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84 results for “mRNA”
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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 ↗
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Transcriptome regulation by PARP13 in basal and antiviral states in human cells.
iScience · 2024 · 27(4): 109251
The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including …
PMID 38495826 DOI ↗
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Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery.
Nucleic acids research · 2023 · 51(19): 10768-10781
Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). …
PMID 37739431 DOI ↗
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A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
bioRxiv : the preprint server for biology · 2023
Large-genome bacteriophages (jumbo phages) of the <i>Chimalliviridae</i> family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, …
PMID 37790334 DOI ↗
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A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
Nature communications · 2023 · 14(1): 5195
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that …
PMID 37673892 DOI ↗
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Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology · 2023 · 19(7): 825-836
Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants …
PMID 36864190 DOI ↗
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Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.
Nucleic acids research · 2023 · 51(12): 6461-6478
In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome …
PMID 37224531 DOI ↗
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Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.
bioRxiv : the preprint server for biology · 2023
Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) in diverse ribonucleoprotein complexes (RNPs) during distinct life-cycle stages for their processing and maturation. While substantial attention has focused on understanding RNA regulation by assigning proteins, particularly RBPs, to specific RNA substrates, …
PMID 37333282 DOI ↗
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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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Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.
Nature communications · 2023 · 14(1): 551
Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it …
PMID 36759613 DOI ↗
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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 ↗
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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 ↗
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AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay.
Molecular cell · 2022 · 82(15): 2779-2796.e10
Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in destroying faulty, disease-causing mRNAs and maintaining normal, physiologic mRNA abundance, additional effectors that regulate NMD activity in mammalian cells continue to be identified. Here, we describe a …
PMID 35675814 DOI ↗
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Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
Research square · 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 35313591 DOI ↗
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Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.
Cell reports · 2022 · 38(10): 110481
Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this …
PMID 35263585 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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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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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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Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.
Molecular cell · 2021 · 81(9): 1905-1919.e12
Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative …
PMID 33852893 DOI ↗
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DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.
Life science alliance · 2020 · 3(10)
Tumorigenesis in different segments of the intestinal tract involves tissue-specific oncogenic drivers. In the colon, complement component 3 (C3) activation is a major contributor to inflammation and malignancies. By contrast, tumorigenesis in the small intestine involves fatty acid-binding protein 1 …
PMID 32817263 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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Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development · 2020 · 34(19-20): 1373-1391
The N6-methyladenosine (m<sup>6</sup>A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader …
PMID 32943573 DOI ↗
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …
PMID 32848060 DOI ↗
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A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
Genes & development · 2020 · 34(15-16): 1089-1105
The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic …
PMID 32616519 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
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
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]
GPL24676
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
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
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
6239 · GPL19757
The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
6239 · GPL13657
Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
Mus musculus · GPL9115
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution
Homo sapiens · GPL15520
Showing first 25 dataset results.
Analyses 25+
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)
GSE199650 · 11 steps · RIP-Seq · code_examples
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor. (2025)
GSE278725 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279064 · 3 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279065 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE284636 · 10 steps · OTHER · code_examples
The IFIT2-IFIT3 antiviral complex targets short 5' untranslated regions on viral mRNAs for translation inhibition. (2025)
GSE193134 · 18 steps · RIP-Seq · code_examples
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. (2024)
GSE230717 · 9 steps · RIP-Seq · code_examples
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
GSE253825 · 1 step · RNA-Seq · code_examples
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
GSE206674 · 10 steps · eCLIP · geo_data_processing
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)
GSE230349 · 8 steps · OTHER · code_examples
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)
GSE123613 · 9 steps · OTHER · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE90963 · 35 steps · RNA-Seq · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE157467 · 6 steps · RNA-Seq · code_examples
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. (2021)
GSE117290 · 7 steps · OTHER · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117291 · 5 steps · RNA-Seq · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117293 · 5 steps · RNA-Seq · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117294 · 5 steps · GSE · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE124714 · 14 steps · OTHER · code_examples
The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics. (2020)
GSE98869 · 13 steps · RNA-Seq · code_examples
The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis. (2017)
GSE80664 · 9 steps · RNA-Seq · code_examples
Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes. (2016)
GSE66696 · 6 steps · GSE · code_examples
Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects. (2015)
Showing first 25 analysis results.