bims-ribost 2026-03-22 papers

bims-ribost

Biomed News

on Ribostasis and translation stress

Issue of 2026–03–22
forty-one papers selected by
Cédric Chaveroux, CNRS

Structure of a specialized 70S initiation complex.
RNA modifications in gene regulation: Functions and pathways.
An RNA structural switch controlling bacterial toxin translation.
Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.
The Arabidopsis FRIENDLY (FMT) protein interacts with NAC and determines where nuclear-encoded mitochondrial proteins are translated.
Functional characterization of dynamic nascent RNA folding ensembles in real time.
Reprogramming mRNA localization by targeted RNA-protein interference.
The unphosphorylated, closed form of ezrin binds to RNA to maintain a metastatic phenotype in osteosarcoma cells.
Discrete 3' UTR sequence motifs regulate nanos RNA enrichment in Drosophila germ granules.
RNA m6A modification is a driver and therapeutic target in gastric cancer.
Local Translation in Glial Cells of the Brain.
YTHDF proteins differentially regulate a subset of m6A-modified transcripts to restrain endothelial inflammation during homeostasis.
Human DEAH-box helicase 8 regulates HSF1-mediated stress response and cancer-associated pre-mRNA splicing in tumour cells.
Mutually exclusive alternative pre-mRNA splicing promotes adaptive metabolic stress signaling by JNK.
Ribosome-associated quality control and related mechanisms.
VIRMA modulates function of photoreceptor cells through m6A modification and alternative splicing.
The role of TDP-43 fragments in regular cellular functions and homeostatic failure.
Profiling RNA metabolism to understand tissue and subcellular clearance of therapeutic RNA.
Intrinsically disordered SERBP1 regulates translation through topology-driven G-quadruplex recognition.
(Lnc)ing MALAT1-SRSF1 condensates to hypoxia-induced RNA alternative splicing and cancer.
Myofibrillar protein accumulation but reduced protein synthesis in PDCD4-depleted myotubes.
The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.
Targeting CPSF73, the mRNA 3' End Processing Endonuclease, Moves Cancer Cells Away from the Mesenchymal State.
Revealing and Exploiting the Biochemistry of O-GlcNAc through Protein Semisynthesis.
Hydroxyl radical footprinting modification reveals an intradomain communication pathway in EFL1 disrupted by a Shwachman-Diamond syndrome-associated mutation.
Drugging cold-response networks for neuroprotection.
Genome-wide Identification and expression analysis of TOR signaling pathway components in apple in response to low nitrogen.
FScanR reveals widespread programmed ribosomal frameshifting consistent with neutral evolution in a ciliate model.
LENG8 mediates RNA nuclear retention and degradation in eukaryotes.
Caution in Interpreting Regulatory RNA Associations With Eusocial Evolution in Bees.
Mistranslation from an endogenous tRNA variant in human pan-genome cell lines.
Competition for the conserved branch point sequence influences physiological outcomes in pre-mRNA splicing.
The stress responsive transcription factor ATF4: from molecular structure to disease mechanisms.
The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation.
The dual regulatory role of METTL14-mediated m6A modification in tumorigenesis and its underlying mechanisms.
Damage to newly synthesized proteins is a major cause of Cd(II) toxicity counteracted by proteasomes and integrated stress response in human cells.
IGF2BP3-TRIM37-P53 axis promotes tumor progression in LUAD.
Skin Colour in Salamanders Is Modulated by Both Epitranscriptomic Methylation and Gene Expression.
MATR3 regulates METTL3-Mediated m6A modification of MSI2 mRNA to activate the Wnt/β-Catenin pathway, exacerbating myocardial fibrosis and atrial fibrillation.
Sequence motif dynamics in RNA pools.
Huntingtin (HTT) interactome in regulation of DNA repair/remodeling and RNA processing pathways.

Nucleic Acids Res. 2026 Mar 19. pii: gkag094. [Epub ahead of print]54(6):

Structure of a specialized 70S initiation complex.

Dominic Arpin, Bappaditya Roy, Fawwaz M Naeem, Kurt Fredrick, Joaquin Ortega.

Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.

DOI: https://doi.org/10.1093/nar/gkag094
Cell. 2026 Mar 19. pii: S0092-8674(26)00053-X. [Epub ahead of print]189(6): 1591-1619

RNA modifications in gene regulation: Functions and pathways.

Jiangbo Wei, Chuan He.

RNA is frequently chemically modified, with over 170 types of chemical modifications identified to date in cellular RNAs. These modifications, along with their effector proteins, constitute new layers of gene expression regulation by controlling either the fate of modified RNAs at nearly every stage of their life cycle or local transcription through modulating the nearby chromatin state and transcriptional complexes. This is especially evident in dynamic biological contexts such as cellular state transitions, signaling, immune responses, and stress adaptation. In this review, we discuss recent breakthroughs and promising avenues for future exploration. Particular attention is given to the functional significance of mRNA modifications, the emerging roles of modifications on chromatin-associated regulatory RNAs in chromatin and transcriptional regulation, and mechanistic insights that will guide future scientific interrogation of RNA modifications in gene expression regulation. We also highlight how these fundamental understandings are beginning to catalyze the development of novel therapeutic strategies.

DOI: https://doi.org/10.1016/j.cell.2026.01.006
Nucleic Acids Res. 2026 Mar 19. pii: gkag240. [Epub ahead of print]54(6):

An RNA structural switch controlling bacterial toxin translation.

Athina Eleftheraki, Andrés Escalera-Maurer, Elsa D M Hien, Alice Virciglio, Maéva Conangle, Nicolas J Tourasse, Anaïs Le Rhun, Erik Holmqvist.

Type I toxin-antitoxin systems (T1TAs) rely on tight posttranscriptional control to prevent inadvertent toxin synthesis, yet the molecular mechanisms underlying this control are highly diverse. Here, we uncover an RNA-based mechanism that controls translation initiation in the enterobacterial timPR system. Unlike most T1TAs, which typically rely on ribonucleolytic messenger RNA (mRNA) processing to relieve ribosome binding site sequestration, the primary timP toxin mRNA is activated through a purely structural RNA switch. Using a FASTBAC-Seq loss-of-function screen with biochemical and phenotypic assays, we here identify key RNA interactions that govern this switch. Translation initiation at timP requires formation of (i) a pseudoknot in the 5' untranslated region, and (ii) a long-range interaction that destabilizes the ribosome-binding-site-sequestering stem-loop, rendering the Shine-Dalgarno sequence accessible for pre-initiation complex formation. Conversely, an alternative interaction locks the mRNA in an inactive state. Our findings reveal a structural RNA switch that controls toxin expression without the need for enzymatic processing and demonstrate an alternative mechanism for translation initiation in bacteria.

DOI: https://doi.org/10.1093/nar/gkag240
Curr Opin Struct Biol. 2026 Mar 17. pii: S0959-440X(26)00028-X. [Epub ahead of print]98 103246

Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.

Brennan Ashwood, Victoria Stalls, Ruben L Gonzalez.

During eukaryotic translation initiation, initiation factor proteins and the ribosomal small subunit undergo binding and dissociation reactions and conformational rearrangements that properly assemble a ribosome at the start codon of a messenger RNA. Building on extensive genetic and biochemical studies, single-molecule fluorescence experiments are revealing the time-dependent pathways of factor binding to, and dissociation from, the ribosomal small subunit and messenger RNA during initiation. Nonetheless, essential binding and/or dissociation events, conformational rearrangements, and the coupling between binding and conformational changes remain kinetically uncharacterized. Here, we summarize the status of single-molecule investigations of initiation and advocate for integrating single-molecule microscopy, structural biology, and molecular simulations to enable a time-dependent, molecular description of this fundamental step in gene expression.

DOI: https://doi.org/10.1016/j.sbi.2026.103246
Proc Natl Acad Sci U S A. 2026 Mar 24. 123(12): e2521483123

The Arabidopsis FRIENDLY (FMT) protein interacts with NAC and determines where nuclear-encoded mitochondrial proteins are translated.

Valentina Montoya-Brach, Jeanne Roignant, Grégory Renard, Johana Chicher, Anne-Marie Duchêne.

  Mitochondria are not only the powerhouses of the cell. They are also dynamic signaling hubs, playing a key role in cellular metabolism and adaptation. Proper mitochondrial function depends largely on the import of proteins encoded by the nucleus. Using proximity labeling (TurboID), we show that Arabidopsis thaliana FRIENDLY (FMT) protein is in close proximity to several organellar-destined proteins, mostly mitochondrial, during their translation. Many of the corresponding mRNAs are immunoprecipitated with FMT. Remarkably, when FMT is absent, its target mRNAs lose their correct cellular localization. Our TurboID approach, associated with immunoprecipitations and confocal microscopy, also demonstrates the interaction between FMT and the Nascent polypeptide Associated Complex (NAC), a ribosome-associated platform involved in the maturation and sorting of nascent peptides. Taken together, these results suggest that FMT, through its interaction with NAC and the ribosome, is involved in the spatial regulation of translation in the cell.

