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146 results for “RNA binding proteins”

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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. RNA dysregulation as a determinant of aging and neurodegenerative vulnerability.

    Trends in cell biology · 2026

    In the nervous system, aging causes deterioration of cellular and molecular processes that are associated with declines in cognition, sensory perception, and motor coordination. Aging is also the strongest risk factor for neurodegenerative disease, yet the mechanisms by which aging …

    PMID 42711219 DOI ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.

    Cell systems · 2026 : 101588

    RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated RBP resource integrates data from 92 additional RBPs (286 in total) profiled by enhanced CLIP (eCLIP), enabling comprehensive characterization of RNA elements within human K562 …

    PMID 42025161 DOI ↗

  8. 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 ↗

  9. Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.

    bioRxiv : the preprint server for biology · 2026

    Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for …

    PMID 41959526 DOI ↗

  10. 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 ↗

  11. 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 ↗

  12. 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 ↗

  13. 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 ↗

  14. KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS.

    bioRxiv : the preprint server for biology · 2025

    Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as …

    PMID 41279899 DOI ↗

  15. RNA triggers chronic stress during neuronal aging.

    bioRxiv : the preprint server for biology · 2025

    Neurodegenerative diseases are linked with dysregulation of the integrated stress response (ISR), which coordinates cellular homeostasis during and after stress events. Cellular stress can arise from several sources, but there is significant disagreement about which stress might contribute to aging …

    PMID 40799579 DOI ↗

  16. Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.

    RNA (New York, N.Y.) · 2025 · 31(8): 1103-1124

    RNA-binding proteins (RBP) play diverse roles in mRNA processing and function. However, from thousands of RBPs encoded in the human genome, a detailed molecular understanding of their interactions with RNA is available only for a small fraction. In most cases, …

    PMID 40399037 DOI ↗

  17. Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.

    Nature neuroscience · 2025 · 28(6): 1174-1184

    Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged …

    PMID 40456907 DOI ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.

    Cell systems · 2025 · 16(4): 101204

    The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the …

    PMID 40054464 DOI ↗

  22. 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 ↗

  23. Rational design yields RNA-binding zinc finger domains with altered sequence specificity.

    RNA (New York, N.Y.) · 2025 · 31(2): 150-163

    Targeting and manipulating endogenous RNAs in a sequence-specific manner is essential for both understanding RNA biology and developing RNA-targeting therapeutics. RNA-binding zinc fingers (ZnFs) are excellent candidates as designer proteins to expand the RNA-targeting toolbox, due to their compact size …

    PMID 39658359 DOI ↗

  24. 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 ↗

  25. Strategies for programmable manipulation of alternative splicing.

    Current opinion in genetics & development · 2024 · 89: 102272

    Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …

    PMID 39471777 DOI ↗

Datasets 25+

GSE254209 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).

Homo sapiens · GPL24676

GSE254208 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).

Homo sapiens · Illumina

GSE328331 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]

Homo sapiens · Illumina

GSE290625 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]

Homo sapiens · Illumina

GSE290765 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]

Homo sapiens · Illumina

GSE290755 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]

Homo sapiens · Illumina

GSE166404 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens · GPL28352

GSE34992 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Homo sapiens · GPL15106

GSE77629 GSE · GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]

Homo sapiens · GPL16791

GSE145968 GSE · GEO

CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production

Homo sapiens · GPL20301

GSE149767 GSE · GEO

Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces

Homo sapiens · GPL11154

GSE232519 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)

Homo sapiens · GPL15520

GSE155708 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens · GPL24106

GSE86035 GSE · GEO

SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

Homo sapiens · GPL20301

GSE232518 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (4)

Homo sapiens · GPL24676

GSE80039 GSE · GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]

Homo sapiens · GPL16791

GSE77339 GSE · GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]

Homo sapiens · GPL17585

GSE232513 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)

Homo sapiens · GPL15520

GSE155726 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Homo sapiens · GPL24676

GSE232514 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)

Homo sapiens · GPL24676

GSE34993 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)

Homo sapiens · GPL9052

GSE232515 GSE · GEO

Expanded repertoire for RNA-editing-based detection for RNA binding protein interactions (3)

Homo sapiens · GPL24676

GSE155649 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

Homo sapiens · GPL20301

GSE155728 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Homo sapiens · GPL16791

GSE155729 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Homo sapiens · GPL16791

Showing first 25 dataset results.

Analyses 12

GSE145968 Processing Pipeline

GSE145968 · 6 steps · OTHER · code_examples

A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. (2021)

GSE155649 Processing Pipeline

GSE155649 · 6 steps · OTHER · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE155708 Processing Pipeline

GSE155708 · 11 steps · RNA-Seq · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE155726 Processing Pipeline

GSE155726 · 12 steps · RNA-Seq · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE155728 Processing Pipeline

GSE155728 · 21 steps · RIP-Seq · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE155729 Processing Pipeline

GSE155729 · 6 steps · GSE · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE166402 Processing Pipeline

GSE166402 · 18 steps · RIP-Seq · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE166404 Processing Pipeline

GSE166404 · 9 steps · OTHER · code_examples

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)

GSE102497 Processing Pipeline

GSE102497 · 5 steps · miRNA-Seq · code_examples

Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels. (2018)

GSE88722 Processing Pipeline

GSE88722 · 11 steps · RIP-Seq · code_examples

CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. (2017)

GSE90650 Processing Pipeline

GSE90650 · 6 steps · ncRNA-Seq · code_examples

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing. (2017)

GSE86035 Processing Pipeline

GSE86035 · 32 steps · RIP-Seq · code_examples

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. (2016)