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88 results for “gene regulation”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. 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 ↗

  11. 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 ↗

  12. 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 ↗

  13. 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 ↗

  14. 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 ↗

  15. 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 ↗

  16. 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 ↗

  17. 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 ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. Transcriptome regulation by PARP13 in basal and antiviral states in human cells.

    iScience · 2024 · 27(4): 109251

    The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including …

    PMID 38495826 DOI ↗

  22. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.

    Nature communications · 2023 · 14(1): 5195

    Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that …

    PMID 37673892 DOI ↗

  23. 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 ↗

  24. 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 ↗

  25. Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration.

    bioRxiv : the preprint server for biology · 2023

    Muscular atrophy is a mortality risk factor that happens with disuse, chronic disease, and aging. Recovery from atrophy requires changes in several cell types including muscle fibers, and satellite and immune cells. Here we show that Zfp697/ZNF697 is a damage-induced …

    PMID 37398033 DOI ↗

Datasets 14

GSE290248 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]

Homo sapiens · Illumina

GSE290282 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]

Homo sapiens · Illumina

GSE290281 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]

Homo sapiens · Illumina

GSE147005 GSE · GEO

Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration

Mus musculus · GPL21103

GSE202881 GSE · GEO

Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling

Homo sapiens · GPL24676

GSE266924 GSE · GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Homo sapiens · GPL30173

GSE230097 GSE · GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Homo sapiens · GPL24676

GSE277160 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]

Homo sapiens · GPL24676

GSE277047 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RBNS]

synthetic construct · GPL34014

GSE268963 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]

Homo sapiens · GPL24676

GSE249245 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]

Homo sapiens · GPL24676

GSE213867 GSE · GEO

Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

Homo sapiens · GPL24676

GSE249246 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]

Homo sapiens · GPL24676

GSE277161 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]

Homo sapiens · GPL24676

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