Search publications

20 results for “CRISPR”

Clear

  1. Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.

    Cancer research · 2025

    RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies, such as triple negative breast cancer (TNBC). Here, we employed both in vitro …

    PMID 41411621 DOI ↗

  2. Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.

    bioRxiv : the preprint server for biology · 2025

    RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …

    PMID 40655003 DOI ↗

  3. 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 ↗

  4. 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 ↗

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

    Blood cancer discovery · 2023 · 4(3): 180-207

    Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) …

    PMID 36763002 DOI ↗

  6. An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models.

    Nature neuroscience · 2023 · 26(1): 27-38

    Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAG<sup>EX</sup> …

    PMID 36510111 DOI ↗

  7. VPS13A and VPS13C Influence Lipid Droplet Abundance.

    Contact (Thousand Oaks (Ventura County, Calif.)) · 2022 · 5: 25152564221125613

    Lipid transfer proteins mediate the exchange of lipids between closely apposed membranes at organelle contact sites and play key roles in lipid metabolism, membrane homeostasis, and cellular signaling. A recently discovered novel family of lipid transfer proteins, which includes the …

    PMID 36147729 DOI ↗

  8. Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.

    Nature medicine · 2022 · 28(7): 1372-1376

    RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …

    PMID 35668177 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. 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 ↗

  11. A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.

    Blood advances · 2021 · 5(5): 1310-1323

    The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …

    PMID 33656539 DOI ↗

  12. The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.

    Nature biomedical engineering · 2021 · 5(2): 157-168

    Myotonic dystrophy type I (DM1) is a multisystemic autosomal-dominant inherited human disorder that is caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of DMPK. Toxic RNAs expressed from such repetitive sequences can be eliminated using CRISPR-mediated …

    PMID 32929188 DOI ↗

  13. Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.

    Molecular cell · 2020 · 80(3): 452-469.e9

    Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens …

    PMID 33157015 DOI ↗

  14. Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.

    Cell reports · 2020 · 33(5): 108350

    Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …

    PMID 33147453 DOI ↗

  15. 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 ↗

  16. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.

    Nature methods · 2020 · 17(6): 636-642

    Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and …

    PMID 32393832 DOI ↗

  17. 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 ↗

  18. RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering.

    Nature cell biology · 2020 · 22(2): 143-150

    Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, …

    PMID 32015437 DOI ↗

  19. Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.

    Cell · 2017 · 170(5): 899-912.e10

    Microsatellite repeat expansions in DNA produce pathogenic RNA species that cause dominantly inherited diseases such as myotonic dystrophy type 1 and 2 (DM1/2), Huntington's disease, and C9orf72-linked amyotrophic lateral sclerosis (C9-ALS). Means to target these repetitive RNAs are required for …

    PMID 28803727 DOI ↗

  20. Applications of Cas9 as an RNA-programmed RNA-binding protein.

    BioEssays : news and reviews in molecular, cellular and developmental biology · 2015 · 37(7): 732-9

    The Streptococcus pyogenes CRISPR-Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can …

    PMID 25880497 DOI ↗

Datasets 25+

GSE286096 GSE · GEO

Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq

Homo sapiens · 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

ENCSR226KWO ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04_B)

Homo sapiens

ENCSR000SKS ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPLP0. (RPLP0_BGHcLV03)

Homo sapiens

ENCSR637EFF ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against CEBPZ. (CEBPZ_BGKcLV02)

Homo sapiens

ENCSR380RRP ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGKcLV02)

Homo sapiens

ENCSR395HQT ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 30. (NT-D30_BGKcLV02)

Homo sapiens

ENCSR619GAS ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 41. (NT-D41_BGKcLV02)

Homo sapiens

ENCSR231RKU ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGHcLV03)

Homo sapiens

ENCSR384LKC ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGKcLV02)

Homo sapiens

ENCSR268XHM ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGHcLV03)

Homo sapiens

ENCSR105NML ENCSR · ENCODE

Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV03)

Homo sapiens

ENCSR163JUC ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV02)

Homo sapiens

ENCSR599NNK ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGHcLV03)

Homo sapiens

ENCSR721CNY ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 30. (DGCR8-D30_BGKcLV02)

Homo sapiens

ENCSR376GHG ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against FXR2. (FXR2_BGKcLV04)

Homo sapiens

ENCSR599PZD ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 22. (NT-D22_BGKcLV02)

Homo sapiens

ENCSR278NFF ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDC40. (CDC40_BGHcLV05)

Homo sapiens

ENCSR481WJH ENCSR · ENCODE

Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV05)

Homo sapiens

ENCSR991XFO ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against DROSHA. (DROSHA_BGHcLV05)

Homo sapiens

ENCSR845MNM ENCSR · ENCODE

RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGHcLV03)

Homo sapiens

ENCSR096WVE ENCSR · ENCODE

RNA-seq on K562 cells treated with a CRISPR gRNA against EIF3H. (EIF3H_BGKcLV04)

Homo sapiens

ENCSR828YEB ENCSR · ENCODE

Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04)

Homo sapiens

Showing first 25 dataset results.

Analyses 22

GSE280897 RNA-seq Data Processing

GSE280897 · 6 steps · RNA-seq · geo_data_processing

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)

GSE280898 eCLIP Data Processing

GSE280898 · 5 steps · eCLIP · geo_data_processing

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)

GSE280899 Processing Pipeline

GSE280899 · 6 steps · GSE · code_examples

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)

GSE313324 Data Processing

GSE313324 · 2 steps · geo_data_processing

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)

GSE217735 Processing Pipeline

GSE217735 · 2 steps · OTHER · code_examples

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

GSE214108 Processing Pipeline

GSE214108 · 3 steps · RNA-Seq · code_examples

An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. (2023)

GSE214109 Processing Pipeline

GSE214109 · 5 steps · RNA-Seq · code_examples

An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. (2023)

GSE214110 Processing Pipeline

GSE214110 · 3 steps · GSE · code_examples

An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. (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)

GSE167466 Processing Pipeline

GSE167466 · 18 steps · RIP-Seq · code_examples

Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)

GSE55887 Processing Pipeline

GSE55887 · 5 steps · ChIP-Seq · code_examples

Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)

GSE145968 Processing Pipeline

GSE145968 · 6 steps · OTHER · code_examples

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

GSE134971 Processing Pipeline

GSE134971 · 32 steps · RIP-Seq · code_examples

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)

GSE135012 Processing Pipeline

GSE135012 · 2 steps · RNA-Seq · code_examples

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)

GSE135300 Processing Pipeline

GSE135300 · 2 steps · RNA-Seq · code_examples

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)

GSE139815 Processing Pipeline

GSE139815 · 2 steps · OTHER · code_examples

Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. (2020)

GSE142307 Processing Pipeline

GSE142307 · 2 steps · ChIP-Seq · code_examples

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)

GSE152684 Processing Pipeline

GSE152684 · 8 steps · RNA-Seq · code_examples

Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing. (2020)

GSE68172 Processing Pipeline

GSE68172 · 2 steps · GSE · code_examples

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)

GSE88722 Processing Pipeline

GSE88722 · 11 steps · RIP-Seq · code_examples

CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. (2017)