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29 results for “RNA localization”

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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. Localized regulation of cell junction mRNAs is required for epithelial cell integrity.

    RNA (New York, N.Y.) · 2026 · 32(5): 635-653

    Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. …

    PMID 41535088 DOI ↗

  3. 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 ↗

  4. 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 ↗

  5. Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.

    Nature communications · 2024 · 15(1): 10796

    Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal …

    PMID 39737952 DOI ↗

  6. Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes.

    Neuron · 2024 · 112(24): 4033-4047.e8

    Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear …

    PMID 39486415 DOI ↗

  7. 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 ↗

  8. Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.

    bioRxiv : the preprint server for biology · 2024

    Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …

    PMID 38915553 DOI ↗

  9. ePRINT: exonuclease assisted mapping of protein-RNA interactions.

    Genome biology · 2024 · 25(1): 140

    RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new …

    PMID 38807229 DOI ↗

  10. Transcriptome regulation by PARP13 in basal and antiviral states in human cells.

    iScience · 2024 · 27(4): 109251

    The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including …

    PMID 38495826 DOI ↗

  11. Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.

    Cell genomics · 2023 · 3(6): 100317

    Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts …

    PMID 37388912 DOI ↗

  12. RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.

    Nucleic acids research · 2023 · 51(D1): D1549-D1557

    RNA binding proteins (RBPs) are central regulators of gene expression implicated in all facets of RNA metabolism. As such, they play key roles in cellular physiology and disease etiology. Since different steps of post-transcriptional gene expression tend to occur in …

    PMID 36321651 DOI ↗

  13. APEX Proximity Labeling of Stress Granule Proteins.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2428: 381-399

    Ascorbate peroxidase (APEX)-catalyzed proximity labeling has been recently established as a robust approach to uncover localized protein environments and transient protein-protein interactions occurring across mammalian cells. This molecular tool enables improved identification of individual proteins localized to and involved in …

    PMID 35171492 DOI ↗

  14. Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.

    Acta neuropathologica · 2022 · 144(3): 413-435

    Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by aberrant alternative splicing (AS). Nuclear loss and cytoplasmic accumulation of the splicing factor TDP-43 in motor neurons (MN) are hallmarks of ALS at late stages of the disease. However, it …

    PMID 35778567 DOI ↗

  15. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.

    Nature communications · 2021 · 12(1): 6324

    Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart …

    PMID 34732726 DOI ↗

  16. Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.

    Cell reports · 2021 · 36(10): 109685

    Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). …

    PMID 34496257 DOI ↗

  17. G<sub>4</sub>C<sub>2</sub> Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD.

    Neuron · 2020 · 107(6): 1124-1140.e11

    Through mechanisms that remain poorly defined, defects in nucleocytoplasmic transport and accumulations of specific nuclear-pore-complex-associated proteins have been reported in multiple neurodegenerative diseases, including C9orf72 Amyotrophic Lateral Sclerosis and Frontotemporal Dementia (ALS/FTD). Using super-resolution structured illumination microscopy, we have explored …

    PMID 32673563 DOI ↗

  18. A large-scale binding and functional map of human RNA-binding proteins.

    Nature · 2020 · 583(7818): 711-719

    Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …

    PMID 32728246 DOI ↗

  19. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.

    Scientific reports · 2019 · 9(1): 11071

    AATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role …

    PMID 31363146 DOI ↗

  20. Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas.

    Bioconjugate chemistry · 2018 · 29(1): 126-135

    The intracellular delivery of synthetic nucleic acids represents a major challenge in biotechnology and in biomedicine. Methods to deliver short, double-stranded RNA to living cells are of particular interest because of the potential to engage the RNA interference machinery and …

    PMID 29286237 DOI ↗

  21. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.

    Nucleic acids research · 2017 · 45(21): 12509-12528

    To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, …

    PMID 29069457 DOI ↗

  22. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

    Advances in experimental medicine and biology · 2016 · 907: 1-28

    After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. …

    PMID 27256380 DOI ↗

  23. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.

    Advances in experimental medicine and biology · 2016 · 907: 61-88

    Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …

    PMID 27256382 DOI ↗

  24. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

    Neuron · 2016 · 92(4): 780-795

    HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …

    PMID 27773581 DOI ↗

  25. Programmable RNA Tracking in Live Cells with CRISPR/Cas9.

    Cell · 2016 · 165(2): 488-96

    RNA-programmed genome editing using CRISPR/Cas9 from Streptococcus pyogenes has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target RNA would allow alteration and imaging of endogenous RNA transcripts analogous to CRISPR/Cas-based genomic …

    PMID 26997482 DOI ↗

Datasets 2

GSE106493 GSE · GEO

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

Homo sapiens · GPL11154

GSE157467 GSE · GEO

Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress

Homo sapiens · GPL20301

Analyses 1

GSE157467 Processing Pipeline

GSE157467 · 6 steps · RNA-Seq · code_examples

Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. (2021)