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74 results for “RNA biology”

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  1. RNA dysregulation as a determinant of aging and neurodegenerative vulnerability.

    Trends in cell biology · 2026

    In the nervous system, aging causes deterioration of cellular and molecular processes that are associated with declines in cognition, sensory perception, and motor coordination. Aging is also the strongest risk factor for neurodegenerative disease, yet the mechanisms by which aging …

    PMID 42711219 DOI ↗

  2. ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSC-derived models.

    Nature communications · 2026 · 17(1)

    RNA-binding proteins (RBPs) are key regulators of gene expression that shape cellular function in health and disease. However, the roles of RBPs in immune cells within the central nervous system (CNS) remain poorly understood. Here, we identify ARID5A as an …

    PMID 42717200 DOI ↗

  3. ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing.

    bioRxiv : the preprint server for biology · 2026

    Chemical proteomics has identified covalent ligands targeting cysteine residues across many hundreds of human proteins. The functional effects of these liganding events, however, remain challenging to assign at scale. Here we describe ESCAPE (Endogenous Site-specific Competition Assays using Prime Editors), …

    PMID 42619774 DOI ↗

  4. Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response.

    bioRxiv : the preprint server for biology · 2026

    RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment into Ebola virus condensates under basal and IFN-stimulated states. We …

    PMID 42465340 DOI ↗

  5. Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.

    bioRxiv : the preprint server for biology · 2026

    Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for …

    PMID 41959526 DOI ↗

  6. Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.

    Cell chemical biology · 2026 · 33(2): 256-267.e11

    RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We previously described a chloroacetamide compound (R)-SKBG-1 that covalently binds …

    PMID 41534524 DOI ↗

  7. Dosage-sensitive <i>RBFOX2</i> autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome.

    bioRxiv : the preprint server for biology · 2025

    Haploinsufficiency of the RNA splicing regulator, <i>RBFOX2</i> , is linked to congenital heart disease (CHD), yet its pathogenic mechanisms remain unclear. Here, we demonstrate that RBFOX2 is essential for progressing cardiomyocyte (CM) differentiation by shifting exon usage profiles to more …

    PMID 41280054 DOI ↗

  8. KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS.

    bioRxiv : the preprint server for biology · 2025

    Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as …

    PMID 41279899 DOI ↗

  9. Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.

    bioRxiv : the preprint server for biology · 2025

    Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope …

    PMID 41279865 DOI ↗

  10. Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.

    bioRxiv : the preprint server for biology · 2025

    The <i>AUTS2</i> gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2's chromatin-and RNA-related functions are recognized, its direct binding to RNA in human neural progenitors has not been …

    PMID 41278797 DOI ↗

  11. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.

    Nature chemical biology · 2025

    Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …

    PMID 40968292 DOI ↗

  12. RNA triggers chronic stress during neuronal aging.

    bioRxiv : the preprint server for biology · 2025

    Neurodegenerative diseases are linked with dysregulation of the integrated stress response (ISR), which coordinates cellular homeostasis during and after stress events. Cellular stress can arise from several sources, but there is significant disagreement about which stress might contribute to aging …

    PMID 40799579 DOI ↗

  13. Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.

    Nature neuroscience · 2025 · 28(6): 1174-1184

    Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged …

    PMID 40456907 DOI ↗

  14. Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.

    bioRxiv : the preprint server for biology · 2025

    RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We recently reported a chloroacetamide compound ( <i>R</i> )-SKBG-1 that …

    PMID 40661397 DOI ↗

  15. Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites.

    bioRxiv : the preprint server for biology · 2025

    The global impact of the COVID-19 pandemic underscores the critical need for a comprehensive understanding of SARS-CoV-2 replication mechanisms. While the central roles of the RNA dependent RNA polymerase (NSP12), primase protein (NSP8), and nucleocapsid protein (N) in the virus …

    PMID 40501555 DOI ↗

  16. Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.

    bioRxiv : the preprint server for biology · 2025

    RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …

    PMID 40655003 DOI ↗

  17. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.

    Cell systems · 2025 · 16(4): 101204

    The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the …

    PMID 40054464 DOI ↗

  18. Phenylpyrazoles as Inhibitors of the m<sup>6</sup>A RNA-Binding Protein YTHDF2.

    JACS Au · 2025 · 5(2): 618-630

    The <i>N</i>6-methyladenosine (m<sup>6</sup>A) modification, which is the most common RNA modification in eukaryotes, is regulated by the "writer" methyltransferases, the "reader" m<sup>6</sup>A binding proteins, and the "eraser" demethylases. m<sup>6</sup>A plays a multifunctional role in physiological and pathological processes, regulating all …

    PMID 40017738 DOI ↗

  19. Rational design yields RNA-binding zinc finger domains with altered sequence specificity.

    RNA (New York, N.Y.) · 2025 · 31(2): 150-163

    Targeting and manipulating endogenous RNAs in a sequence-specific manner is essential for both understanding RNA biology and developing RNA-targeting therapeutics. RNA-binding zinc fingers (ZnFs) are excellent candidates as designer proteins to expand the RNA-targeting toolbox, due to their compact size …

    PMID 39658359 DOI ↗

  20. LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.

    bioRxiv : the preprint server for biology · 2025

    Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality …

    PMID 39868246 DOI ↗

  21. Strategies for programmable manipulation of alternative splicing.

    Current opinion in genetics & development · 2024 · 89: 102272

    Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …

    PMID 39471777 DOI ↗

  22. Decoding protein-RNA interactions using CLIP-based methodologies.

    Nature reviews. Genetics · 2024 · 25(12): 879-895

    Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding …

    PMID 38982239 DOI ↗

  23. Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.

    Genome research · 2024 · 34(11): 2012-2024

    Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …

    PMID 38906680 DOI ↗

  24. Localized synthesis of molecular chaperones sustains neuronal proteostasis.

    bioRxiv : the preprint server for biology · 2024

    Neurons are challenged to maintain proteostasis in neuronal projections, particularly with the physiological stress at synapses to support intercellular communication underlying important functions such as memory and movement control. Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted …

    PMID 37873158 DOI ↗

  25. High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.

    Nature communications · 2024 · 15(1): 7067

    RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE (IN situ Sensitive Capture of RNA-protein Interactions in Biological Environments), circumventing the challenges through …

    PMID 39152130 DOI ↗

Datasets 3

GSE276986 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]

Homo sapiens · GPL24676

GSE276985 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]

Mus musculus · GPL24676

GSE277082 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]

Homo sapiens · GPL24676

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