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13 results for “Cas9”
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
Cell · 2016 · 165(2): 488-96
RNA-programmed genome editing using CRISPR/Cas9 from Streptococcus pyogenes has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target RNA would allow alteration and imaging of endogenous RNA transcripts analogous to CRISPR/Cas-based genomic …
PMID 26997482 DOI ↗
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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 21
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
GPL24676
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Identifying differentially expressed genes in Zmat3 knockout cells
Mus musculus · GPL13112
RNA-targeting Cas9 corrects molecular and physiological features in pre-clinical model of myotonic dystrophy type 1
Mus musculus · GPL21103
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells (RNA-Seq)
Homo sapiens · GPL11154
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
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
Crosstalk between CRISPR-Cas9 and the human transcriptome
Homo sapiens · GPL20301
Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)
Mus musculus · GPL21626
Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9
Homo sapiens · GPL20301
A two-step in vivo CRISPR screen unveils pervasive RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a therapeutic target
Homo sapiens · GPL18460
Discovery and evaluation of CRISPR/Cas-mediated systems for site-specific RNA editing
Homo sapiens · GPL20301
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins
Homo sapiens · GPL20301
A role for alternative splicing in circadian control of insulin secretion and glucose homeostasis
Mus musculus · GPL19057
Analyses 6
GSE167466 · 18 steps · RIP-Seq · code_examples
Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)
GSE55887 · 5 steps · ChIP-Seq · code_examples
Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)
GSE145968 · 6 steps · OTHER · code_examples
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. (2021)
GSE152033 · 8 steps · RNA-Seq · code_examples
The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1. (2021)
GSE100943 · 7 steps · RNA-Seq · code_examples
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9. (2017)
GSE88722 · 11 steps · RIP-Seq · code_examples
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. (2017)