA), ribosomal RNA(rRNA), messenger RNA(mRNA), and long non-coding RNA(lncRNA) via its specific localization and expression. However, its systematic functions in tumor immunity and metabolic reprogramming have not been comprehensively summarized for clinical translation.
METHODS: This review systematically synthesizes recent research on NAT10-mediated ac4C modification in oncology, covering data from cell experiments, animal models, and clinical sample analyses across multiple tumor types (e.g. breast cancer(BC), liver, cervical cancer(CC). It integrates findings on NAT10's dual enzymatic activities, subcellular localization, regulation of cell cycle and DNA damage repair, mechanisms in TME remodeling and metabolic reprogramming, as well as preclinical progress of NAT10 inhibitors.
MAIN BODY: NAT10 possesses dual enzymatic activities of protein acetylation and RNA acetylation. Its subcellular localization is redistributed in tumor tissues, which is closely associated with tumorigenesis and progression. In TME remodeling, the NAT10-ac4C axis regulates inflammasome activation, suppresses T-cell function, promotes M2 macrophage polarization, andrecruits tumor- associated macrophages, thereby creating an immunosuppressive microenvironment.In metabolic reprogramming, this axis drives glycolysis by stabilizing hexokinase 2(HK2)/lactate dehydrogenase A (LDHA) mRNA, regulates amino acid metabolism through the Khib-ac4C cascade, and modulates fatty acid metabolism and ferroptosis resistance. Furthermore, high NAT10 expression is associated with chemotherapy and radiotherapy resistance in various tumors, and its inhibitor Remodelin has shown synergistic antitumor effects when combined with immune checkpoint inhibitors in preclinical studies.
CONCLUSION: NAT10-mediated ac4C modification is a critical regulatory node integrating tumor immunity and metabolism, serving as a promising potential target for precision cancer therapy. Current research still faces challenges such as insufficient sensitivity and specificity of ac4C detection technologies, unclearcell-type-specific mechanisms of NAT10, limited delivery efficiency of inhibitors, and the existence of compensatory pathways. Future research should focus on optimizing ac4C detection technologies, clarifying cell-type-specific mechanisms, developing targeted delivery systems, and further exploring the clinical translational value of combining NAT10-targeted therapy with immune checkpoint blockade, so as to provide new strategies and technical support for cancer treatment.

Keywords:  NAT10; TME; Tumor metabolism; Tumor progression; ac4C

DOI:  https://doi.org/10.1186/s12967-026-07788-w
Genome Biol. 2026 Feb 20.

Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.

Mahdi Assari, Brandon J Chew, Mohammad Amin Bayat Tork, Marek Sobczyk, Chenyou Zhu, Hoang Anh V Tran, Dominika Rudzka, Wen Zhang, Tao Pan.

   BACKGROUND: Transfer RNA (tRNA) modifications play important roles in regulating gene expression and protein synthesis, yet their dynamic interplay remains elusive. The human tRNAome contains approximately 40 modification types, distributed on average at 13 sites in cytosolic tRNAs and 6 sites in mitochondrial tRNAs. tRNA modifications exhibit dynamic patterns dependent on cell types and cell states, underscoring the need for advancing methodologies to assess their variations and crosstalk transcriptome-wide.
RESULTS: Here, we develop enhanced single-read analysis of tRNA crosstalks (eSLAC), an integrative platform combining multiplex small RNA sequencing (MSR-seq) with expanded detection of pseudouridine (Ψ), 5-formylcytidine (f5C), N4-acetylcytidine (ac4C), and a single-read analysis pipeline to map modifications and their crosstalk (eSLAC). eSLAC enables the detection of over 60% of all human tRNA modification sites and assigns sites to three Ψ writer enzymes. The analysis reveals strong positive Ψ-Ψ and Ψ-charging crosstalks. Applying polysome tRNA profiling, we identify differential tRNA isodecoder usage and site-specific tRNA Ψ variations on the polysome.
CONCLUSIONS: This study establishes a framework for dissecting the interconnected architecture of tRNA modome and its functional complexity.

Keywords:  Crosstalk; Modification; Pseudouridine; Single-read data analysis; TRNA

DOI:  https://doi.org/10.1186/s13059-026-04009-x
Biochem Biophys Res Commun. 2026 Feb 11. pii: S0006-291X(26)00218-4. [Epub ahead of print]807 153454

Intestinal stem cell damage caused by specific amino acid deprivation is linked to a potent integrated stress response triggered by the direct sensing of stem cells.

