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103 results for “RNA targeting”

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  1. 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 ↗

  2. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.

    bioRxiv : the preprint server for biology · 2024

    Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses …

    PMID 37745562 DOI ↗

  3. 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 ↗

  4. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

    Nucleic acids research · 2024 · 52(8): 4440-4455

    Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against …

    PMID 38554115 DOI ↗

  5. 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 ↗

  6. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.

    Current opinion in biotechnology · 2024 · 85: 103048

    Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the …

    PMID 38142648 DOI ↗

  7. LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.

    RNA (New York, N.Y.) · 2024 · 30(3): 223-239

    Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified …

    PMID 38164626 DOI ↗

  8. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

    Nature communications · 2024 · 15(1): 875

    RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize …

    PMID 38287010 DOI ↗

  9. 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 ↗

  10. FLARE: a fast and flexible workflow for identifying RNA editing foci.

    BMC bioinformatics · 2023 · 24(1): 370

    Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable …

    PMID 37784060 DOI ↗

  11. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

    bioRxiv : the preprint server for biology · 2023

    RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize …

    PMID 37808757 DOI ↗

  12. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

    bioRxiv : the preprint server for biology · 2023

    Large-genome bacteriophages (jumbo phages) of the <i>Chimalliviridae</i> family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, …

    PMID 37790334 DOI ↗

  13. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.

    Nature communications · 2023 · 14(1): 5195

    Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that …

    PMID 37673892 DOI ↗

  14. Remodeling oncogenic transcriptomes by small molecules targeting NONO.

    Nature chemical biology · 2023 · 19(7): 825-836

    Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants …

    PMID 36864190 DOI ↗

  15. 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 ↗

  16. 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 ↗

  17. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.

    bioRxiv : the preprint server for biology · 2023

    Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) in diverse ribonucleoprotein complexes (RNPs) during distinct life-cycle stages for their processing and maturation. While substantial attention has focused on understanding RNA regulation by assigning proteins, particularly RBPs, to specific RNA substrates, …

    PMID 37333282 DOI ↗

  18. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.

    Blood cancer discovery · 2023 · 4(3): 180-207

    Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) …

    PMID 36763002 DOI ↗

  19. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders.

    RNA (New York, N.Y.) · 2023 · 29(4): 489-497

    Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies …

    PMID 36693761 DOI ↗

  20. Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.

    Nature communications · 2023 · 14(1): 551

    Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it …

    PMID 36759613 DOI ↗

  21. RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation.

    Science advances · 2023 · 9(5): eadd6165

    Retinoid-related orphan receptor (RAR) gamma (RORγt)-expressing regulatory T cells (RORγt<sup>+</sup> T<sub>regs</sub>) play pivotal roles in preventing T cell hyperactivation and maintaining tissue homeostasis, in part by secreting the anti-inflammation cytokine interleukin-10 (IL-10). Here, we report that hypoxia-induced factor 1α (HIF1α) …

    PMID 36724232 DOI ↗

  22. An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models.

    Nature neuroscience · 2023 · 26(1): 27-38

    Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAG<sup>EX</sup> …

    PMID 36510111 DOI ↗

  23. 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 ↗

  24. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.

    Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53

    Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …

    PMID 35378331 DOI ↗

  25. 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 ↗

Datasets 2

GSE127743 GSE · GEO

In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]

Mus musculus · GPL18480

GSE230717 GSE · GEO

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Homo sapiens · GPL24676

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No analyses match this query.