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20 results for “RNA context”

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  1. Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.

    RNA (New York, N.Y.) · 2025 · 31(8): 1103-1124

    RNA-binding proteins (RBP) play diverse roles in mRNA processing and function. However, from thousands of RBPs encoded in the human genome, a detailed molecular understanding of their interactions with RNA is available only for a small fraction. In most cases, …

    PMID 40399037 DOI ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.

    Molecular cell · 2023 · 83(19): 3421-3437.e11

    The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the …

    PMID 37751740 DOI ↗

  6. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.

    Molecular cell · 2023 · 83(14): 2595-2611.e11

    RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier …

    PMID 37421941 DOI ↗

  7. Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.

    PLoS biology · 2023 · 21(1): e3001983

    During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the …

    PMID 36716323 DOI ↗

  8. Author Correction: Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.

    Nature communications · 2023 · 14(1): 136

    PMID 36627300 DOI ↗

  9. Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2463: 67-80

    Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …

    PMID 35344168 DOI ↗

  10. 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 ↗

  11. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.

    Nature communications · 2022 · 13(1): 7506

    Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains …

    PMID 36473869 DOI ↗

  12. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.

    Nature · 2022 · 609(7925): 101-108

    As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which …

    PMID 35798029 DOI ↗

  13. Engineered U1 snRNAs to modulate alternatively spliced exons.

    Methods (San Diego, Calif.) · 2022 · 205: 140-148

    Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

    PMID 35764245 DOI ↗

  14. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.

    medRxiv : the preprint server for health sciences · 2022

    As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also …

    PMID 35411350 DOI ↗

  15. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.

    Critical reviews in biochemistry and molecular biology · 2021 · 56(1): 31-53

    Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG<sub>50-3,500</sub> in <i>DMPK</i>; DM2, CCTG<sub>75-11,000</sub> in …

    PMID 33172304 DOI ↗

  16. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  17. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses.

    Science immunology · 2020 · 5(50)

    Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal …

    PMID 32826341 DOI ↗

  18. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

    Nature · 2020 · 583(7818): 699-710

    The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded …

    PMID 32728249 DOI ↗

  19. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.

    Cell stem cell · 2019 · 25(5): 622-638.e13

    Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells …

    PMID 31588046 DOI ↗

  20. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

    Molecular cell · 2018 · 70(5): 854-867.e9

    RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by …

    PMID 29883606 DOI ↗

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