Keywords:  mRNA sorting; nascent polypeptide associated complex; protein import; ribosome; “clustered mitochondria” family

DOI:  https://doi.org/10.1073/pnas.2521483123
Sci Adv. 2026 Mar 20. 12(12): eaec4037

Functional characterization of dynamic nascent RNA folding ensembles in real time.

Kavan Gor, Eva Maria Geissen, Olivier Duss.

RNA structure starts forming cotranscriptionally as the nascent RNA emerges from the RNA polymerase and is dynamically modulated by cellular factors. How individual RNA conformations, out of an ensemble of RNA molecules, relate to function is not well understood. Here, developing multicolor single-molecule fluorescence microscopy experiments, we track in real time nascent RNA structure formation, functionally characterizing up to eight different types of RNA molecules. We find that ribosomal proteins, RNA modification enzymes or antisense oligonucleotides specifically modulate a subset of the RNA folding classes. For example, we provide direct evidence that increased local RNA accessibility at specific sites correlates with the chaperoning activity of ribosomal proteins during ribosome assembly. These experiments provide a general framework to study how dynamic RNA folding, and misfolding, relates to function.

DOI: https://doi.org/10.1126/sciadv.aec4037
bioRxiv. 2026 Mar 02. pii: 2026.02.27.708609. [Epub ahead of print]

Reprogramming mRNA localization by targeted RNA-protein interference.

Devon E Mason, Diptankar Bandyopadhyay, Neal Jiwnani, Brigitte Meyer, Stavroula Mili.

RNA binding proteins (RBPs) associate with RNAs in intricate ribonucleoprotein complexes and regulate various aspects of RNA life cycle and, by extension, cell functions. Despite their significance, elucidating the functional contributions of specific RNA-RBP binding events, particularly in long-term phenotypic assays, remains challenging. Here, we harness the specificity of CRISPR/dCas13 to interfere with specific RNA-RBP interactions. We apply this methodology to GA-rich mRNA localization elements which recruit the RNA-binding protein CNBP and serve as platforms for the assembly of mRNA trafficking complexes. We show that dCas13/gRNA binds to target transcripts in a highly specific manner and sterically interferes with CNBP recruitment leading to altered target mRNA localization and cell motility, consistent with the function of the targeted mRNAs. The effectiveness of dCas13/gRNA as a functional interference tool is curtailed by the strength of target mRNA binding as well as by the amount of cytoplasmic gRNA. We describe optimizations and considerations for the stable implementation of this system, to allow the investigation of long-term functional consequences of altered mRNA distributions.
GRAPHICAL ABSTRACT:

DOI: https://doi.org/10.64898/2026.02.27.708609
Sci Signal. 2026 Mar 17. 19(929): eady8367

The unphosphorylated, closed form of ezrin binds to RNA to maintain a metastatic phenotype in osteosarcoma cells.

Emre Deniz, Prakriti Tiwari, Purushottam B Tiwari, Eric Glasgow, Brent T Harris, Anup Tiwari, Chunyan Hou, Junfeng Ma, Jeffrey A Toretsky, Aykut Üren.

Ezrin is a cytoplasmic protein that can exist in multiple conformations that are regulated by phosphorylation at Thr567. The phosphorylated, open form of ezrin generally has been considered the active form because it translocates to the plasma membrane. In contrast, the unphosphorylated, closed form of ezrin is sequestered in the cytoplasm and is considered inactive, although it directly interacts with cytoplasmic RNA binding proteins. Here, we found that the closed form of ezrin is itself an RNA binding protein with biological activity. The abundance of ezrin correlated with that of RBPs in human osteosarcoma samples. Purified recombinant ezrin protein engineered to maintain a closed conformation (rEZRIN-T567A) directly bound RNA, with greatest affinity for guanine-rich sequences and RNA G-quadruplexes (G4 RNAs). Expressing closed ezrin in ezrin-null osteosarcoma cells restored the transcriptomic and proteomic profiles. Closed ezrin bound to endogenous mRNAs associated with pathways related to RNA processing and splicing, DNA maintenance, and cellular metabolism. In zebrafish, expression of closed ezrin rescued the metastatic capability of ezrin-null osteosarcoma xenografts. Our findings demonstrate that the closed conformation of ezrin-previously thought to be inactive-can directly bind RNA, regulate transcription and translation, and contribute to a metastatic phenotype in osteosarcoma cells.

DOI: https://doi.org/10.1126/scisignal.ady8367
Dev Biol. 2026 Mar 13. pii: S0012-1606(26)00063-1. [Epub ahead of print]

Discrete 3' UTR sequence motifs regulate nanos RNA enrichment in Drosophila germ granules.

Kira Mitchel, Elizabeth R Gavis.

Germ granules are ribonucleoprotein condensates that concentrate key maternal mRNAs needed for germ cell development. In Drosophila, nanos mRNA is selectively enriched in germ granules but the specific cis-acting elements mediating this process remain poorly defined. Here, we identify discrete sequence motifs in the nanos 3' UTR that regulate nanos enrichment specifically by promoting the growth of homotypic nanos mRNA clusters within granules, without affecting the initial targeting of nanos to germ granules. These sequence motifs are binding sites for the hnRNP M homolog Rumpelstiltskin (Rump) and mutation of Rump binding sites or Rump attenuates nanos homotypic cluster growth, reducing the amount of nanos inherited by germ cells. Consequently, germ cells exhibit defective migration to the gonad. Together, our findings reveal how small repeated sequence motifs and cognate RNA-binding proteins can tune enrichment of germ granule mRNAs by driving self-assembly into large RNA clusters. This strategy ensures sufficient inheritance of mRNAs to support germ cell development and may represent a general mechanism by which RNP condensates regulate transcript dosage.

DOI: https://doi.org/10.1016/j.ydbio.2026.03.007
Cell Biol Toxicol. 2026 Mar 14.

RNA m6A modification is a driver and therapeutic target in gastric cancer.

Qingjuan Chen, Hongzhao Lu, Dezhi Li, Tao Liu.

  N6-methyladenosine (m6A), the most abundant modification in eukaryotic RNAs, plays a critical role in regulating RNA stability, expression, and translation. Key m6A regulators are up- or down-regulated in human gastric cancer tissues, by Helicobacter pylori and transcription factors, and the aberrant expression is associated with poor patient prognosis. Dynamic m6A modification, orchestrated by methyltransferases, demethylases, and m6A-binding proteins, profoundly impacts gastric cancer tumorigenesis, metastasis, cancer cell stemness, immune evasion, and resistance to chemotherapy, radiotherapy, and immunotherapy. While aberrant m6A modifications and the expression levels of its regulatory factors in blood samples are novel biomarkers in gastric cancer patients, therapies targeting m6A regulators have emerged as promising approaches for treating the disease. In summary, m6A RNA methylation represents a pivotal epitranscriptomic mechanism with significant implications for gastric cancer biology and precision oncology.

Keywords:  Cancer therapy; Drug resistance; Gastric cancer; M6A methylation; M6A regulators; Tumorigenesis

DOI:  https://doi.org/10.1007/s10565-026-10141-y
Annu Rev Cell Dev Biol. 2026 Mar 16.

Local Translation in Glial Cells of the Brain.

Martine Cohen-Salmon.

Local protein synthesis is a conserved mechanism that allows cells with intricate architectures to perform compartment-specific functions. By translating messenger RNAs (mRNAs) at distinct subcellular locations, cells can respond swiftly and precisely to localized stimuli. This strategy is crucial in neurons, whose long processes extend far from the cell body. Disruptions in neuronal local translation have been implicated in neurological disorders, including fragile X syndrome, amyotrophic lateral sclerosis, and spinal muscular atrophy. While much of the spotlight has been on neurons, glial cells-microglia, astrocytes, oligodendrocytes, and radial glia-are increasingly recognized for their own dynamic use of local translation. These support cells exhibit asymmetric mRNA localization, suggesting that local protein synthesis plays key roles in their diverse functions. This review explores the emerging landscape of local translation in glial cells and examines how this finely tuned process contributes to both normal brain function and the development of neurological disease.

DOI: https://doi.org/10.1146/annurev-cellbio-111524-124159
Mol Biol Rep. 2026 Mar 18. pii: 510. [Epub ahead of print]53(1):

YTHDF proteins differentially regulate a subset of m6A-modified transcripts to restrain endothelial inflammation during homeostasis.

