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229 results for “RNA”
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration.
bioRxiv : the preprint server for biology · 2023
Muscular atrophy is a mortality risk factor that happens with disuse, chronic disease, and aging. Recovery from atrophy requires changes in several cell types including muscle fibers, and satellite and immune cells. Here we show that Zfp697/ZNF697 is a damage-induced …
PMID 37398033 DOI ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Nature methods · 2023 · 20(1): 65-69
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the …
PMID 36550273 DOI ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]
Homo sapiens · Illumina
RBP Footprint Grand Challenge: An evaluation of novel computational approaches to RNA-binding protein target prediction from structural data
Homo sapiens · GPL20301
RNA secondary structome of different cell lines
Homo sapiens, Mus musculus · GPL20795, GPL21273
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]
Homo sapiens · Illumina
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]
GPL21626
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE)
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Showing first 25 dataset results.
Analyses 25+
GSE244832 · 9 steps · scRNA-seq · geo_data_processing
RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis. (2026)
GSE275091 · 1 step · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE275133 · 2 steps · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE290248 · 1 step · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290281 · 1 step · eCLIP · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290282 · 3 steps · RNA-seq · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE299099 · 3 steps · RNA-Seq · code_examples
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)
GSE302648 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302649 · 11 steps · eCLIP · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302651 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE314058 · 7 steps · scRNA-seq · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE314059 · 4 steps · scRNA-seq · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE315347 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315406 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315407 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315443 · 2 steps · scRNA-seq · geo_data_processing
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
GSE125970 · 4 steps · RNA-Seq · code_examples
Stratification of enterochromaffin cells by single-cell expression analysis. (2025)
GSE137810 · 8 steps · RNA-seq · geo_data_processing
Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in … (2025)
GSE145805 · 7 steps · SHAPE-seq · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE199650 · 11 steps · RIP-Seq · code_examples
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor. (2025)
GSE227455 · 7 steps · eCLIP · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE228444 · 4 steps · OTHER · code_examples
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. (2025)
GSE247544 · 3 steps · scRNA-seq · geo_data_processing
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner. (2025)
GSE262542 · 4 steps · RNA-Seq · code_examples
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
Showing first 25 analysis results.