Ayumi Kozai, Takumi Satoh, Yoshiko Sugita-Konishi, Makoto Shimizu, Ken Iwatsuki, Miki Tadaishi, Kazuo Kobayashi-Hattori.

  Amino acid deprivation, particularly deficiencies in methionine (Met) or glutamine (Gln), disrupts intestinal stem cells (ISCs), causes growth suppression, and induces cell death. We previously found that among the branched-chain amino acid (BCAA), leucine and isoleucine deprivation maintain ISC survival, whereas valine (Val) deprivation induces ISC impairment, which is characterized by suppressed proliferation and increased cell death; however, the mechanisms underlying these divergent cell fates remain largely unclear. We here focused on the integrated stress response (ISR) as a regulator of cell fate under amino acid deprivation using mouse intestinal organoids and ISCs isolated from organoids. Deprivation of each BCAA uniformly suppressed global translation, whereas only Val deprivation induced activation through phosphorylation of eukaryotic initiation factor 2 alpha (eIF2α) and a persistent increase in the mRNA expressions of activating transcription factor 4, C/EBP homologous protein, and growth arrest and DNA damage-inducible 34, indicating a potent and sustained ISR. Analysis using ISCs isolated by cell sorting revealed that only Val deprivation markedly increased p-eIF2α levels and reduced organoid formation. Furthermore, Met and Gln deprivation resulted in similar responses to Val deprivation in organoids and isolated ISCs. Taken together, these results suggest that Val, Met, and Gln deprivation induce a potent ISR through direct sensing by ISCs, with the response associated with stem cell damage.

Keywords:  Amino acids; Glutamine; Integrated stress response; Intestinal stem cells; Methionine; Organoids; Valine

DOI:  https://doi.org/10.1016/j.bbrc.2026.153454
Front Med (Lausanne). 2025 ;12 1735826

Mechanistic insights into non-coding RNAs regulate autophagy in chondrocytes and their contribution to osteoarthritis.

Bo Wang, Zhihong Wang.

  Osteoarthritis (OA), a chronic degenerative joint disease, arises from a confluence of factors including aging, mechanical injury, and obesity. Autophagy, a fundamental cellular process involving the degradation and recycling of cellular components, plays a critical role in chondrocyte homeostasis and survival under stress. Non-coding RNAs (ncRNAs), a diverse class of RNA molecules with no protein-coding potential, exert significant influence on gene expression through post-transcriptional and epigenetic mechanisms. Growing evidence suggests a crucial interplay between ncRNAs, autophagy, and OA pathogenesis. This review summarizes the multifaceted role of autophagy in OA chondrocytes and delves into the regulatory mechanisms of ncRNAs on OA-associated autophagy, aiming to elucidate the intricate pathological network underlying OA development and identify novel therapeutic targets.

Keywords:  autophagy; non-coding RNAs; osteoarthritis; pathological network; therapeutic targets

DOI:  https://doi.org/10.3389/fmed.2025.1735826
Nat Commun. 2026 Feb 19. pii: 1934. [Epub ahead of print]17(1):

Composite SMG5-SMG6 PIN domain formation is essential for NMD.

Katharina Kurscheidt, Sophie Theunissen, Natalia Pasquali, Kerstin Becker, Volker Boehm, Elena Conti, Niels H Gehring.

Nonsense-mediated mRNA decay (NMD) relies on the coordinated assembly and action of multiple protein factors. Degradation of target mRNAs begins with endonucleolytic cleavage near premature stop codons, but the mechanisms of endonuclease activation and regulation remain unclear. Using structural predictions, biochemical in vitro assays, and cell-based NMD analysis, we show that SMG5 and SMG6 interact via their PIN domains to form a composite interface (cPIN) with full endonuclease activity. In vitro reconstituted SMG5-SMG6 cPIN heterodimers show high activity, as SMG5 completes the SMG6 active site and substrate binding site. Mutations in residues at their predicted interaction surfaces, RNA-binding sites, or active site attenuate or abolish cPIN activity in vitro and impair cellular NMD. Our findings demonstrate how paralogous PIN domains complement each other to assemble a highly active endonuclease in NMD, providing a structural and mechanistic explanation for efficient NMD substrate degradation.

