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17 results for “enhanced CLIP”

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  1. Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.

    Cell systems · 2026 : 101588

    RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated RBP resource integrates data from 92 additional RBPs (286 in total) profiled by enhanced CLIP (eCLIP), enabling comprehensive characterization of RNA elements within human K562 …

    PMID 42025161 DOI ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. 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 ↗

  8. 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 ↗

  9. Crosstalk between CRISPR-Cas9 and the human transcriptome.

    Nature communications · 2022 · 13(1): 1125

    CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …

    PMID 35236841 DOI ↗

  10. 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 ↗

  11. 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 ↗

  12. 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 ↗

  13. 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 ↗

  14. 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 ↗

  15. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

    Cell reports · 2016 · 15(3): 666-679

    Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad …

    PMID 27068461 DOI ↗

  16. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.

    Molecular cell · 2013 · 50(2): 223-35

    SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …

    PMID 23562324 DOI ↗

  17. High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.

    Journal of virology · 2012 · 86(1): 226-35

    Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely fine-tuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small …

    PMID 22013051 DOI ↗

Datasets 23

GSE315407 GSE · GEO

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

GPL20301, GPL24676, GPL34284

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

GSE137258 GSE · GEO

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

Homo sapiens · GPL20301

GSE210437 GSE · GEO

Enhanced CLIP (eCLIP) identified differential UPF1 binding sites in mouse neural progenitor cells (NPCs) samples

Mus musculus · GPL24247

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

GSE109423 GSE · GEO

A transcriptome-wide divergence in protein translation scales with LIN28B expression

Mus musculus · GPL20301

GSE167466 GSE · GEO

Crosstalk between CRISPR-Cas9 and the human transcriptome

Homo sapiens · GPL20301

GSE86035 GSE · GEO

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

Homo sapiens · GPL20301

GSE221870 GSE · GEO

HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence

Homo sapiens · GPL16791

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

GSE78509 GSE · GEO

Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival

Homo sapiens · GPL11154

GSE232597 GSE · GEO

Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]

Homo sapiens · GPL24676

GSE77633 GSE · GEO

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

Homo sapiens · GPL16791

GSE232598 GSE · GEO

Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [RNA-seq]

Homo sapiens · GPL24676

GSE78508 GSE · GEO

Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [RNA-Seq]

Homo sapiens · GPL11154

GSE213867 GSE · GEO

Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

Homo sapiens · GPL24676

GSE77634 GSE · GEO

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

Homo sapiens · GPL16791

GSE78507 GSE · GEO

Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [eCLIP-Seq]

Homo sapiens · GPL16791

GSE178259 GSE · GEO

Non-microRNA Binding Competitively Inhibits LIN28 Regulation

Mus musculus · GPL20301

GSE180686 GSE · GEO

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

Homo sapiens · GPL24676

GSE205536 GSE · GEO

Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

Homo sapiens · GPL18573

Analyses 12

GSE315347 eCLIP Data Processing

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 eCLIP Data Processing

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 eCLIP Data Processing

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)

GSE210437 Processing Pipeline

GSE210437 · 9 steps · RNA-Seq · code_examples

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)

GSE77339 Processing Pipeline

GSE77339 · 7 steps · GSE · code_examples

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). (2016)

GSE77629 Processing Pipeline

GSE77629 · 32 steps · OTHER · code_examples

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). (2016)

GSE77633 Processing Pipeline

GSE77633 · 7 steps · RIP-Seq · code_examples

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). (2016)

GSE77634 Processing Pipeline

GSE77634 · 7 steps · GSE · code_examples

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). (2016)

GSE78507 Processing Pipeline

GSE78507 · 33 steps · OTHER · code_examples

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. (2016)

GSE78508 Processing Pipeline

GSE78508 · 5 steps · RNA-Seq · code_examples

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. (2016)

GSE78509 Processing Pipeline

GSE78509 · 33 steps · GSE · code_examples

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. (2016)

GSE80039 Processing Pipeline

GSE80039 · 33 steps · OTHER · code_examples

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). (2016)