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29 results for “RNA editing”

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  1. ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing.

    bioRxiv : the preprint server for biology · 2026

    Chemical proteomics has identified covalent ligands targeting cysteine residues across many hundreds of human proteins. The functional effects of these liganding events, however, remain challenging to assign at scale. Here we describe ESCAPE (Endogenous Site-specific Competition Assays using Prime Editors), …

    PMID 42619774 DOI ↗

  2. High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay.

    Cell reports · 2026 · 45(5): 117348

    The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA turnover through interactions with RNA-binding proteins (RBPs) and the microRNA (miRNA)-induced silencing complex. However, identifying which RBP- and miRNA-associated RNA elements recruit CCR4-NOT remains challenging, due in part …

    PMID 42154591 DOI ↗

  3. 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 ↗

  4. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.

    Nature chemical biology · 2025

    Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …

    PMID 40968292 DOI ↗

  5. Strategies for programmable manipulation of alternative splicing.

    Current opinion in genetics & development · 2024 · 89: 102272

    Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …

    PMID 39471777 DOI ↗

  6. 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 ↗

  7. Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.

    bioRxiv : the preprint server for biology · 2024

    Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …

    PMID 38915553 DOI ↗

  8. 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 ↗

  9. FLARE: a fast and flexible workflow for identifying RNA editing foci.

    BMC bioinformatics · 2023 · 24(1): 370

    Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable …

    PMID 37784060 DOI ↗

  10. 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 ↗

  11. Engineered U1 snRNAs to modulate alternatively spliced exons.

    Methods (San Diego, Calif.) · 2022 · 205: 140-148

    Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

    PMID 35764245 DOI ↗

  12. 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 ↗

  13. 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 ↗

  14. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.

    The Journal of experimental medicine · 2021 · 218(9)

    Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA …

    PMID 34297039 DOI ↗

  15. 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 ↗

  16. 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 ↗

  17. 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 ↗

  18. Regulation of RNA editing by RNA-binding proteins in human cells.

    Communications biology · 2019 · 2: 19

    Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of …

    PMID 30652130 DOI ↗

  19. Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.

    Cell reports · 2019 · 27(4): 1244-1253.e4

    A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …

    PMID 31018137 DOI ↗

  20. 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 ↗

  21. Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.

    Nucleic acids research · 2018 · 46(14): 7323-7338

    Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of …

    PMID 29733375 DOI ↗

  22. The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.

    eLife · 2017 · 6

    ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …

    PMID 28925356 DOI ↗

  23. 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 ↗

  24. 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 ↗

  25. 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 ↗

Datasets 18

GSE98869 GSE · GEO

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

6239 · GPL19757

GSE240014 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]

Mus musculus · GPL24247

GSE263371 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]

Mus musculus · GPL30172

GSE166404 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens · GPL28352

GSE107896 GSE · GEO

Widespread RNA editing dysregulation in Autism Spectrum Disorders

Homo sapiens · GPL20301

GSE167466 GSE · GEO

Crosstalk between CRISPR-Cas9 and the human transcriptome

Homo sapiens · GPL20301

GSE155708 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens · GPL24106

GSE113193 GSE · GEO

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9

Homo sapiens · GPL18573

GSE107895 GSE · GEO

Widespread RNA editing dysregulation in Autism Spectrum Disorders [eCLIP-seq]

Homo sapiens · GPL20301

GSE117776 GSE · GEO

Widespread RNA editing dysregulation in Autism Spectrum Disorders II

Homo sapiens · GPL11154

GSE215252 GSE · GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Homo sapiens · GPL24676

GSE263870 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]

Homo sapiens · GPL34382

GSE107867 GSE · GEO

Widespread RNA editing dysregulation in Autism Spectrum Disorders [RNA-Seq]

Homo sapiens · GPL20301

GSE152684 GSE · GEO

Discovery and evaluation of CRISPR/Cas-mediated systems for site-specific RNA editing

Homo sapiens · GPL20301

GSE110701 GSE · GEO

Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing

6239 · GPL18245

GSE240325 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]"

Homo sapiens · GPL28352

GSE248461 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]

Homo sapiens · GPL30173

GSE51556 GSE · GEO

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

6239 · GPL9269

Analyses 10

GSE215252 Processing Pipeline

GSE215252 · 5 steps · RNA-Seq · code_examples

FLARE: a fast and flexible workflow for identifying RNA editing foci. (2023)

GSE152684 Processing Pipeline

GSE152684 · 8 steps · RNA-Seq · code_examples

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

GSE107867 Processing Pipeline

GSE107867 · 14 steps · RNA-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE107895 Processing Pipeline

GSE107895 · 32 steps · RIP-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE107896 Processing Pipeline

GSE107896 · 14 steps · GSE · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE117776 Processing Pipeline

GSE117776 · 14 steps · RNA-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE51264 Processing Pipeline

GSE51264 · 5 steps · RNA-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE59288 Processing Pipeline

GSE59288 · 3 steps · RNA-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

GSE113193 Processing Pipeline

GSE113193 · 32 steps · OTHER · code_examples

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9. (2018)

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)