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50 results for “translation”
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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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Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023 · 3(6): 100317
Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts …
PMID 37388912 DOI ↗
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The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
Nature communications · 2022 · 13(1): 3833
Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival. Here, we demonstrate that upregulation of the splicing factor, RBM17 preferentially marks and sustains LSCs and …
PMID 35781533 DOI ↗
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MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
Science translational medicine · 2022 · 14(651): eabn2375
Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (<i>DMPK</i>) gene. Despite its prominence as the most common adult-onset muscular dystrophy, …
PMID 35767654 DOI ↗
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Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.
Nucleic acids research · 2022 · 50(8): 4685-4702
The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved …
PMID 35438785 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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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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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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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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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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AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
Genes & development · 2020 · 34(19-20): 1330-1344
Despite being the frontline therapy for type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of …
PMID 32912901 DOI ↗
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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 ↗
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Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.
Circulation · 2020 · 142(4): 365-379
Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth …
PMID 32393053 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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RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering.
Nature cell biology · 2020 · 22(2): 143-150
Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, …
PMID 32015437 DOI ↗
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The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019 · 25(5): 622-638.e13
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells …
PMID 31588046 DOI ↗
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A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell · 2019 · 73(2): 304-313.e3
LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …
PMID 30527666 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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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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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 ↗
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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 ↗
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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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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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The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression.
Cell · 2007 · 130(1): 179-91
Proper neuronal function and several forms of synaptic plasticity are highly dependent on precise control of mRNA translation, particularly in dendrites. We find that eIF4AIII, a core exon junction complex (EJC) component loaded onto mRNAs by pre-mRNA splicing, is associated …
PMID 17632064 DOI ↗
Datasets 25+
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
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]
GPL20301, GPL24676
Single cell and isoform-specific translational profiling of the mouse brain
GPL24247, GPL34475, GPL34585
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
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 mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
6239 · GPL13657
Active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells
Homo sapiens · GPL16791
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls
Homo sapiens · GPL20301
ALS implicated protein TDP-43 sustains levels of STMN2 a mediator of motor neuron growth and repair
Homo sapiens · GPL11154
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
Homo sapiens · GPL24676
SerRS mediates translational readthrough of through engagement of the selenocysteine incorporation machinery
Homo sapiens · GPL30173
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
Showing first 25 dataset results.
Analyses 25+
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)
GSE276504 · 1 step · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (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)
GSE314176 · 1 step · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
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)
GSE255844 · 5 steps · RNA-Seq · code_examples
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. (2024)
GSE138197 · 6 steps · RNA-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE202881 · 8 steps · OTHER · code_examples
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. (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)
GSE213867 · 5 steps · RNA-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE224998 · 6 steps · RIP-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE230349 · 8 steps · OTHER · code_examples
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)
GSE126263 · 25 steps · RIP-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE126337 · 3 steps · RNA-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE134597 · 4 steps · RNA-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE195494 · 5 steps · RIP-Seq · code_examples
Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. (2022)
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)
Showing first 25 analysis results.