Ramakrishnan Shyam Kumar, Srinjoy Chakraborty, Hariharan Jayakumar, Manasa Bharath, Niyati Pandya Thakkar, Syamantak Majumder.

   BACKGROUND: N6-methyladenosine (m6A) modification of mRNAs through METTL3 maintains homeostasis in many cell types. The mechanism by which METTL3 complexes together with reader proteins, especially the YTH domain-containing protein, governs endothelial homeostasis is not yet fully understood.
METHODS AND RESULTS: Primary endothelial cells (HUVECs), EA.hy926 cells, and rat aortas were used to modulate METTL3 activity and assess gene expression changes by molecular and biochemical assays. m6A RNA immunoprecipitation and RNA-protein interaction analyses were performed to determine transcript-specific m6A modification and YTHDF-mediated regulation. Interplaying with METTL3 caused abrupt yet selective loss of eNOS gene expression while increasing inflammatory adhesion molecule gene expression in cultured endothelial cells (EC) and rat aorta. Interestingly, many other genes associated with endothelial function/inflammation/senescence including CD31, CD144, KLF2, p65, and p53 remained unaltered upon METTL3 inhbition. MeRIP analysis revealed significant m6A modifications of several gene transcript including eNOS, and inflammatory adhesion molecules. m6A modification of gene transcripts selectively stabilized eNOS while causing degradation of inflammatory adhesion molecules without affecting the stability of other genes such as p65. Interestingly, RIP analysis showed that YTHDF1 was preferentially bound to m6A-modified eNOS while YTHDF2 was selectively associated with inflammatory adhesion molecules, causing differential regulation. Moreover, we failed to detect association of YTHDF1 or YTHDF2 to m6A modified p65 and KLF2 transcript.
CONCLUSION: Taken together, the current study describes the essential role of the METTL3 complex in maintaining endothelial homeostasis through differential association of m6A modified gene transcripts with the reader proteins.

Keywords:  Endothelial Cells; Inflammation; METTL3; YTHDF1; YTHDF2; eNOS

DOI:  https://doi.org/10.1007/s11033-026-11672-7
NAR Cancer. 2026 Mar;8(1): zcag008

Human DEAH-box helicase 8 regulates HSF1-mediated stress response and cancer-associated pre-mRNA splicing in tumour cells.

Jennifer R Tall, Robert Te Poele, Alexandra Vasile, Pradeep Ramagiri, James Campbell, Caitlin R Davies, Marissa V Powers, Toby Roe, Deivendran Sankaran, Hannah Wang, Konstantinos Mitsopoulos, Bissan Al-Lazikani, Rob L M van Montfort, Emmanuel de Billy, Paul Workman, Paul A Clarke.

Transcription factor heat shock factor 1 (HSF1) orchestrates the cellular stress response, promoting malignant transformation, unchecked proliferation, and stress-resilient survival of tumour cells. We set out to discover potentially druggable regulators of HSF1 activation and identified DEAH-box RNA helicase 8 (DHX8). We investigated the role of DHX8 in regulating HSF1 within the broader context of DHX8 function in cancer cells. DHX8 silencing induces intron retention in HSF1 transcripts, reducing HSF1 protein. Importantly, DHX8 loss significantly alters RNA processing of an HSF1-regulated cancer-associated gene signature linked to poor clinical outcomes, as well as additional oncogenic and stress-response pathways. DHX8 binds between the pre-messenger RNA (mRNA) lariat branch point and the 3' splice site, consistent with the predominance of intron-retained transcripts following DHX8 loss. We show that both the ATPase and RNA-binding activities of DHX8 are essential for its role in splicing, including processing of HSF1 mRNA. We also find that DHX8 silencing triggers apoptosis more effectively in human cancer cells than in non-tumorigenic cells. Our findings identify DHX8 as a critical regulator of stress-adaptive gene expression, highlighting its promise as a therapeutic target not only to disrupt HSF1-dependent transcriptional programs but also having broader effects in cancer cells under oncogenic stress.

DOI: https://doi.org/10.1093/narcan/zcag008
Proc Natl Acad Sci U S A. 2026 Mar 24. 123(12): e2527162123

Mutually exclusive alternative pre-mRNA splicing promotes adaptive metabolic stress signaling by JNK.

Alexandra Lee, Autumn Gentzler, Declan Fitzpatrick, Sithara Raju Ponny, Ozkan Aydemir, Myoung Sook Han, Caroline A Lewis, Guangping Gao, Roger J Davis.

  The JUN NH2-terminal kinase (JNK) signal transduction pathway is activated during the hepatic metabolic stress response. The JNK1 and JNK2 pre-mRNAs expressed by hepatocytes exhibit mutually exclusive inclusion of exons 7a or 7b that encode a segment of the substrate binding site that is required for selective protein phosphorylation. We established mice with conditional inclusion of exons 7a or 7b to test the function of these JNK spliceoforms. We report that the JNK27b spliceoform plays a key role in the hepatic metabolic stress response. This function of JNK27b is mediated by coordinated mechanisms that independently regulate circadian gene expression and phosphorylation of Retinoid X Receptor α (RXRα) on Ser265. This analysis identifies an important role for JNK27b in the hepatic adaptive response to metabolic stress.

Keywords:  JNK; alternative pre-mRNA splicing; circadian rhythm; metabolic stress

DOI:  https://doi.org/10.1073/pnas.2527162123
Nat Struct Mol Biol. 2026 Mar;33(3): 394-407

Ribosome-associated quality control and related mechanisms.

Toshifumi Inada.

Ribosome-associated quality control (RQC) safeguards translation by detecting and resolving collided ribosomes and triaging their nascent chains. This Review outlines mechanisms, crosstalk and disease implications of RQC cascades and presents RQC as a 'first responder' that prevents escalation to global stress responses and provides protection against proteostasis collapse.

DOI: https://doi.org/10.1038/s41594-026-01771-1
JCI Insight. 2026 Mar 19. pii: e197880. [Epub ahead of print]

VIRMA modulates function of photoreceptor cells through m6A modification and alternative splicing.

Wenjing Liu, Xiaojing Wu, Rong Zou, Fan Zhang, Yudi Fan, Kuanxiang Sun, Liping Yang, Jiang Hu, Lin Zhang, Xianjun Zhu.

  N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional epigenetic modification in mammalian mRNAs, and it has been implicated in the regulation of nervous system development by modulating mRNA metabolism. VIRMA is the largest core subunit of the m6A methyltransferase complex and essential for the assembly and stability of the m6A methyltransferase complex. In the retina, m6A methylation modification is widely distributed in various cellular layers and is essential for retinal homeostasis. Here, we demonstrate that VIRMA-mediated m6A modification is essential for retinal homeostasis. Loss of Virma in retinal rod cells resulted in abnormal reduction in m6A methylation levels, along with impaired photoreceptor function and degeneration. Mechanically, Virma depletion in photoreceptors dampened the m6A modification level of visual perception-associated genes, resulting compromised visual function and photoreceptors degeneration. Moreover, Virma interacts with splicing factor to regulate the alternative splicing events of retina function-related genes such as Polg2, which contributes to photoreceptor damage. Reintroduction of normal Virma expression colonially rescued photoreceptor degeneration. Collectively, our data elucidate the important role of Virma-mediated m6A modification in photoreceptor function and suggest that epigenetic modulation could serve as potential targets to treat these blinding diseases.

Keywords:  Epigenetics; Neurodegeneration; Neuroscience; Ophthalmology; RNA processing

DOI:  https://doi.org/10.1172/jci.insight.197880
Neurobiol Dis. 2026 Mar 15. pii: S0969-9961(26)00094-X. [Epub ahead of print] 107349

The role of TDP-43 fragments in regular cellular functions and homeostatic failure.

Regina Dahlhaus, Ralf J Braun.

  Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of motor neurons, leading to severe muscle weakness, loss of voluntary movement, and respiratory failure. A widely noted feature of the disease is the presence of TDP-43 proteinopathies. Under homeostatic conditions, the RNA/DNA-binding protein TDP-43 mainly resides in the nucleus, where it functions to regulate gene expression, controlling not only RNA transcription and splicing, but also stability and transport to the cytoplasm. Upon the arrival at ribosomes, TDP-43 may further moderate translation, acting as a global repressor of protein synthesis. However, in over 95% of ALS cases, TDP-43 mislocalies from the nucleus to the cytoplasm, where it enriches in cytoplasmic inclusions that are marked by the presence of misfolded, ubiquitinated, phosphorylated and fragmented protein species of TDP-43. Although recent studies have tried to untangle the relationship between TDP fragments on the one hand, and cytotoxicity as well as neurodegeneration on the other, the results are still a matter of debate. Here, we review our current understanding of the different TDP fragments derived from proteolytic cleavage as well as alternative splicing, addressing the different N-terminal and C-terminal species and evaluating differences in rodent and primate models. We focus our analysis on the potential homeostatic functions of TDP fragments in the context of viral infections and myelination control, which are potentially pivotally interconnected. The findings illustrate several facets of fragmented TDP-43 protein species in scenarios of enhanced cellular stress. Gaining a detailed understanding could help to reveal new treatment options for ALS and other TDP-43 proteinopathies.

