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153 results for “RNA binding”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.

    Molecular cell · 2024 · 84(19): 3826-3842.e8

    RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and …

    PMID 39303722 DOI ↗

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

    Molecular cell · 2024 · 84(19): 3790-3809.e8

    mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map …

    PMID 39303721 DOI ↗

  8. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.

    Nature biotechnology · 2024 · 42(9): 1429-1441

    RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion …

    PMID 38168984 DOI ↗

  9. Author Correction: Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.

    Nature biotechnology · 2024 · 42(9): 1467

    PMID 38418649 DOI ↗

  10. Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.

    Proceedings of the National Academy of Sciences of the United States of America · 2024 · 121(34): e2319724121

    Skeletal muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and aging. The tissue remodeling that happens during recovery from atrophy or injury involves changes in different cell types such as muscle fibers, and …

    PMID 39141348 DOI ↗

  11. 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 ↗

  12. Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

    Cell genomics · 2024 · 4(7): 100603

    The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets …

    PMID 38955188 DOI ↗

  13. Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.

    STAR protocols · 2024 · 5(2): 103040

    Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows …

    PMID 38669139 DOI ↗

  14. 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 ↗

  15. 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 ↗

  16. 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 ↗

  17. 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 ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. 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 ↗

  22. 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 ↗

  23. 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 ↗

  24. 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 ↗

  25. 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 ↗

Datasets 25+

GSE254209 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).

Homo sapiens · GPL24676

GSE254208 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).

Homo sapiens · Illumina

GSE328331 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]

Homo sapiens · Illumina

GSE290625 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]

Homo sapiens · Illumina

GSE290765 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]

Homo sapiens · Illumina

GSE290755 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]

Homo sapiens · Illumina

GSE315026 GSE · GEO

MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]

GPL24676

GSE134971 GSE · GEO

An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia

Homo sapiens · GPL16791

GSE65973 GSE · GEO

RNA sequencing of mice expressing NLS-hTDP-43

Mus musculus · GPL9250

GSE179634 GSE · GEO

Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death

Mus musculus · GPL21103

GSE127944 GSE · GEO

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

Mus musculus · GPL21103

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

GSE166404 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens · GPL28352

GSE34992 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Homo sapiens · GPL15106

GSE77629 GSE · GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]

Homo sapiens · GPL16791

GSE145968 GSE · GEO

CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production

Homo sapiens · GPL20301

GSE277160 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]

Homo sapiens · GPL24676

GSE77700 GSE · GEO

Distinct and shared molecular targets and functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [CLIP-Seq]

Mus musculus · GPL13112

GSE77702 GSE · GEO

Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_human]

Homo sapiens · GPL11154

GSE149767 GSE · GEO

Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces

Homo sapiens · GPL11154

GSE232519 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)

Homo sapiens · GPL15520

GSE155708 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens · GPL24106

GSE86035 GSE · GEO

SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

Homo sapiens · GPL20301

GSE232518 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (4)

Homo sapiens · GPL24676

GSE86227 GSE · GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]

Mus musculus · GPL15520

Showing first 25 dataset results.

Analyses 25+

GSE230717 Processing Pipeline

GSE230717 · 9 steps · RIP-Seq · code_examples

Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)

GSE232513 Processing Pipeline

GSE232513 · 3 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE232514 Processing Pipeline

GSE232514 · 5 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE232515 Processing Pipeline

GSE232515 · 4 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE232518 Processing Pipeline

GSE232518 · 3 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE232519 Processing Pipeline

GSE232519 · 3 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE127743 Processing Pipeline

GSE127743 · 4 steps · RNA-Seq · code_examples

In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. (2023)

GSE127944 Processing Pipeline

GSE127944 · 22 steps · RIP-Seq · code_examples

In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. (2023)

GSE134809 Processing Pipeline

GSE134809 · 5 steps · RNA-Seq · code_examples

RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation. (2023)

GSE157259 Processing Pipeline

GSE157259 · 22 steps · RIP-Seq · code_examples

RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation. (2023)

GSE162335 Processing Pipeline

GSE162335 · 2 steps · GSE · code_examples

RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation. (2023)

GSE205536 Processing Pipeline

GSE205536 · 13 steps · OTHER · code_examples

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)

GSE206674 eCLIP Data Processing

GSE206674 · 10 steps · eCLIP · geo_data_processing

Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)

GSE224548 Processing Pipeline

GSE224548 · 3 steps · RNA-Seq · code_examples

In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. (2023)

GSE230349 Processing Pipeline

GSE230349 · 8 steps · OTHER · code_examples

Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)

GSE126263 Processing Pipeline

GSE126263 · 25 steps · RIP-Seq · code_examples

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)

GSE126337 Processing Pipeline

GSE126337 · 3 steps · RNA-Seq · code_examples

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)

GSE134597 Processing Pipeline

GSE134597 · 4 steps · RNA-Seq · code_examples

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)

GSE146014 Processing Pipeline

GSE146014 · 3 steps · RNA-Seq · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)

GSE180686 Processing Pipeline

GSE180686 · 20 steps · RIP-Seq · code_examples

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. (2022)

GSE184564 Processing Pipeline

GSE184564 · 3 steps · RNA-Seq · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)

GSE75214 Processing Pipeline

GSE75214 · 1 step · GSE · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)

GSE83687 Processing Pipeline

GSE83687 · 4 steps · RNA-Seq · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)

GSE145968 Processing Pipeline

GSE145968 · 6 steps · OTHER · code_examples

A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. (2021)

GSE155649 Processing Pipeline

GSE155649 · 6 steps · OTHER · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

Showing first 25 analysis results.