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18 results for “genome editing”

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  1. MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.

    Neurobiology of disease · 2026 · 221: 107305

    Myotonic dystrophy type 1 (DM1) arises from toxic CUG-expanded DMPK transcripts that sequester Muscleblind-like (MBNL) proteins, yet how this molecular lesion perturbs brain development in congenital DM1 (CDM) remains unknown. Here, we identify an unanticipated developmental role for MBNL2 in …

    PMID 41644016 DOI ↗

  2. Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.

    Genome research · 2024 · 34(11): 2012-2024

    Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …

    PMID 38906680 DOI ↗

  3. 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 ↗

  4. Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors.

    Frontiers in genome editing · 2022 · 4: 923718

    Base editors (BEs) are genome editing agents that install point mutations with high efficiency and specificity. Due to their reliance on uracil and inosine DNA damage intermediates (rather than double-strand DNA breaks, or DSBs), it has been hypothesized that BEs …

    PMID 35910415 DOI ↗

  5. 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 ↗

  6. Reintroduction of the archaic variant of <i>NOVA1</i> in cortical organoids alters neurodevelopment.

    Science (New York, N.Y.) · 2021 · 371(6530)

    The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (<i>NOVA1</i>) plays a key role in neural development and function. <i>NOVA1</i> also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance …

    PMID 33574182 DOI ↗

  7. Base editing: advances and therapeutic opportunities.

    Nature reviews. Drug discovery · 2020 · 19(12): 839-859

    Base editing - the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells - is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due …

    PMID 33077937 DOI ↗

  8. 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 ↗

  9. 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 ↗

  10. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

    Nature communications · 2020 · 11(1): 550

    Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that …

    PMID 31992716 DOI ↗

  11. Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells.

    Angewandte Chemie (International ed. in English) · 2019 · 58(44): 15646-15649

    The scarcity of effective means to deliver functional proteins to living cells is a central problem in biotechnology and medicine. Herein, we report the efficient delivery of an active DNA-modifying enzyme to human stem cells through high-density cell penetrating peptide …

    PMID 31404473 DOI ↗

  12. Widespread RNA editing dysregulation in brains from autistic individuals.

    Nature neuroscience · 2019 · 22(1): 25-36

    Transcriptomic analyses of postmortem brains have begun to elucidate molecular abnormalities in autism spectrum disorder (ASD). However, a crucial pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here we profiled global patterns …

    PMID 30559470 DOI ↗

  13. 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 ↗

  14. 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 ↗

  15. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.

    Genome medicine · 2016 · 8(1): 94

    Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human …

    PMID 27655340 DOI ↗

  16. 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 ↗

  17. 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 ↗

  18. Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.

    PLoS genetics · 2015 · 11(4): e1005123

    Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative …

    PMID 25835743 DOI ↗

Datasets 11

GSE286096 GSE · GEO

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

Homo sapiens · GPL24676

GSE55887 GSE · GEO

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

Homo sapiens · GPL15520

GSE153279 GSE · GEO

Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq, Cut&Run]

Homo sapiens · GPL24676

GSE153264 GSE · GEO

Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [RNA-seq]

Homo sapiens · GPL18573

GSE122069 GSE · GEO

Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

Homo sapiens · GPL20301

GSE176060 GSE · GEO

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (eCLIP)

Homo sapiens · GPL16791

GSE175886 GSE · GEO

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing

Homo sapiens · GPL16791

GSE164666 GSE · GEO

Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor mutant neoplasms

Homo sapiens · GPL20301

GSE176045 GSE · GEO

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (WTB RNA-Seq)

Homo sapiens · GPL20301

GSE113947 GSE · GEO

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing [RNA-Seq]

Homo sapiens · GPL16791

GSE175885 GSE · GEO

RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (RiboMinus RNA-Seq)

Homo sapiens · GPL16791

Analyses 5

GSE113947 Processing Pipeline

GSE113947 · 4 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE175885 Processing Pipeline

GSE175885 · 5 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE175886 Processing Pipeline

GSE175886 · 4 steps · GSE · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE176045 Processing Pipeline

GSE176045 · 4 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE176060 Processing Pipeline

GSE176060 · 3 steps · OTHER · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)