Keywords:  Amyotrophic lateral sclerosis; Glial function; Neuronal function; Proteases; TDP-43 fragments; TDP-43 proteinopathies

DOI:  https://doi.org/10.1016/j.nbd.2026.107349
Drug Metab Dispos. 2026 Jan 23. pii: S0090-9556(26)00012-7. [Epub ahead of print]54(3): 100243

Profiling RNA metabolism to understand tissue and subcellular clearance of therapeutic RNA.

Harvey Andersen, Ryan Hill, Alec Bell, Shane Lowery, Anthony Murphy, Michael Huskin, Michael Mohutsky, Christopher M Wiethoff.

  Recent clinical success for RNA therapeutics supports the promise of these modalities to unlock additional drug targets with pharmacodynamic responses that are considerably more durable than other drug classes. Metabolic clearance in tissue is a key determinant of dosing requirements and therapeutic durability. To build our understanding of the mechanisms of RNA metabolic clearance, we quantified the catalytic efficiency of 3'- and 5'-exonucleases, and endonucleases in S9 fractions from various rat tissues using novel fluorescent RNA probes. We validated the specificity of these probes using recombinant nucleases and rat liver S9 fractions, demonstrating their ability to accurately report enzyme activity without cross-reactivity between nuclease classes. Key experimental parameters, such as solution pH and enzyme-substrate ratios, were optimized to maximize dynamic range. Profiling nuclease activity across various rat tissues revealed tissue-specific variations, with kidney, muscle, and plasma showing the highest catalytic efficiency for 3' exonuclease, 5' exonuclease, and endonuclease, respectively. Using a model siRNA targeting hypoxanthine phosphoribosyltransferase, comparative degradation studies in rat liver homogenate, liver S9 fractions, and liver tritosomes revealed divergent metabolic profiles; S9 fractions and homogenate processed both double-stranded siRNA and single-stranded antisense RNA to a similar extent, whereas in tritosomes single-stranded RNA was observed to be degraded more rapidly than a double-stranded form. These differences are consistent with distinct nuclease activities in each compartment, reflecting both enzyme identity and relative abundance as revealed by the probe analyses. Collectively, these findings offer critical mechanistic insights into RNA metabolism and establish a robust platform to improve the development and predictability of siRNA therapeutics. SIGNIFICANT STATEMENT: Metabolic clearance of RNA therapeutics is a critical determinant of their pharmacological durability and potency. This work quantitatively describes the activity of 3 major classes of ribonucleases within various tissues and subcellular compartments, revealing specific patterns of RNA metabolism and enable discovery of novel RNA therapeutics with improved pharmacokinetic properties.

Keywords:  clearance; fluorescence; metabolism; nuclease; siRNA

DOI:  https://doi.org/10.1016/j.dmd.2026.100243
bioRxiv. 2026 Mar 05. pii: 2026.03.03.709370. [Epub ahead of print]

Intrinsically disordered SERBP1 regulates translation through topology-driven G-quadruplex recognition.

Antoine Baudin, Hoang H Dinh, Kira Breunig, Xuifen Lei, Xiaoping Xu, Luiz O Penalva, David S Libich.

Serpine mRNA-binding protein 1 (SERBP1) is an intrinsically disordered RNA-binding protein that regulates translation and ribosome biogenesis through interactions with ribosomes and other molecular complexes. Despite its regulatory importance and implication in cancer development, the molecular basis of SERBP1 RNA recognition remains poorly understood. Here, we characterize the G-quadruplex (G4)-binding properties of SERBP1. Using NMR spectroscopy and biophysical assays, we show that SERBP1 binds parallel G4s, both RNA and DNA, with low micromolar affinity through a conserved mechanism. Molecular dynamics and docking simulations reveal an encircling mechanism in which the RGG box wraps around the G4 while downstream C-terminal serine residues stabilize the complex through hydrogen bonding. Phosphomimetic mutations of key serines disrupt this stabilization and reduce binding affinity, identifying phosphorylation as a regulatory switch for SERBP1 activity. Recognition is driven by G4 topology rather than nucleotide sequence, establishing SERBP1 as a broad-specificity G4-binding protein. We further demonstrate that SERBP1 regulates mTOR expression in glioblastoma cell lines through G4 elements in the mTOR 5' UTR, and that SERBP1 depletion synergizes with mTOR inhibition to reduce cell growth. These results establish SERBP1 as a G4 adaptor protein and represent, to our knowledge, the first detailed characterization of G4 recognition by a fully disordered domain, providing a molecular framework for targeting SERBP1-G4 interactions in cancer.
Significance Statement: SERBP1 is overexpressed in multiple cancers and regulates key cellular processes, yet how it recognizes its RNA targets has remained unclear. We show that SERBP1 binds G-quadruplex structures through an encircling mechanism in which its RGG box and adjacent C-terminal serine residues lock around the G4 topology, and that phosphorylation of these serines acts as a switch to modulate binding. Recognition is driven by G4 topology rather than nucleotide sequence, positioning SERBP1 as a general G4 adaptor that recruits helicases to resolve these structures and license translation. We demonstrate this principle in glioblastoma, where SERBP1 regulates mTOR expression through direct recognition of G4 elements in the mTOR 5' UTR, and its depletion synergizes with mTOR inhibition. These findings provide the first molecular characterization of G4 recognition by a fully disordered domain and establish a direct link between SERBP1-G4 interactions and cancer-relevant translational regulation.

DOI: https://doi.org/10.64898/2026.03.03.709370
Mol Cell. 2026 Mar 19. pii: S1097-2765(26)00134-6. [Epub ahead of print]86(6): 993-995

(Lnc)ing MALAT1-SRSF1 condensates to hypoxia-induced RNA alternative splicing and cancer.

Jodi L Bubenik, Maurice S Swanson.

In this issue of Molecular Cell, Song et al.1 focus on the regulation of hypoxia-induced alternative splicing (AS) in cancer cells and provide evidence for key regulatory roles for MALAT1-SRSF1 condensates in preferential pre-mRNA binding and RNAPII recruitment.

DOI: https://doi.org/10.1016/j.molcel.2026.02.020
PLoS One. 2026 ;21(3): e0345305

Myofibrillar protein accumulation but reduced protein synthesis in PDCD4-depleted myotubes.

Stephen Mora, Lilia Alihemmat, Logan D Davari, Termeh Ataie, Parsa Nafari Mehranjani, Luke Flewwelling, Arthur J Cheng, Olasunkanmi A J Adegoke.

Skeletal muscle is critical to whole-body functionality and homeostasis. The mammalian/mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient/growth-factor sensitive positive regulator of skeletal muscle mass. Amongst other substrates, mTORC1 phosphorylates the ribosomal protein S6 kinase (S6K1). Activated S6K1 acts through multiple effectors, including programmed cell death 4 (PDCD4), to promote mRNA translation and protein synthesis. Much of what is known about PDCD4 is in non-muscle cells. We previously demonstrated that the effect of PDCD4 differs between myoblasts and myotubes. Here, we showed that PDCD4 depletion in myotubes enhanced myotube diameter (+36%) and accumulation of myofibrillar proteins (+163-237%). These effects occurred along with increased phosphorylation of AKTser473 (+85%) and of the mTORC1 substrate S6K1thr389 (+152%), but protein synthesis was suppressed. There was increased phosphorylation of FoxO3aser253 (+250%) and a corresponding reduction in the expression of the muscle protein ubiquitin ligase MuRF1 (-44%), but there was no significant effect on measures of proteolysis or autophagy. In starved myotubes treated with the proteasome inhibitor MG132, accumulation of ubiquitinated proteins was attenuated in PDCD4-depleted cells. PDCD4 depletion did not augment sarcoplasmic reticulum (SR) Ca2+ release capacity but was associated with reduced ATP and intracellular amino acid levels. Finally, AKT inhibition partially attenuated the effect of PDCD4 depletion on myofibrillar protein abundance. In summary, myofibrillar protein accumulation in PDCD4-depleted myotubes did not lead to improved intracellular Ca2+ handling, likely due to reduced energy level. Our data point to a pivotal role for PDCD4 in regulating myotube size.

