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144 results for “Regulation”
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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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The YTHDF proteins modulate Alzheimer's disease-associated brain gene signatures.
Molecular neurodegeneration · 2026 · 21(1)
Gene signatures of Alzheimer's disease (AD) brains reflect the output of a complex interplay of genetic, epigenetic, epi-transcriptomic, and post-transcriptional regulations. To nominate candidate factors modulating these signatures, we developed a machine learning model to integrate cellular and molecular features …
PMID 42811341 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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Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response.
bioRxiv : the preprint server for biology · 2026
RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment into Ebola virus condensates under basal and IFN-stimulated states. We …
PMID 42465340 DOI ↗
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Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection.
Molecular cell · 2026
Alternative polyadenylation (APA) generates transcript isoforms with distinct 3' ends, yet the repertoire of its protein regulators remains poorly defined. Using a large-scale tethered function screen, we profiled 879 human RNA-binding proteins (RBPs) and identified 63 high-confidence activators of poly(A) …
PMID 42361791 DOI ↗
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High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay.
Cell reports · 2026 · 45(5): 117348
The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA turnover through interactions with RNA-binding proteins (RBPs) and the microRNA (miRNA)-induced silencing complex. However, identifying which RBP- and miRNA-associated RNA elements recruit CCR4-NOT remains challenging, due in part …
PMID 42154591 DOI ↗
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Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
RNA (New York, N.Y.) · 2026 · 32(5): 635-653
Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. …
PMID 41535088 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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MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.
Neurobiology of disease · 2026 · 221: 107305
Myotonic dystrophy type 1 (DM1) arises from toxic CUG-expanded DMPK transcripts that sequester Muscleblind-like (MBNL) proteins, yet how this molecular lesion perturbs brain development in congenital DM1 (CDM) remains unknown. Here, we identify an unanticipated developmental role for MBNL2 in …
PMID 41644016 DOI ↗
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Identification of RBP binding sites using RNA deaminases.
Methods in enzymology · 2025 · 713: 287-297
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly …
PMID 40250958 DOI ↗
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Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies, such as triple negative breast cancer (TNBC). Here, we employed both in vitro …
PMID 41411621 DOI ↗
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Dosage-sensitive <i>RBFOX2</i> autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome.
bioRxiv : the preprint server for biology · 2025
Haploinsufficiency of the RNA splicing regulator, <i>RBFOX2</i> , is linked to congenital heart disease (CHD), yet its pathogenic mechanisms remain unclear. Here, we demonstrate that RBFOX2 is essential for progressing cardiomyocyte (CM) differentiation by shifting exon usage profiles to more …
PMID 41280054 DOI ↗
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A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies.
bioRxiv : the preprint server for biology · 2025
Variants in ion channel genes are common causes of pediatric epilepsy, often leading to intractable seizures, developmental delay and other comorbidities, which increases risk of death. Pathogenic variants in the <i>SCN8A</i> gene, which encodes a voltage-gated sodium channel critical for …
PMID 41278710 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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Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.
bioRxiv : the preprint server for biology · 2025
The <i>AUTS2</i> gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2's chromatin-and RNA-related functions are recognized, its direct binding to RNA in human neural progenitors has not been …
PMID 41278797 DOI ↗
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Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites.
bioRxiv : the preprint server for biology · 2025
The global impact of the COVID-19 pandemic underscores the critical need for a comprehensive understanding of SARS-CoV-2 replication mechanisms. While the central roles of the RNA dependent RNA polymerase (NSP12), primase protein (NSP8), and nucleocapsid protein (N) in the virus …
PMID 40501555 DOI ↗
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Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …
PMID 40655003 DOI ↗
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Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner.
Science immunology · 2025 · 10(106): eadn1894
Tissue-resident memory CD8 T (T<sub>RM</sub>) cells serve as a front-line defense against microbial pathogens in barrier and mucosal tissues. Accurately predicting the roles of tissue-specific transcription factors (TFs) that regulate T<sub>RM</sub> biology remains a challenge. Here, by applying integrated transcriptomic …
PMID 40215325 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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Decoding protein-RNA interactions using CLIP-based methodologies.
Nature reviews. Genetics · 2024 · 25(12): 879-895
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding …
PMID 38982239 DOI ↗
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Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
Nature communications · 2024 · 15(1): 10796
Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal …
PMID 39737952 DOI ↗
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Localized synthesis of molecular chaperones sustains neuronal proteostasis.
bioRxiv : the preprint server for biology · 2024
Neurons are challenged to maintain proteostasis in neuronal projections, particularly with the physiological stress at synapses to support intercellular communication underlying important functions such as memory and movement control. Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted …
PMID 37873158 DOI ↗
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Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.
Molecular cell · 2024 · 84(19): 3826-3842.e8
RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and …
PMID 39303722 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
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 (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
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
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
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner
GPL24247
Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes
Mus musculus · GPL9250
Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
Mus musculus · GPL9115
Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons
Mus musculus · GPL5188
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
Alternative polyadenylation mediates genetic regulation of gene expression
Homo sapiens · GPL18573
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
Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells
Homo sapiens · GPL16791
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Homo sapiens · GPL15520
Showing first 25 dataset results.
Analyses 25+
GSE104949 · 9 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE106493 · 4 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE215251 · 5 steps · GSE · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE249245 · 5 steps · OTHER · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE249246 · 3 steps · RIP-Seq · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE249247 · 5 steps · GSE · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE268963 · 1 step · OTHER · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE277047 · 2 steps · OTHER · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE277160 · 8 steps · RNA-Seq · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE277161 · 4 steps · RNA-Seq · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE138197 · 6 steps · RNA-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE56504 · 2 steps · GSE · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE113947 · 4 steps · RNA-Seq · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE118347 · 10 steps · OTHER · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE175885 · 5 steps · RNA-Seq · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE175886 · 4 steps · GSE · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE176045 · 4 steps · RNA-Seq · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE176060 · 3 steps · OTHER · code_examples
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE178259 · 6 steps · RNA-Seq · code_examples
Non-microRNA binding competitively inhibits LIN28 regulation. (2021)
GSE157048 · 14 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157049 · 14 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157050 · 6 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157051 · 14 steps · GSE · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE55727 · 5 steps · RNA-Seq · code_examples
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. (2020)
GSE107867 · 14 steps · RNA-Seq · code_examples
Widespread RNA editing dysregulation in brains from autistic individuals. (2019)
Showing first 25 analysis results.