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30 results for “RNA metabolism”
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Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 signaling and hepatic inflammation in liver disease.
Molecular metabolism · 2026 : 102457
Liver diseases driven by metabolic dysfunction, inflammation, and fibrosis such as metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis (MASH), and acute liver injury represent a growing global health burden. The zinc finger protein Zfp697 (ZNF697 in humans) …
PMID 42875003 DOI ↗
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ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSC-derived models.
Nature communications · 2026 · 17(1)
RNA-binding proteins (RBPs) are key regulators of gene expression that shape cellular function in health and disease. However, the roles of RBPs in immune cells within the central nervous system (CNS) remain poorly understood. Here, we identify ARID5A as an …
PMID 42717200 DOI ↗
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RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis.
The Journal of clinical investigation · 2026
Metabolic syndrome and excessive alcohol consumption (MetALD) result in liver injury and fibrosis, which is driven by increased collagen production by activated hepatic stellate cells (HSCs). Our previous studies demonstrated that LARP6, an RNA-binding protein, may facilitate collagen production. However, …
PMID 41746718 DOI ↗
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Single-cell and isoform-specific translational profiling of the mouse brain.
Nature · 2026
The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …
PMID 41708856 DOI ↗
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Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.
bioRxiv : the preprint server for biology · 2025
Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope …
PMID 41279865 DOI ↗
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Phenylpyrazoles as Inhibitors of the m<sup>6</sup>A RNA-Binding Protein YTHDF2.
JACS Au · 2025 · 5(2): 618-630
The <i>N</i>6-methyladenosine (m<sup>6</sup>A) modification, which is the most common RNA modification in eukaryotes, is regulated by the "writer" methyltransferases, the "reader" m<sup>6</sup>A binding proteins, and the "eraser" demethylases. m<sup>6</sup>A plays a multifunctional role in physiological and pathological processes, regulating all …
PMID 40017738 DOI ↗
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LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.
bioRxiv : the preprint server for biology · 2025
Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality …
PMID 39868246 DOI ↗
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High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications · 2024 · 15(1): 7067
RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE (IN situ Sensitive Capture of RNA-protein Interactions in Biological Environments), circumventing the challenges through …
PMID 39152130 DOI ↗
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HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.
Molecular cell · 2023 · 83(14): 2595-2611.e11
RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier …
PMID 37421941 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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RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.
Nucleic acids research · 2023 · 51(D1): D1549-D1557
RNA binding proteins (RBPs) are central regulators of gene expression implicated in all facets of RNA metabolism. As such, they play key roles in cellular physiology and disease etiology. Since different steps of post-transcriptional gene expression tend to occur in …
PMID 36321651 DOI ↗
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The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.
Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53
Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …
PMID 35378331 DOI ↗
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RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
Gut · 2022 · 71(9): 1790-1802
Tuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in …
PMID 34853057 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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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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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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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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Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions.
Neuron · 2019 · 102(2): 294-320
RNA binding proteins are critical to the maintenance of the transcriptome via controlled regulation of RNA processing and transport. Alterations of these proteins impact multiple steps of the RNA life cycle resulting in various molecular phenotypes such as aberrant RNA …
PMID 30998900 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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Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.
Nucleic acids research · 2017 · 45(21): 12509-12528
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, …
PMID 29069457 DOI ↗
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Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.
Cell metabolism · 2017 · 25(5): 1160-1175.e11
Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of …
PMID 28467932 DOI ↗
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Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Neuron · 2016 · 92(4): 780-795
HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …
PMID 27773581 DOI ↗
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SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.
Molecular cell · 2016 · 64(2): 282-293
RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down …
PMID 27720645 DOI ↗
Datasets 25
ALS implicated protein TDP-43 sustains levels of STMN2 a mediator of motor neuron growth and repair
Homo sapiens · GPL11154
Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration
Mus musculus · GPL21103
Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death
Mus musculus · GPL21103
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Homo sapiens · GPL15520
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
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]
Mus musculus · GPL30172
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]
Homo sapiens · GPL24676
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]
Mus musculus · GPL24676
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]
Homo sapiens · GPL24676
Distinct and shared molecular targets and functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [CLIP-Seq]
Mus musculus · GPL13112
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_human]
Homo sapiens · GPL11154
SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.
Homo sapiens · GPL20301
HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence
Homo sapiens · GPL16791
Spatial transcriptomic studies of the small intestine from WT and DDX5â³IEC (KO) mice
Mus musculus · GPL24247
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_mouse]
Mus musculus · GPL13112
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [array]
Mus musculus · GPL13185
The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism
Thermus thermophilus HB27 · GPL27012
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_Stability]
Homo sapiens · GPL11154
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]
Homo sapiens · GPL34382
Non-microRNA Binding Competitively Inhibits LIN28 Regulation
Mus musculus · GPL20301
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]"
Homo sapiens · GPL28352
Overriding FUS autoregulation triggers gain-of-toxic dysfunctions in autophagy-lysosome axis and RNA metabolism
Mus musculus · GPL21103
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]
Homo sapiens · GPL30173
Analyses 5
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE276986 · 1 step · RNA-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE277082 · 2 steps · RNA-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE135435 · 29 steps · RIP-Seq · code_examples
The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism. (2020)
GSE125125 · 3 steps · RNA-Seq · code_examples
Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis. (2019)