DOI: https://doi.org/10.1371/journal.pone.0345305
Nucleic Acids Res. 2026 Feb 24. pii: gkag186. [Epub ahead of print]54(5):

The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.

Ravinth Reddy Ramireddy, Matthew D Shortridge, Venkata Vidalala, Bhawna Chaubey, Changyan Tang, Gregory L Olsen, Gabriele Varani.

We report that the kinase inhibitor Palbociclib is a very low nanomolar ligand for the HIV-1 TAR, a paradigmatic 'difficult-to-drug' RNA. Binding is exquisitely specific, since simple chemical modifications of the small molecule, single nucleotide substitutions, or base pair inversions abolish high affinity binding, and is independent from kinase inhibition. Palbociclib also inhibits recruitment of the super elongation complex (SEC) at low nM concentration, the long-standing aim of Tat-TAR targeting efforts. Thus, we demonstrate that low nM affinity, specificity, and potent biochemical activity against 'undruggable' RNAs can be readily found within the chemical space of drugs. The structural basis for binding and biochemical activity is demonstrated in the accompanying manuscript.

DOI: https://doi.org/10.1093/nar/gkag186
bioRxiv. 2026 Mar 03. pii: 2026.03.01.708894. [Epub ahead of print]

Targeting CPSF73, the mRNA 3' End Processing Endonuclease, Moves Cancer Cells Away from the Mesenchymal State.

Marzieh Naseri, Huiyun Liu, Luyang Wang, Salwa Mohd Mostafa, Ehsan Ranaei Pirmardan, Bin Tian, Claire L Moore.

Background: Metastasis significantly contributes to cancer-related mortality and therapeutic failure. Cancer cells acquire metastatic potential by losing epithelial characteristics and gaining mesenchymal properties through the epithelial-mesenchymal transition (EMT). Differential poly(A) site (PAS) usage, known as alternative polyadenylation (APA), generates mRNA isoforms differing in coding sequence, subcellular localization, stability, or translation efficiency. In cancer, 3'UTR shortening increases expression of proto-oncogenes by escaping miRNA-mediated repression. High expression of CPSF73, which cleaves mRNA precursors at PASs, is associated with unfavorable prognoses in cancer patients. However, the role of APA in regulating EMT remains poorly understood.
Methods: In this study, to investigate the role of APA in EMT, we employed JTE-607, a small-molecule inhibitor of CPSF73 activity, to examine the impact of catalytic inhibition of CPSF73 on proliferation and EMT in MDA-MB-231, MCF7, A549, and HepG2 cancer cells. To identify differential usage of PASs, global profiling of APA changes, and differential gene expression analysis were performed in MDA-MB-231 cells. Additionally, antisense oligonucleotides were used to block the use of a specific PAS whose APA change may be a driver of EMT reversal.
Results: Our findings showed that catalytic inhibition of CPSF73 not only attenuates cancer cell proliferation but also moves the cells away from the mesenchymal state across all four cell lines tested. Global profiling of APA changes following CPSF73 inhibition revealed widespread 3'UTR lengthening and suppression of intronic PASs in MDA-MB-231 cells. APA shifts were observed in key EMT-related genes, accompanied by decreased expression of corresponding proteins across all four cell lines. We used antisense morpholino oligonucleotides to block the proximal PAS of AKT2, shifting the balance of AKT2 mRNA isoforms toward the long isoform. This shift caused EMT reversal, marked by reduced AKT2 protein expression, changes in EMT-related markers, and impaired invasion by MDA-MB-231 cells.
Conclusion: Together, these findings identify APA-mediated 3'UTR lengthening, with functional consequences in EMT-related genes, as a coordinated mechanism leading to an attenuated EMT phenotype, highlighting a significant connection between APA and the EMT process. Interfering with these APA changes may offer a promising therapeutic strategy to suppress metastasis, with potential efficacy across multiple pathways.
Statement of Significance: Our findings highlight APA-mediated 3' UTR lengthening as a coordinated mechanism that promotes EMT reversal and support CPSF73 inhibition or APA-targeting strategies as potential therapeutic approaches to suppress metastasis across multiple pathways.

DOI: https://doi.org/10.64898/2026.03.01.708894
Biochemistry. 2026 Mar 18.

Revealing and Exploiting the Biochemistry of O-GlcNAc through Protein Semisynthesis.

Gilbert B Ampomah, Matthew R Pratt.

O-GlcNAcylation is a dynamic posttranslational modification regulated by the enzymes O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA). It involves the attachment of N-acetylglucosamine to serine or threonine residues of proteins in the cytosol, nucleus, and mitochondria. As a dynamic and abundant modification, O-GlcNAcylation functions as a sensor of the cell's metabolic state. Fluctuations in O-GlcNAc levels of the adenosine (O-GlcNAc) signal cellular stress or metabolic changes and have been implicated in various human diseases. The overall impact of this modification is protein-dependent, underscoring the importance of studying its biochemical consequences in a protein- and site-specific manner. To achieve this, enzymatic and chemical strategies have been developed to incorporate O-GlcNAc into peptides and proteins. These synthetic glycopeptides and glycoproteins have been instrumental in elucidating how O-GlcNAcylation influences protein structure, function, and diverse biochemical pathways. Recently, the O-GlcNAcylation has also emerged as a tool for glycosylation-assisted folding of proteins and as a solubility tag for the chemical synthesis of glycopeptides and proteins. Here, we overview the current methods enabling the preparation of specific O-GlcNAc-modified proteins and highlight recent developments.

DOI: https://doi.org/10.1021/acs.biochem.6c00095
Protein Sci. 2026 Apr;35(4): e70504

Hydroxyl radical footprinting modification reveals an intradomain communication pathway in EFL1 disrupted by a Shwachman-Diamond syndrome-associated mutation.

Jonathan A Zúñiga-Domínguez, Rohit Jain, Martín González-Andrade, Erik R Farquhar, Mark R Chance, Abril Gijsbers, Nuria Sánchez-Puig.

  Shwachman-Diamond syndrome (SDS) is a rare genetic disorder characterized by pancreatic insufficiency and neutropenia. While most cases are linked to mutations in the SBDS gene, some involve mutations in the GTPase EFL1. This protein works with SBDS to release the anti-association factor eIF6 from the 60S ribosomal subunit during ribosome biogenesis. The pathogenic EFL1 R1095Q mutant (R1086Q in yeast) exhibits altered guanine nucleotide recognition and impaired eIF6 release, prompting an investigation into its structural consequences. Using the yeast Efl1 orthologue in X-ray hydroxyl radical footprinting experiments, we tracked changes in solvent accessibility caused by the mutation. Although the mutation is situated in domain IV, widespread conformational changes were observed across the protein, particularly in domain I, suggesting a long-range intramolecular communication. Strikingly, the growth defect caused by the pathogenic mutation was rescued by a second mutation located in a allosteric pathway that spans from the nucleotide-binding pocket to domain IV. This compensatory mutation restored proper nuclear localization of eIF6 (Tif6 in yeast). These findings reveal that the R1086Q mutation disrupts a structural communication network within Efl1, impairing the conformational dynamics required for its activity. The loss of this coordination likely underlies the ribosome maturation defects observed in SDS cases linked to EFL1, offering new insights into the molecular basis of the disease.

Keywords:  EFL1; Shwachman‐Diamond syndrome; X‐ray footprinting; long‐range communication

DOI:  https://doi.org/10.1002/pro.70504
Trends Pharmacol Sci. 2026 Mar 19. pii: S0165-6147(26)00033-7. [Epub ahead of print]

Drugging cold-response networks for neuroprotection.

Min Zhang, Chengli Liu, Aifang Cheng, Mingchang Li.

  Therapeutic hypothermia is robustly neuroprotective in models but slow to initiate and hard to sustain clinically. This gap motivates pharmacological strategies that capture 'cold' protection at normothermia. Recent advances across the cold-response landscape have made RNA layer mechanisms operational. These include temperature-gated alternative splicing coupled to nonsense-mediated decay and temperature-sensitive RNA secondary structure elements such as RNA G-quadruplexes (rG4) thermometers, which are now quantifiable and tractable. In this review, we present a development-oriented framework that spans membrane thermosensors, intracellular temperature decoders, and downstream cold effectors. We focus on RNA layer mechanisms while treating upstream non-RNA elements as contextual adjuncts. We outline an RNA-binding motif protein 3 (RBM3)-first translational roadmap mainly built on two orthogonal modalities: splice-switching antisense oligonucleotides and rG4-oriented chemotypes. Lastly, we define pharmacodynamic anchors, realistic clinical windows, and safety gates for early-phase testing of normothermic hypothermia mimetics.

