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103 results for “RNA targeting”

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  1. 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 ↗

  2. ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing.

    bioRxiv : the preprint server for biology · 2026

    Chemical proteomics has identified covalent ligands targeting cysteine residues across many hundreds of human proteins. The functional effects of these liganding events, however, remain challenging to assign at scale. Here we describe ESCAPE (Endogenous Site-specific Competition Assays using Prime Editors), …

    PMID 42619774 DOI ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  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. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. 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 ↗

  11. 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 ↗

  12. The IFIT2-IFIT3 antiviral complex targets short 5' untranslated regions on viral mRNAs for translation inhibition.

    Nature microbiology · 2025 · 10(11): 2934-2948

    Recognition of foreign RNA is critical for the innate immune response to viruses. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFIT) 2 and 3 are highly upregulated following viral infection, but mechanistic insight into their antiviral role is lacking. Here we …

    PMID 41093992 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. 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 ↗

  15. Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor.

    RNA (New York, N.Y.) · 2025 · 31(8): 1195-1205

    Translation elongation stalls trigger mRNA decay and degradation of the nascent polypeptide via translation-dependent quality control pathways. One such pathway, non-stop mRNA decay (NSD), targets aberrant mRNAs that lack stop codons, for example, due to premature polyadenylation. Here we identify …

    PMID 40441874 DOI ↗

  16. 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 ↗

  17. 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 ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. 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 ↗

  22. 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 ↗

  23. Steering research on mRNA splicing in cancer towards clinical translation.

    Nature reviews. Cancer · 2024 · 24(12): 887-905

    Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome …

    PMID 39384951 DOI ↗

  24. 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 ↗

  25. 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 ↗

Datasets 2

GSE127743 GSE · GEO

In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]

Mus musculus · GPL18480

GSE230717 GSE · GEO

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Homo sapiens · GPL24676

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