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229 results for “RNA”
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Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery · 2022 · 12(3): 836-855
Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …
PMID 34620690 DOI ↗
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Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis.
Cellular and molecular life sciences : CMLS · 2022 · 79(3): 147
In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we …
PMID 35195778 DOI ↗
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Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
bioRxiv : the preprint server for biology · 2022
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …
PMID 35233578 DOI ↗
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Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Molecular cell · 2022 · 82(3): 645-659.e9
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …
PMID 35051350 DOI ↗
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A multi-scale map of cell structure fusing protein images and interactions.
Nature · 2021 · 600(7889): 536-542
The cell is a multi-scale structure with modular organization across at least four orders of magnitude<sup>1</sup>. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are …
PMID 34819669 DOI ↗
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Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs.
mSystems · 2021 · 6(6): e0113621
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with coronavirus disease 2019 (COVID-19) and inform appropriate infection mitigation responses. Research groups have reported detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces …
PMID 34726486 DOI ↗
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SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp.
medRxiv : the preprint server for health sciences · 2021
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can …
PMID 34909793 DOI ↗
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Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
Nature communications · 2021 · 12(1): 6324
Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart …
PMID 34732726 DOI ↗
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fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
STAR protocols · 2021 · 2(3): 100762
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein …
PMID 34485935 DOI ↗
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Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.
Cell reports · 2021 · 36(10): 109685
Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). …
PMID 34496257 DOI ↗
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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 ↗
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Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports · 2021 · 36(6): 109517
RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct …
PMID 34380031 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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Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence.
bioRxiv : the preprint server for biology · 2021
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks …
PMID 34312621 DOI ↗
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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods · 2021 · 18(5): 507-519
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …
PMID 33963355 DOI ↗
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S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD.
Proceedings of the National Academy of Sciences of the United States of America · 2021 · 118(11)
Rare genetic mutations result in aggregation and spreading of cognate proteins in neurodegenerative disorders; however, in the absence of mutation (i.e., in the vast majority of "sporadic" cases), mechanisms for protein misfolding/aggregation remain largely unknown. Here, we show environmentally induced …
PMID 33692125 DOI ↗
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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 ↗
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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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Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.
Critical reviews in biochemistry and molecular biology · 2021 · 56(1): 31-53
Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG<sub>50-3,500</sub> in <i>DMPK</i>; DM2, CCTG<sub>75-11,000</sub> in …
PMID 33172304 DOI ↗
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Author Correction: A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2021 · 589(7842): E5
PMID 33402748 DOI ↗
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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 ↗
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Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
Genome medicine · 2020 · 12(1): 112
Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …
PMID 33287884 DOI ↗
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Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
Molecular cell · 2020 · 80(5): 903-914.e8
Discovering the interaction mechanism and location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four …
PMID 33242392 DOI ↗
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The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.
RNA (New York, N.Y.) · 2020 · 26(11): 1557-1574
RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate …
PMID 32669294 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 ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]
Homo sapiens · Illumina
RBP Footprint Grand Challenge: An evaluation of novel computational approaches to RNA-binding protein target prediction from structural data
Homo sapiens · GPL20301
RNA secondary structome of different cell lines
Homo sapiens, Mus musculus · GPL20795, GPL21273
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]
Homo sapiens · Illumina
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]
GPL21626
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE)
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Showing first 25 dataset results.
Analyses 25+
GSE244832 · 9 steps · scRNA-seq · geo_data_processing
RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis. (2026)
GSE275091 · 1 step · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE275133 · 2 steps · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE290248 · 1 step · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290281 · 1 step · eCLIP · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290282 · 3 steps · RNA-seq · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE299099 · 3 steps · RNA-Seq · code_examples
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)
GSE302648 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302649 · 11 steps · eCLIP · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302651 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE314058 · 7 steps · scRNA-seq · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE314059 · 4 steps · scRNA-seq · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
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 · 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 · 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)
GSE315443 · 2 steps · scRNA-seq · geo_data_processing
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. (2026)
GSE125970 · 4 steps · RNA-Seq · code_examples
Stratification of enterochromaffin cells by single-cell expression analysis. (2025)
GSE137810 · 8 steps · RNA-seq · geo_data_processing
Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in … (2025)
GSE145805 · 7 steps · SHAPE-seq · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE199650 · 11 steps · RIP-Seq · code_examples
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor. (2025)
GSE227455 · 7 steps · eCLIP · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE228444 · 4 steps · OTHER · code_examples
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. (2025)
GSE247544 · 3 steps · scRNA-seq · geo_data_processing
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner. (2025)
GSE262542 · 4 steps · RNA-Seq · code_examples
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
Showing first 25 analysis results.