Keywords:  RBM3; RNA G-quadruplexes; antisense oligonucleotides; cold-response networks; hypothermia mimicry; neuroprotection

DOI:  https://doi.org/10.1016/j.tips.2026.02.003
Plant Genome. 2026 Mar;19(1): e70215

Genome-wide Identification and expression analysis of TOR signaling pathway components in apple in response to low nitrogen.

Dehai Liu, Siyuan Cheng, Yanghao Long, Qinyao Jin, Yujie Zhou, Fengwang Ma, Xuan Liu, Xiaoqing Gong.

Target of rapamycin (TOR) is an evolutionarily conserved serine/threonine kinase that plays a central role in regulating biological growth, development, and stress responses in eukaryotes. However, the TOR signaling pathway has not been thoroughly studied in apple (Malus domestica). Here, through sequence alignment with homologous genes in Arabidopsis thaliana, 14 conserved members of the TOR signaling pathway, encoded by 28 sequences, were identified in the apple genome. A comprehensive analysis of these members was subsequently performed by integrating their structural features, phylogenetic relationships, and expression profiles under low-nitrogen stress conditions. The results showed that the functional motifs of these members are highly conserved across species, while there are significant differences in the physicochemical properties of each member in apple. Subcellular localization predictions indicated that most members are likely localized to the nucleus; a few may reside in the cytoplasm or chloroplast. Quantitative PCR analysis showed that TOR pathway members are differentially regulated under low-nitrogen stress, suggesting their potential involvement in nitrogen stress response. Furthermore, MdTORs were found to directly interact with several autophagy-related (ATG) proteins in apple plants, in addition to its canonical target ATG13. Collectively, this study systematically characterizes the components of the TOR pathway in the apple genome, examines their expression dynamics under low nitrogen stress, and identifies novel interactions between TOR and ATGs. These research findings broaden our understanding of TOR-regulated autophagic pathways, provide a valuable foundation for future studies into their regulatory mechanisms, and also provide data support for clarifying the responses of TOR signaling pathway members in apple to low-nitrogen stress.

DOI: https://doi.org/10.1002/tpg2.70215
Eur J Protistol. 2026 Mar 16. pii: S0932-4739(26)00017-9. [Epub ahead of print]104 126196

FScanR reveals widespread programmed ribosomal frameshifting consistent with neutral evolution in a ciliate model.

Juan Yang, Yuhao Yang, Ruanlin Wang, Saleh A Al-Farraj, Naomi Stover, Yuan Li, Xiao Chen.

  Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism that allows multiple functionally distinct proteins to be synthesized from a single mRNA transcript. Although PRF is widespread among both prokaryotic and eukaryotic organisms, accurately assessing its full scope in biological systems using conventional genomic or proteomic data alone remains challenging. To address this, we have developed FScanR, a computational tool that identifies PRF events with high confidence by systematically comparing in-frame and out-of-frame nucleotide sequences with corresponding peptide datasets. Our results show that (1) FScanR detects PRF events in protein-coding genes across phylogenetically distinct organisms, enabling us to characterize the sequence features surrounding the PRF sites; (2) euplotid ciliates exhibit widespread PRF events, with no significant bias in GC content or inter-site distance observed in genomic regions flanking the PRF sites; (3) genes associated with PRF events participate in critical physiological processes, including phosphorylation, ubiquitination and metabolic regulation; and (4) PRF in euplotids occurs across genes with varying expression levels and appears to be under neutral selection. These findings highlight the value of FScanR in revealing recoding mechanisms and offer new insights into the evolutionary dynamics of PRF in single-celled eukaryotes.

Keywords:  Cross-species; Euplotid; FScanR; Neutral selection; Programmed ribosomal frameshifting

DOI:  https://doi.org/10.1016/j.ejop.2026.126196
Mol Cell. 2026 Mar 19. pii: S1097-2765(26)00137-1. [Epub ahead of print]

LENG8 mediates RNA nuclear retention and degradation in eukaryotes.

Lusong Tian, Liang Liu, Yoseop Yoon, Lindsey V Soles, Marielle Valdez, Joshua Jeong, Clinton Yu, Lan Huang, Yongsheng Shi.

  In eukaryotes, incompletely and aberrantly processed mRNAs as well as numerous noncoding RNAs are retained in the nucleus and often degraded, but the underlying quality-control mechanisms remain poorly defined. Here, we identify LENG8 as a conserved RNA nuclear retention and degradation factor. LENG8 is recruited to pre-mRNAs by splicing factors, including the U1 small nuclear ribonucleoprotein particle (snRNP). It associates with PCID2 and SEM1 to form the REX (repressor of export) complex, which is conserved from yeast to humans, and causes RNA nuclear retention by acting as a dominant-negative factor for the essential mRNA export factor TREX (transcription-export)-2. Loss of LENG8 results in cytoplasmic leakage of misprocessed mRNAs, including intronically polyadenylated and intron-retained mRNAs, as well as noncoding RNAs. Moreover, LENG8 promotes nuclear RNA degradation through interactions with the RNA exosome adaptor PAXT. Together, these findings uncover a conserved RNA quality-control mechanism that ensures only correctly processed RNAs are exported.

Keywords:  RNA degradation; RNA export; RNA nuclear retention; RNA polyadenylation; intron retention; splicing

DOI:  https://doi.org/10.1016/j.molcel.2026.02.023
Genome Biol Evol. 2026 Mar 02. pii: evag032. [Epub ahead of print]18(3):

Caution in Interpreting Regulatory RNA Associations With Eusocial Evolution in Bees.

Petr Heneberg.

  Recent advances in transcriptomics and regulatory genomics have expanded interest in the potential roles of alternative splicing and noncoding RNAs in the evolution of eusociality in bees. A recently published review by Brenman-Suttner and Zayed synthesized this literature, highlighting numerous associations between the expression patterns of regulatory RNA and caste, task, and developmental states. However, there is a distinction between molecular associations and demonstrated causal roles in evolutionary processes, particularly for complex social traits. Drawing on established principles from evolutionary genomics and regulatory biology, we discuss the limitations of correlational transcriptomic data and highlight ongoing debates over the functional inference of circular RNAs and long noncoding RNAs. Clarifying these interpretive boundaries is essential for aligning conclusions with current evidence and for guiding future experimental research on the molecular basis of social evolution.

Keywords:  Hymenoptera; circular RNA; eusociality; evolution; long noncoding RNA; regulatory RNA

DOI:  https://doi.org/10.1093/gbe/evag032
Nucleic Acids Res. 2026 Feb 24. pii: gkag224. [Epub ahead of print]54(5):

Mistranslation from an endogenous tRNA variant in human pan-genome cell lines.

Peter Rozik, Henry Moore, Jeremy T Lant, Kyle S Hoffman, Sarah K Schultz, Baasil Afzal, Patricia P Chan, Lauren E Flynn, Ilka U Heinemann, Todd M Lowe, Patrick O'Donoghue.

Human transfer RNA (tRNA) anticodon variants are a source of translation error. The tRNASerAGA-2-3 variant (G35A) occurs in 2% of the human population and causes mis-incorporation of serine at phenylalanine codons. Here, we developed a dual fluorescent reporter to quantify mis-incorporation levels in live human and murine cells and validated mistranslation by mass spectrometry. In β-lymphocytes from individuals in the 1000 genomes project, we confirmed the anticipated genotype of cells with A35 minor alleles, and tRNA sequencing demonstrated expression, C32 hypo-modification, and partial 5'-fragmentation of the endogenous mutant tRNASerAAA. Nanoparticle delivery of the fluorescent reporter confirmed serine mis-incorporation in the pan-genome cell lines. The data demonstrate that a natural genome-encoded human tRNA mutant causes mistranslation in cells derived from healthy individuals. Our findings have important implications for translation fidelity in humans and the application of missense suppressor tRNAs to medicine.

DOI: https://doi.org/10.1093/nar/gkag224
Elife. 2026 Mar 20. pii: RP103167. [Epub ahead of print]13

Competition for the conserved branch point sequence influences physiological outcomes in pre-mRNA splicing.

Karen Larisssa Pereira de Castro, Jose M Abril, Kuo-Chieh Liao, Haiping Hao, John Paul Donohue, William K Russell, William S Fagg.

  Recognition of the intron branch point during spliceosome assembly is a multistep process that can influence mRNA structure and levels. A branch point sequence motif UACUAAC is variably conserved in eukaryotic genomes, but in some organisms, more than one protein can recognize it. Here, we show that SF1 and Quaking (QKI) compete for a subset of intron branch sites with the sequence ACUAA in mammalian cells. SF1 activates exon inclusion through this sequence, but QKI represses the inclusion of alternatively spliced exons with this intron branch point sequence. Using mutant reporters derived from a natural intron with two branch site-like sequences, we find that when either branch point sequence is mutated, the other is utilized; however, when both are present, neither is used due to high-affinity binding and strong splicing repression by QKI. QKI occupancy at the dual branch site directly prevents SF1 binding and the subsequent recruitment of spliceosome-associated factors. Finally, ectopic expression of QKI in budding yeast (which lacks QKI) is lethal, at least in part due to widespread splicing repression. In conclusion, QKI can function as a splicing repressor by directly competing with SF1/BBP for a subset of branch point sequences that closely mirror its high-affinity binding site.

