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84 results for “mRNA”
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Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Genome biology · 2020 · 21(1): 90
A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …
PMID 32252787 DOI ↗
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The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.
Current biology : CB · 2020 · 30(5): 865-876.e7
mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA …
PMID 31983639 DOI ↗
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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 ↗
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Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Nature communications · 2019 · 10(1): 1338
Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …
PMID 30902979 DOI ↗
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Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
eLife · 2019 · 8
Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked …
PMID 30747709 DOI ↗
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Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica · 2018 · 136(3): 405-423
Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …
PMID 29881994 DOI ↗
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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 ↗
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Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas.
Bioconjugate chemistry · 2018 · 29(1): 126-135
The intracellular delivery of synthetic nucleic acids represents a major challenge in biotechnology and in biomedicine. Methods to deliver short, double-stranded RNA to living cells are of particular interest because of the potential to engage the RNA interference machinery and …
PMID 29286237 DOI ↗
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Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology · 2017 · 24(12): 1057-1063
Poly(A) tails are important elements in mRNA translation and stability, although recent genome-wide studies have concluded that poly(A) tail length is generally not associated with translational efficiency in nonembryonic cells. To investigate whether poly(A) tail size might be coupled to …
PMID 29106412 DOI ↗
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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 ↗
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Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.
Nature genetics · 2017 · 49(3): 457-464
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg<sup>2+</sup>-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) …
PMID 28092684 DOI ↗
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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 ↗
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Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts.
Scientific reports · 2016 · 6: 30896
Hypoplastic left heart syndrome (HLHS) is a fatal congenital heart disease in which the left side of the heart is underdeveloped, impairing the systemic circulation. Underdeveloped left ventricle exerts biomechanical stress on the right ventricle that can progress into heart …
PMID 27485310 DOI ↗
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Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Cell reports · 2016 · 15(3): 666-679
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad …
PMID 27068461 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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The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.
Annual review of biochemistry · 2015 · 84: 325-54
Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind …
PMID 25784054 DOI ↗
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Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity.
Molecular cell · 2015 · 59(3): 413-25
RNA quality-control pathways get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the adenosine triphosphatase (ATPase) cycle of the SF1 helicase Upf1 is required for …
PMID 26253027 DOI ↗
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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 ↗
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Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles.
Journal of the American Chemical Society · 2014 · 136(21): 7615-8
We present an untemplated, single-component antisense oligonucleotide delivery system capable of regulating mRNA abundance in live human cells. While most approaches to nucleic acid delivery rely on secondary carriers and complex multicomponent charge-neutralizing formulations, we demonstrate efficient delivery using a …
PMID 24827740 DOI ↗
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Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nature structural & molecular biology · 2013 · 20(12): 1434-42
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …
PMID 24213538 DOI ↗
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Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases.
Frontiers in neuroscience · 2012 · 6: 144
Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the …
PMID 23060744 DOI ↗
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LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 DOI ↗
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Misregulated RNA processing in amyotrophic lateral sclerosis.
Brain research · 2012 · 1462: 3-15
Amyotrophic lateral sclerosis (ALS) research is undergoing an era of unprecedented discoveries with the identification of new genes as major genetic causes of this disease. These discoveries reinforce the genetic, clinical and pathological overlap between ALS and frontotemporal lobar degeneration …
PMID 22444279 DOI ↗
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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 DOI ↗
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Comprehensive identification of miRNA target sites in live animals.
Methods in molecular biology (Clifton, N.J.) · 2011 · 732: 169-85
MicroRNAs (miRNAs) are small RNA molecules that posttranscriptionally regulate the expression of protein-coding genes. The mature miRNAs are loaded into Argonaute-containing protein complexes (miRISC, miRNA Induced S ilencing Complex), and guide these complexes to the 3' UTR of targeted mRNA …
PMID 21431713 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.