DOI: https://doi.org/10.1038/s41467-026-69819-w
Angew Chem Int Ed Engl. 2026 Feb 17. e20273

Fluorescence Amplification Tags for Single-Molecule Imaging and Tracking of Proteins, RNA, and DNA in Live Cells.

Yifan Bao, Tianle Xiong, Arnaud Gautier, Murat Sunbul, Lu Wang.

  Single-molecule imaging and tracking of DNA, RNA, and proteins have revolutionized molecular and cellular biology by shifting the focus from population-level analyses to the direct observation of individual molecular events. However, conventional fluorescent labeling strategies, which tag biomolecules with a single fluorophore, are often hindered by low brightness, suboptimal signal-to-noise ratio (SNR), and rapid photobleaching, limiting localization precision and tracking duration. To overcome these challenges in single-molecule imaging, fluorescence amplification tags (FATs) have been developed to enable the multiplexed labeling of individual macromolecules with multiple fluorescent reporters, enhancing signal intensity and photostability. This review presents a comprehensive overview of FAT design principles, working mechanisms, and their applications in labeling DNA, RNA, and proteins. We highlight their impact on elucidating dynamic genetic processes, including chromatin remodeling, gene expression regulation, mRNA translation, and protein interactions. Finally, we discuss existing challenges and propose future directions to further optimize FATs for single-molecule imaging and tracking.

Keywords:  DNA; RNA; fluorescence amplification tag; protein; single‐molecule imaging

DOI:  https://doi.org/10.1002/anie.202520273
Mol Metab. 2026 Feb 17. pii: S2212-8778(26)00021-9. [Epub ahead of print] 102337

METTL18 Ensures Pancreatic Function by Maintaining Proper Translation and Proteostasis.

Tadahiro Shimazu, Megumi Gowa, Ayane Kataoka, Takehiro Suzuki, Kotaro Tomuro, Yuichi Shichino, Naoshi Dohmae, Shintaro Iwasaki, Yoichi Shinkai.

  Methyltransferases fine-tune various biomolecules by site-specific methylation. METTL18, an N3-position-specific histidine methyltransferase, modifies H245 of the ribosomal protein RPL3 (uL3), thereby regulating translation dynamics and proteostasis. However, the physiological role of this enzyme in vivo remains to be elucidated. Here, we show that METTL18 is essential for pancreatic function by regulating translation and suppressing protein aggregation. Mettl18 knockout (KO) mice exhibited partial preweaning lethality, and the surviving mice showed a marked reduction in N3-histidine methylation in the pancreas, diabetic phenotypes, and accumulation of pancreatitis-associated proteins. Ribosome profiling in a pancreatic acinar cell line revealed that loss of METTL18 caused global translational alterations, including accelerated elongation at proline codons. The improper ribosome traverse compromises protein folding, resulting in the aggregation of pancreatitis-associated proteins, including Reg1, and activation of the unfolded protein response. Our findings establish histidine methylation as a physiologically important post-translational modification and highlight METTL18 as a key regulator of pancreatic function through the maintenance of proteostasis.

Keywords:  Glucose homeostasis; Histidine methylation; METTL18; Pancreatic function; RPL3/uL3; Ribosome function; Translation regulation

DOI:  https://doi.org/10.1016/j.molmet.2026.102337
Nucleic Acids Res. 2026 Feb 05. pii: gkag140. [Epub ahead of print]54(4):

A reprogrammed genetic code consisting of 32 distinct amino acids.

Takayuki Katoh, Hiroaki Suga.

Sense codon reassignment enables ribosomal incorporation of nonproteinogenic amino acids (npAAs) at any of the 61 sense codons. Because npAAs replace proteinogenic amino acids (pAAs), the total number of available building blocks usually remains limited to 20. To overcome this, we previously introduced "artificial codon box division", where four-codon boxes (e.g. Val GUN) are split into distinct sets (e.g. GUY and GUG) using in vitro transcribed transfer RNAs (tRNAs) lacking nucleotide modifications. This allows two different amino acids-a pAA and an npAA-to be assigned within the same original box. While we previously demonstrated this by incorporating 23 amino acids, low incorporation efficiency hindered further expansion. Here, we applied our engineered tRNAs, tRNAPro1E2 and tRNAiniP, to the codon box division framework and optimized translation conditions to facilitate multiple npAA incorporations. Consequently, we successfully expanded the genetic code to 32 amino acids, incorporating 11 elongator npAAs and 1 initiator npAA while maintaining all 20 pAAs. Notably, these npAAs include therapeutically significant monomers such as β-amino, d-amino, and N-methyl amino acids, as well as an initiator N-chloroacetyl-d-tyrosine for peptide macrocyclization. This platform offers vast potential for generating diverse macrocyclic peptide libraries with unique chemical entities for drug discovery.

