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51 results for “RBP”

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  1. 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 ↗

  2. Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.

    Bioinformatics advances · 2022 · 2(1): vbac083

    Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often indicative of its molecular function in RNA processing. As an example, the binding sites …

    PMID 36388152 DOI ↗

  3. Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.

    Acta neuropathologica · 2022 · 144(3): 413-435

    Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by aberrant alternative splicing (AS). Nuclear loss and cytoplasmic accumulation of the splicing factor TDP-43 in motor neurons (MN) are hallmarks of ALS at late stages of the disease. However, it …

    PMID 35778567 DOI ↗

  4. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

    Nature protocols · 2022 · 17(5): 1223-1265

    Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which …

    PMID 35322209 DOI ↗

  5. Non-microRNA binding competitively inhibits LIN28 regulation.

    Cell reports · 2021 · 36(6): 109517

    RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct …

    PMID 34380031 DOI ↗

  6. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.

    Molecular cell · 2021 · 81(15): 3048-3064.e9

    RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in …

    PMID 34216543 DOI ↗

  7. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

    Nature methods · 2021 · 18(5): 507-519

    RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …

    PMID 33963355 DOI ↗

  8. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  9. Large-scale tethered function assays identify factors that regulate mRNA stability and translation.

    Nature structural & molecular biology · 2020 · 27(10): 989-1000

    The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. Here, we develop a plasmid resource of 690 human RBPs that we subject to luciferase-based 3'-untranslated-region …

    PMID 32807991 DOI ↗

  10. A large-scale binding and functional map of human RNA-binding proteins.

    Nature · 2020 · 583(7818): 711-719

    Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …

    PMID 32728246 DOI ↗

  11. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.

    Nature cancer · 2020 · 1(4): 410-422

    Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …

    PMID 34109316 DOI ↗

  12. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Genome biology · 2020 · 21(1): 90

    A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

    PMID 32252787 DOI ↗

  13. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

    Cell · 2019 · 178(1): 107-121.e18

    Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …

    PMID 31251911 DOI ↗

  14. 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 ↗

  15. 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 ↗

  16. 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 ↗

  17. 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 ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. 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 ↗

  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. 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 ↗

  24. 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 ↗

  25. Resources for the Comprehensive Discovery of Functional RNA Elements.

    Molecular cell · 2016 · 61(6): 903-13

    Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck …

    PMID 26990993 DOI ↗

Datasets 25+

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

GSE227455 GSE · GEO

RBP Footprint Grand Challenge: An evaluation of novel computational approaches to RNA-binding protein target prediction from structural data

Homo sapiens · GPL20301

GSE145805 GSE · GEO

RNA secondary structome of different cell lines

Homo sapiens, Mus musculus · GPL20795, GPL21273

GSE302649 GSE · GEO

Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]

GPL18573

GSE302648 GSE · GEO

Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]

GPL18573

GSE290248 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]

Homo sapiens · Illumina

GSE290282 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]

Homo sapiens · Illumina

GSE290281 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]

Homo sapiens · Illumina

GSE315406 GSE · GEO

Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]

GPL20301, GPL24676, GPL34284

GSE315347 GSE · GEO

Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]

GPL20301, GPL24676

GSE313324 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]

GPL24676

GSE280898 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]

GPL24676

GSE280897 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]

GPL24676

ENCSR752YLF ENCSR · ENCODE

eCLIP control experiment on K562 against SERBP1

Homo sapiens

ENCSR121GQH ENCSR · ENCODE

eCLIP experiment on K562 against SERBP1

Homo sapiens

ENCSR925RNE ENCSR · ENCODE

shRNA knockdown against SERBP1 in K562 cells followed by RNA-seq. (SERBP1_BGKLV19)

Homo sapiens

ENCSR230ORC ENCSR · ENCODE

shRNA knockdown against CIRBP in HepG2 cells followed by RNA-seq. (CIRBP-BGHLV12)

Homo sapiens

ENCSR056QEW ENCSR · ENCODE

shRNA knockdown against CIRBP in K562 cells followed by RNA-seq. (CIRBP-LV11)

Homo sapiens

ENCSR820ROH ENCSR · ENCODE

shRNA knockdown against SERBP1 in HepG2 cells followed by RNA-seq. (SERBP1_BGHLV16)

Homo sapiens

ENCSR452KAP ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGKcLV11)

Homo sapiens

ENCSR010XIH ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGHcLV12)

Homo sapiens

GSE137258 GSE · GEO

Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer

Homo sapiens · GPL20301

Showing first 25 dataset results.

Analyses 9

GSE227455 eCLIP Data Processing

GSE227455 · 7 steps · eCLIP · geo_data_processing

Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)

GSE232513 Data Processing

GSE232513 · 3 steps · geo_data_processing

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. (2024)

GSE232514 RNA-seq Data Processing

GSE232514 · 5 steps · RNA-seq · geo_data_processing

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. (2024)

GSE232515 Data Processing

GSE232515 · 4 steps · geo_data_processing

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. (2024)

GSE232518 Data Processing

GSE232518 · 3 steps · geo_data_processing

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. (2024)

GSE232519 Data Processing

GSE232519 · 3 steps · geo_data_processing

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. (2024)

GSE232520 Processing Pipeline

GSE232520 · 3 steps · GSE · code_examples

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

GSE145968 Processing Pipeline

GSE145968 · 6 steps · OTHER · code_examples

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

GSE51556 Processing Pipeline

GSE51556 · 14 steps · RNA-Seq · code_examples

The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome. (2014)