Keywords:  Quaking; RNA; S. cerevisiae; SF1; branch site; genetics; genomics; human; intron; mouse; splicing

DOI:  https://doi.org/10.7554/eLife.103167
J Adv Res. 2026 Mar 12. pii: S2090-1232(26)00236-5. [Epub ahead of print]

The stress responsive transcription factor ATF4: from molecular structure to disease mechanisms.

Jian-Rong Yuan, Jie Tang, Rui Sheng.

   BACKGROUND: Activating transcription factor 4 (ATF4), a member of the ATF/CREB family, regulates cell survival and death via governing the expression of genes involved in integrated stress response, endoplasmic reticulum stress, autophagy, and metabolism. ATF4's protein level is tightly controlled by translational regulation (via eIF2α phosphorylation), epigenetic modifications, and post-translational modifications (PTMs) under stress, which are linked to cancer, cardiovascular, neurodegenerative, and metabolic diseases.
AIM: This review aims to summarize recent advances in epigenetic- and PTM-mediated regulation of ATF4 stability and function, and to clarify its multifaceted roles in relevant pathological processes.
KEY SCIENTIFIC CONCEPTS: Emerging evidence highlights that epigenetic modifications and PTMs are critical for fine-tuning ATF4 activity. These regulatory mechanisms not only modulate ATF4-dependent stress responses but also contribute to disease progression, providing potential therapeutic targets for ATF4-associated disorders.

Keywords:  ATF4; Autophagy; Epigenetic modification; Integrated stress response; Oxidative stress; Post-translational modification

DOI:  https://doi.org/10.1016/j.jare.2026.03.017
Nature. 2026 Mar 18.

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation.

Jakob Farnung, Elena Slobodyanyuk, Peter Y Wang, Lianne W Blodgett, Daniel H Lin, Susanne von Gronau, Brenda A Schulman, David P Bartel.

MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes1-3. Within each complex, the miRNA pairs to target RNAs, and AGO provides effector function while also protecting the miRNA from cellular nucleases2-5. Although much is known about miRNA-directed gene regulation, less is known about how miRNAs themselves are regulated. One pathway that regulates miRNAs involves unusual targets called 'trigger' RNAs, which reverse the canonical regulatory logic and instead down-regulate miRNAs6-9. This target-directed miRNA degradation (TDMD) is thought to require a cullin-RING E3 ligase because it depends on the cullin protein CUL3 and other ubiquitylation components, including the BC-box protein ZSWIM8 (refs. 10,11). ZSWIM8 is required for murine perinatal viability and for destabilization of most short-lived miRNAs, which suggests biological importance of TDMD11-13. Here, biochemical and cellular assays establish AGO binding and polyubiquitylation by the ZSWIM8-CUL3 E3 ligase as the key regulatory steps of TDMD, and thereby define a unique cullin-RING E3 ligase class. Cryogenic electron microscopy analyses show ZSWIM8 recognizing distinct AGO and RNA conformations shaped by pairing of the miRNA to the trigger. Specificity of AGO ubiquitylation is established through generalizable RNA-RNA, RNA-protein and protein-protein interactions. The substrate features recognized by the E3 ligase do not conform to a conventional degron14,15 but instead establish a two-RNA-factor authentication mechanism for specifying a protein ubiquitylation substrate.

DOI: https://doi.org/10.1038/s41586-026-10232-0
Front Oncol. 2026 ;16 1771313

The dual regulatory role of METTL14-mediated m6A modification in tumorigenesis and its underlying mechanisms.

Yulan Yang, Lemuge Chao, Xudong Ao, Junqing Liang.

  N6-methyladenosine (m6A), as the most abundant RNA epitranscriptional modification in eukaryotes, its key component of the methyltransferase complex, METTL14, not only cooperates in catalyzing m6A deposition but also has functions independent of methyltransferase activity. This article systematically reviews the dual regulatory role of METTL14 in tumors and its molecular mechanisms, mainly organizing the relevant research in a logical sequence of "tumor suppressive effect - tumor promoting effect - controversial or context-dependent". Studies have shown that METTL14 often plays a tumor suppressive role in tumors such as hepatocellular carcinoma and colorectal cancer, while in pancreatic cancer and nasopharyngeal carcinoma, it mostly promotes malignant progression, showing a high degree of context dependence. This article focuses on two key mechanisms: on the one hand, METTL14 precisely regulates the processing, stability, and function of non-coding RNAs (including miRNAs, lncRNAs, and circRNAs) through m6A modification, reshaping the competitive endogenous RNA (ceRNA) network; on the other hand, it shapes an immunosuppressive tumor microenvironment by directly upregulating immune checkpoints such as PD-L1, mediating metabolism-immune interactions, and regulating the function of immune cells. Its functional duality also stems from the selective regulation of key pathways such as PI3K/AKT, as well as the differential interpretation by different m6A readers (such as YTHDF2 and IGF2BPs). Given the close association of these mechanisms with clinical prognosis, the expression level of METTL14 shows significant potential as a prognostic marker and therapeutic target; in the future, it is necessary to combine single-cell multi-omics and other technologies to analyze its dynamic regulatory network in specific tumor contexts and explore precise treatment strategies based on synthetic lethality or targeting downstream effector molecules.

Keywords:  METTL14; m6A modification; non-coding RNA; targeted therapy; tumor microenvironment

DOI:  https://doi.org/10.3389/fonc.2026.1771313
Chem Biol Interact. 2026 Mar 18. pii: S0009-2797(26)00153-5. [Epub ahead of print] 112045

Damage to newly synthesized proteins is a major cause of Cd(II) toxicity counteracted by proteasomes and integrated stress response in human cells.

Giorgiana Madalina Ursu, Anatoly Zhitkovich.

  Cadmium (Cd) is a biopersistent metal causing cancer and toxicity in several human tissues. Cd(II) lacks DNA binding or direct redox activity and its toxicity may result from protein damage. However, it is unclear what proteins are preferentially damaged by Cd(II) and whether global or protein-specific damage underlies its main pathologies. We examined the origin and toxicological significance of the global proteotoxic stress induced by Cd(II) in human lung and kidney cells, including primary renal proximal tubule cells. In all cells, low doses of Cd(II) induced proteolytic K48-polyubiquitination and insolubility (denaturation) of proteins. Ubiquitination-inactive cells showed hyperaccumulation of Cd-denatured proteins and transient suppression of ubiquitination or proteasome activity severely impaired cell viability at otherwise nontoxic doses of Cd. Inhibition of the ubiquitin-proteasome system after Cd(II) treatments was also detrimental to cell viability, indicating ongoing protein damage. Newly synthesized polypeptides were the main source of Cd(II)-denatured proteins and inhibition of translation prevented the formation of cytosolic aggresomes with amyloid-like structures. Short-lived transcription (p53, c-MYC) or antiapoptotic (MCL1) factors were especially sensitive to unfolding/denaturation by Cd(II). Activation of integrated stress response by Cd(II) increased cell survival and lowered the burden of structurally damaged proteins although to a lesser extent than proteasome activity. Our findings identified newly synthesized proteins as the major target of toxic damage by Cd(II) and revealed a high vulnerability of short-lived proteins. Ubiquitin-proteasome system was critically important for removal of damaged proteins and Cd(II) tolerance by human cells.

Keywords:  cadmium; proteasomes; protein damage; proteotoxicity; unfolded proteins

DOI:  https://doi.org/10.1016/j.cbi.2026.112045
Cell Signal. 2026 Mar 12. pii: S0898-6568(26)00131-2. [Epub ahead of print]143 112480

IGF2BP3-TRIM37-P53 axis promotes tumor progression in LUAD.

Ting Ji, Tingting Zhao, Shuni Wang, Xiaotong Guo, Ting Wang, Hai Tan, Shaojin Wang, Ma Gang, Juan Chen.

