Search publications
146 results for “RNA binding protein”
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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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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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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 ↗
Datasets 25+
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 (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
An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia
Homo sapiens · GPL16791
Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death
Mus musculus · GPL21103
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
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
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]
Homo sapiens · GPL28352
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)
Homo sapiens · GPL15106
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]
Homo sapiens · GPL16791
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens · GPL11154
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)
Homo sapiens · GPL15520
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
Homo sapiens · GPL24106
SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.
Homo sapiens · GPL20301
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (4)
Homo sapiens · GPL24676
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
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]
Homo sapiens · GPL16791
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]
Homo sapiens · GPL17585
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)
Homo sapiens · GPL15520
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens · GPL24676
DDX5 targets tissue specific RNAs to promote intestine tumorigenesis
Mus musculus · GPL21103
Showing first 25 dataset results.
Analyses 25+
GSE230717 · 9 steps · RIP-Seq · code_examples
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
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 · 5 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
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 · 3 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
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 · 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 · 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 · 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 · 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 · 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 · 13 steps · OTHER · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
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)
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 · 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 · 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 · 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 · 20 steps · RIP-Seq · code_examples
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. (2022)
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 · 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 · 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 · 6 steps · OTHER · code_examples
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. (2021)
GSE155649 · 6 steps · OTHER · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
GSE155708 · 11 steps · RNA-Seq · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
GSE155726 · 12 steps · RNA-Seq · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
Showing first 25 analysis results.