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107 results for “gene expression”
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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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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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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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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
Cell chemical biology · 2026 · 33(2): 256-267.e11
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We previously described a chloroacetamide compound (R)-SKBG-1 that covalently binds …
PMID 41534524 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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Dual-targeting snRNA gene therapy rescues STMN2 and UNC13A splicing in TDP-43 proteinopathies.
bioRxiv : the preprint server for biology · 2025
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder caused by the selective deterioration of motor neurons in the central nervous system (CNS). A key driver of this pathogenesis is nuclear loss of ALS-associated protein TDP-43, leading to mis-splicing of TDP-43 …
PMID 41573891 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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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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Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.
Nature chemical biology · 2025
Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …
PMID 40968292 DOI ↗
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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We recently reported a chloroacetamide compound ( <i>R</i> )-SKBG-1 that …
PMID 40661397 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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Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
Nature · 2025 · 639(8054): 483-492
Tissue-resident memory CD8 T (T<sub>RM</sub>) cells provide protection from infection at barrier sites. In the small intestine, T<sub>RM</sub> cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential<sup>1</sup>. …
PMID 39843748 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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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024 · 34(11): 2012-2024
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …
PMID 38906680 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 ↗
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Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes.
Cell reports · 2024 · 43(8): 114637
Reactive changes of glial cells during neuroinflammation impact brain disorders and disease progression. Elucidating the mechanisms that control reactive gliosis may help us to understand brain pathophysiology and improve outcomes. Here, we report that adult ablation of autism spectrum disorder …
PMID 39154337 DOI ↗
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Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America · 2024 · 121(34): e2319724121
Skeletal muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and aging. The tissue remodeling that happens during recovery from atrophy or injury involves changes in different cell types such as muscle fibers, and …
PMID 39141348 DOI ↗
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Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.
bioRxiv : the preprint server for biology · 2024
Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …
PMID 38915553 DOI ↗
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circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.
bioRxiv : the preprint server for biology · 2024
Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses …
PMID 37745562 DOI ↗
Datasets 25+
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
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
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
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Expression data from reactive astrocytes acutely purified from young adult mouse brains
Mus musculus · GPL1261
Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factors
Homo sapiens · GPL570
Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
Homo sapiens · GPL11154
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
6239 · GPL19757
Disruption of human-specific synaptogenesis program in autism [RNA-seq]
9598 · GPL11154
Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
9544 · GPL11154
Chronic viral infection of naive, effector, memory and exhausted virus-specific CD8 T cells
Mus musculus · GPL81
Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression
Mus musculus · GPL17021
A seven-gene signature aggregates a subgroup of stage II colon cancers with stage III.
Homo sapiens · GPL570
Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery
Homo sapiens · GPL13497
Gene Expression Profiles in Stage II and III Colon Cancer. Application of a 128-gene signature
Homo sapiens · GPL570
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)
Homo sapiens · GPL570
Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients
Mus musculus · GPL570
Transactivation-deficient p53 Mutants in Ras-induced Cellular Senescence
Mus musculus · GPL1261
RNA-targeting Cas9 corrects molecular and physiological features in pre-clinical model of myotonic dystrophy type 1
Mus musculus · GPL21103
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation
Mus musculus · GPL17543
Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with normal karyotype and healthy controls
Homo sapiens · GPL6244
Showing first 25 dataset results.
Analyses 18
GSE237099 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
GSE138197 · 6 steps · RNA-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE211676 · 10 steps · GSE · code_examples
RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. (2023)
GSE213470 · 2 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE75214 · 1 step · GSE · code_examples
RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)
GSE17536 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE17538 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE31595 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE95156 · 7 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE76220 · 5 steps · RNA-Seq · code_examples
Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. (2018)
GSE16969 · 2 steps · GSE · code_examples
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. (2016)
GSE72420 · 3 steps · GSE · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72500 · 3 steps · RIP-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72501 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72502 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72509 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE54321 · 3 steps · GSE · code_examples
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses. (2014)