   BACKGROUND: m6A and ubiquitination modifications critically drive lung adenocarcinoma (LUAD) progression and are closely linked to cellular context-such as p53 status. Thus, elucidating how these modifications regulate p53's role in LUAD pathogenesis is vital for targeted therapy.
METHODS: TCGA was used to screen for IGF2BP3, a key m6A regulator in LUAD, and its survival and differential expression were evaluated. Colony formation and CCK8 assays were used to assess the effects of IGF2BP3 on cell proliferation. TRIM37 was identified as a downstream target of IGF2BP3 using the Gene Expression Omnibus (GEO) database for bioinformatics analysis. RIP-qPCR experiments confirmed m6a enrichment of TRIM37 mRNA by IGF2BP3. The pro-tumor effects of IGF2BP3 were validated both in vivo and in vitro.
RESULTS: IGF2BP3 was highly expressed in lung adenocarcinoma (LUAD) and associated with poor patient prognosis. IGF2BP3 recognizes the m6A modification site in the 3'UTR of TRIM37 mRNA, stabilizing its expression. TRIM37 promotes p53 protein degradation through ubiquitination. Silencing TRIM37 reversed IGF2BP3-driven LUAD progression in vivo and in vitro.
CONCLUSION: Here, we found that IGF2BP3, acting as an m6A reader, promotes LUAD cell proliferation both in vivo and in vitro. Mechanistically, IGF2BP3 mediates the ubiquitination and degradation of p53 by reading the m6A-modified TRIM37 mRNA 3'UTR, thereby promoting tumorigenesis in LUAD. Importantly, shTRIM37 significantly inhibited IGF2BP3-driven tumor progression.

Keywords:  IGF2BP3; LUAD; TRIM37; m6A modification; p53

DOI:  https://doi.org/10.1016/j.cellsig.2026.112480
Mol Ecol. 2026 Mar;35(6): e70302

Skin Colour in Salamanders Is Modulated by Both Epitranscriptomic Methylation and Gene Expression.

Nicholas Strowbridge, David R Vieites, Michael G Ritchie, Kathryn R Elmer.

Animal colouration is a key trait in organismal biology, being involved in natural and sexual selection, competition, and communication. Amphibians use their highly diverse colouration in many ecological interactions, but the molecular bases of their colour variation are less well understood than in other vertebrate systems. While the genetic, structural, and cellular bases of pigmentation are increasingly understood in a range of models, potential epigenetic or epitranscriptomic effects are almost completely unexplored. The fire salamander (Salamandra salamandra) has striking colour patterns and polymorphisms, but the extremely large genome size of salamanders makes traditional genetic analyses infeasible. To discover loci and molecular mechanisms underlying colour differences in salamanders, we used long-read direct RNA sequencing to test the roles of RNA methylation, gene expression and their relationship on intra- and inter-individual colour variation in black, yellow and brown skinned salamanders. We found 129 differentially expressed and 281 differentially methylated genes across all pairwise comparisons. Many of the genes involved are related to pigmentation, with several directly associated with melanin production, such as Melan-A (MLANA), Premelanosome protein (PMEL), Tyrosinase (TYR) and Tyrosinase-related protein 1 (TYRP1). We found both a positive overall correlation and a significant overlap in transcripts that are differentially methylated and expressed. These findings suggest multiple molecular mechanisms, including gene expression and RNA methylation, contribute to amphibian colour diversity. RNA modifications as a promising area for understanding morphological variation in non-model animals and their impact on their ecology.

DOI: https://doi.org/10.1111/mec.70302
J Bioenerg Biomembr. 2026 Mar 18.

MATR3 regulates METTL3-Mediated m6A modification of MSI2 mRNA to activate the Wnt/β-Catenin pathway, exacerbating myocardial fibrosis and atrial fibrillation.

Zihan Wei, Jing Li, Pinji Dai, Cheng Qian, Xiaoli Li.

  To investigate the role and molecular mechanisms of the RNA-binding protein MATR3 in myocardial fibrosis of atrial fibrillation (AF). Expression of MATR3 and MSI2 in AF patients was analyzed using GEO datasets (GSE79768, GSE14975, GSE31821). Human atrial fibroblasts (HAFs) induced by Angiotensin II (Ang-II) were used as an in vitro cellular model of myocardial fibrosis. Expression and interactions of MATR3, METTL3, and MSI2 were validated by qRT-PCR and Western blot. The binding between MATR3 and METTL3 was confirmed by co-immunoprecipitation (Co-IP). The m6A modification level of MSI2 mRNA was detected by methylated RNA immunoprecipitation (MeRIP-qPCR). Cell proliferation, migration, and fibrotic phenotypes were evaluated by CCK-8, EdU, scratch, and Transwell assays, as well as detection of fibrosis markers. An Ang-II-induced mouse model of atrial fibrosis was constructed, and the in vivo effects of MATR3 were verified by HE staining, Masson's trichrome staining, and molecular detection. Analysis of GEO datasets showed that both MATR3 and MSI2 were highly expressed in AF patients. Ang-II treatment significantly upregulated the expression of MATR3 in HAFs, while knockdown of MATR3 inhibited Ang-II-induced proliferation, migration, and pro-fibrotic phenotypic changes in HAFs (reducing the expression of α-SMA, collagen I/III). Mechanistically, MATR3 interacted endogenously with METTL3 and stabilized the METTL3 protein by inhibiting proteasomal degradation. METTL3 mediated the m6A modification of MSI2 mRNA, enhancing its stability and promoting its expression. MSI2 exerted a pro-fibrotic effect by activating the Wnt/β-Catenin pathway. In vivo experiments confirmed that silencing MATR3 downregulated the expression of METTL3 and MSI2, inhibited the activation of the Wnt pathway, and alleviated Ang-II-induced atrial fibrosis in mice. MATR3 promotes myocardial fibrosis and exacerbates AF by regulating METTL3-mediated m6A modification of MSI2 mRNA to activate the Wnt/β-Catenin pathway. Targeting MATR3 may represent a potential therapeutic strategy for AF.

Keywords:  Atrial fibrillation; MATR3; METTL3; Wnt/β-Catenin pathway; m6A modification

DOI:  https://doi.org/10.1007/s10863-026-10090-5
Phys Rev E. 2026 Feb;113(2-1): 024407

Sequence motif dynamics in RNA pools.

Johannes Harth-Kitzerow, Tobias Göppel, Ludwig Burger, Torsten A Enßlin, Ulrich Gerland.

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution. In such pools, RNA oligomers hybridize and dehybridize, ligate, and break, ultimately generating longer RNA molecules, which may fold into catalytically active ribozymes. A key process for the elongation of RNA oligomers is templated ligation, which can occur when two RNA strands are adjacently hybridized onto a template strand. Detailed simulations of the dynamics in RNA pools involve a large variety of possible sequences and reactions. Here we develop a reduced description of these complex dynamics within the space of sequence motifs. We then explore to what extent our reduced description can capture the behavior of detailed simulations that account for the full dynamics in the space of RNA strands. Towards this end, we project the dynamics into a motif space, which accounts only for the abundance of all possible four-nucleotide motifs. A system of ordinary differential equations describes the dynamics of those motifs. Its control parameters are effective rate constants for reactions in motif space, which we obtain from the rate constants for the processes underlying the full dynamics in the space of RNA strands. We find that these reduced motif space dynamics indeed capture important aspects of the informational dynamics of RNA pools in sequence space. This approach could also provide a framework to rationalize and interpret features of the sequence dynamics observed in experimental systems.

DOI: https://doi.org/10.1103/y5qv-qm7n
Life Sci Alliance. 2026 Jun;pii: e202503424. [Epub ahead of print]9(6):

Huntingtin (HTT) interactome in regulation of DNA repair/remodeling and RNA processing pathways.

Tamara Ratovitski, Chloe D Holland, Robert N O'Meally, Alexey V Shevelkin, Siddhi V Kamath, Tianze Shi, Matthew J Rodriguez, Robert N Cole, Mali Jiang, Christopher A Ross.

Huntington's disease (HD), an uncurable neurodegenerative disorder, is caused by CAG repeat expansion in the HD gene encoding mutant huntingtin protein. DNA damage response is implicated in HD pathogenesis. We used multiple approaches to assess normal and mutant HTT interactomes in the context of genotoxic stress. We show that double-strand break (DSB) repair response is impaired in HD neurons, which are more vulnerable to DSB-induced stress. We found that S1181 phosphorylation of HTT is regulated by DSB, and can be carried out by DNA-PK. Functional interaction of HTT with a major DSB kinase DNA-PKcs and association of both proteins with nuclear speckles suggest a role of HTT in DSB repair mechanism; however, physiological outcome of these interactions remains to be examined. We revealed HTT interactions with other proteins associated with nuclear speckles, TCERG1 and MED15, whose loci are genetic modifiers for HD, and with chromatin remodeling complex BAF. These interactions may position HTT as an important scaffolding intermediary providing integrated regulation of gene expression and RNA processing in the context of DNA repair mechanisms.

DOI: https://doi.org/10.26508/lsa.202503424