DOI: https://doi.org/10.1093/nar/gkag140
bioRxiv. 2026 Feb 12. pii: 2025.12.22.695711. [Epub ahead of print]

De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response.

Rui Yang, Kaiyuan Zheng, McGuire Metts, Yiluo Wang, Danyan Yin, Kevin P Li, Agnieszka A Prazmowska, David F Kashatus, Brian Kuhlman, Jie Yang.

Mitochondrial stress activates the integrated stress response (ISR) through the mitochondrial protein DELE1, which relays stress signals to the cytosolic kinase HRI to induce ATF4. Dysregulation of DELE1-mediated signaling has been implicated in pathological conditions, yet molecular strategies to modulate DELE1 remain unavailable. Here, we report de novo designed proteins that bind DELE1, block its oligomerization, and inhibit DELE1-mediated ISR activation. Several designs form stable complexes with DELE1 and disrupt its oligomerization in vitro while preserving DELE1's ability to bind HRI. In cells, these designs suppress ATF4 induction during mitochondrial stress and impair the recovery of elongated mitochondrial morphology following transient insult. Crystal structure analysis, structural modeling, and targeted mutagenesis confirm that the designed proteins engage a critical interface required for DELE1 oligomerization. These findings establish DELE1 as a druggable target and demonstrate that de novo designed proteins offer precise tools to modulate this pathway, laying groundwork for therapeutic development.

DOI: https://doi.org/10.64898/2025.12.22.695711
Plant Physiol. 2026 Feb 20. pii: kiag073. [Epub ahead of print]

5'UTR Editing of the Ribosomal Protein UL3Z Gene Unveils Its Critical Roles in Pre-rRNA Processing and Global mRNA Translation Dynamics.

Nier Chen, Minghui Gao, Yongsheng Bai, Mingliang Wang, Meiting Liu, Wei Xiong, Beixin Mo.

  The EMBRYO DEFECTIVE 2207 (EMB2207) gene, encoding ribosomal protein UL3Z, is critical for embryonic development in Arabidopsis, with loss of function resulting in embryo lethality. Despite its importance, the role of UL3Z in the complicated protein translation machinery in plants remains poorly understood due to the lack of viable hypomorphic alleles. In this study, we utilized CRISPR/Cas9 to edit the 5' untranslated region (5'UTR) of UL3Z, generating five ul3z mutants with varying degrees of reduced expression levels of UL3Z proteins. The mutant with the lowest expression exhibited the most severe developmental defects. In contrast, null mutants of its paralog UL3Y displayed no observable phenotypes. Interestingly, expression of UL3Y driven by the UL3Z/EMB2207 promoter successfully rescued the phenotypes of ul3z, demonstrating that these two paralogous RPs actually possess functionally interchangeable roles. GUS staining results showed that UL3Z was constitutively expressed in all examined tissues, while UL3Y was only appreciably expressed in specific tissues. Molecular analysis further revealed the accumulation of rRNA maturation intermediates and increased polysome levels in ul3z mutants, indicating compromised pre-rRNA processing and disturbed global mRNA translation. Interestingly, 3' ends of many rRNA precursors in ul3z had higher frequency of non-encoded tails compared to Col-0. This study demonstrates that CRISPR/Cas9-mediated 5'UTR editing is an effective tool for generating viable hypomorphic alleles of lethal genes and uncovers the critical roles of UL3Z/EMB2207 in pre-rRNA processing and the maintenance of appropriate mRNA translation on ribosomes, underscoring its importance in plant development.

Keywords:  UL3Z/EMB2207; mRNA translation; pre-rRNA processing; ribosomal protein; ribosome

DOI:  https://doi.org/10.1093/plphys/kiag073