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146 results for “RNA binding protein”

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  1. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions.

    Neuron · 2019 · 102(2): 294-320

    RNA binding proteins are critical to the maintenance of the transcriptome via controlled regulation of RNA processing and transport. Alterations of these proteins impact multiple steps of the RNA life cycle resulting in various molecular phenotypes such as aberrant RNA …

    PMID 30998900 DOI ↗

  2. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

    Nature communications · 2019 · 10(1): 1338

    Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …

    PMID 30902979 DOI ↗

  3. RBP-Maps enables robust generation of splicing regulatory maps.

    RNA (New York, N.Y.) · 2019 · 25(2): 193-204

    Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …

    PMID 30413564 DOI ↗

  4. A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.

    Molecular cell · 2019 · 73(2): 304-313.e3

    LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …

    PMID 30527666 DOI ↗

  5. Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.

    Acta neuropathologica · 2018 · 136(3): 405-423

    Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …

    PMID 29881994 DOI ↗

  6. 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 ↗

  7. Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.

    Molecular cell · 2018 · 69(6): 1005-1016.e7

    RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced …

    PMID 29547715 DOI ↗

  8. Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.

    Wiley interdisciplinary reviews. RNA · 2018 · 9(1)

    RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking …

    PMID 28853213 DOI ↗

  9. Erratum to: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

    Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: E1

    PMID 29230720 DOI ↗

  10. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

    Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: 177-200

    Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with …

    PMID 28766298 DOI ↗

  11. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.

    Nucleic acids research · 2017 · 45(21): 12509-12528

    To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, …

    PMID 29069457 DOI ↗

  12. NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.

    Nature structural & molecular biology · 2017 · 24(10): 816-824

    MicroRNA (miRNA) biogenesis is known to be modulated by a variety of RNA-binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small subset of target miRNAs. Here, we report that the RNA-binding NONO-PSF …

    PMID 28846091 DOI ↗

  13. Genetic mutations in RNA-binding proteins and their roles in ALS.

    Human genetics · 2017 · 136(9): 1193-1214

    Mutations in genes that encode RNA-binding proteins (RBPs) have emerged as critical determinants of neurological diseases, especially motor neuron disorders such as amyotrophic lateral sclerosis (ALS). RBPs are involved in all aspects of RNA processing, controlling the life cycle of …

    PMID 28762175 DOI ↗

  14. The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.

    eLife · 2017 · 6

    ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …

    PMID 28925356 DOI ↗

  15. Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.

    Methods (San Diego, Calif.) · 2017 · 126: 29-37

    Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause premature reverse transcription termination and deletions (referred to as crosslink-induced mutation …

    PMID 28790018 DOI ↗

  16. CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.

    Methods (San Diego, Calif.) · 2017 · 118-119: 50-59

    Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous …

    PMID 28003131 DOI ↗

  17. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.

    Advances in experimental medicine and biology · 2016 · 907: 61-88

    Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …

    PMID 27256382 DOI ↗

  18. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

    Advances in experimental medicine and biology · 2016 · 907: 1-28

    After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. …

    PMID 27256380 DOI ↗

  19. RNA-binding protein CPEB1 remodels host and viral RNA landscapes.

    Nature structural & molecular biology · 2016 · 23(12): 1101-1110

    Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …

    PMID 27775709 DOI ↗

  20. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

    Neuron · 2016 · 92(4): 780-795

    HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …

    PMID 27773581 DOI ↗

  21. From Protein-RNA Predictions toward a Peptide-RNA Code.

    Molecular cell · 2016 · 64(3): 437-438

    The RNA field is undergoing a renaissance, with a deluge of proteins being identified to bind RNA. Two reports now introduce proteome-wide approaches that identify the peptides that are crosslinked to RNA (Castello et al., 2016; He et al., 2016).

    PMID 27814488 DOI ↗

  22. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

    Molecular cell · 2016 · 64(2): 282-293

    RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down …

    PMID 27720645 DOI ↗

  23. Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts.

    Scientific reports · 2016 · 6: 30896

    Hypoplastic left heart syndrome (HLHS) is a fatal congenital heart disease in which the left side of the heart is underdeveloped, impairing the systemic circulation. Underdeveloped left ventricle exerts biomechanical stress on the right ventricle that can progress into heart …

    PMID 27485310 DOI ↗

  24. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.

    Nature communications · 2016 · 7: 12143

    The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs …

    PMID 27378374 DOI ↗

  25. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

    Nature methods · 2016 · 13(6): 508-14

    As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically …

    PMID 27018577 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

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

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

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

GSE80039 GSE · GEO

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

GSE77339 GSE · GEO

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

Homo sapiens · GPL17585

GSE232513 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)

Homo sapiens · GPL15520

GSE155726 GSE · GEO

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

Homo sapiens · GPL24676

GSE124023 GSE · GEO

DDX5 targets tissue specific RNAs to promote intestine tumorigenesis

Mus musculus · GPL21103

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)

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)

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)

GSE155708 Processing Pipeline

GSE155708 · 11 steps · RNA-Seq · code_examples

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

GSE155726 Processing Pipeline

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.