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65 results for “cell biology”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  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. 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 ↗

  6. Organizing research at scale: Reflections on leading multi-team scientific collaborations.

    Molecular cell · 2026 · 86(3): 434-438

    Collaborations are critical features of modern academic science. As biological problems get more complex, larger teams become necessary. However, there is an increased level of friction in coordinating activities and attributing credit in large-scale scientific collaborations. Simple organizational principles and …

    PMID 41650944 DOI ↗

  7. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. 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 ↗

  11. 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 ↗

  12. 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 ↗

  13. 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 ↗

  14. 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 ↗

  15. Stratification of enterochromaffin cells by single-cell expression analysis.

    bioRxiv : the preprint server for biology · 2025

    Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine (5-HT) to mediate disparate physiological responses. However, the molecular and cellular basis …

    PMID 37662229 DOI ↗

  16. 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 ↗

  17. 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 ↗

  18. High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.

    Nature communications · 2024 · 15(1): 7067

    RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE (IN situ Sensitive Capture of RNA-protein Interactions in Biological Environments), circumventing the challenges through …

    PMID 39152130 DOI ↗

  19. 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 ↗

  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. ePRINT: exonuclease assisted mapping of protein-RNA interactions.

    Genome biology · 2024 · 25(1): 140

    RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new …

    PMID 38807229 DOI ↗

  22. Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

    Genome biology · 2024 · 25(1): 82

    The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit …

    PMID 38566187 DOI ↗

  23. Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted.

    bioRxiv : the preprint server for biology · 2024

    Tissue-resident memory CD8 T cells (T<sub>RM</sub>) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) T<sub>RM</sub> cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. …

    PMID 38585842 DOI ↗

  24. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.

    Molecular cell · 2023 · 83(19): 3421-3437.e11

    The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the …

    PMID 37751740 DOI ↗

  25. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

    bioRxiv : the preprint server for biology · 2023

    Large-genome bacteriophages (jumbo phages) of the <i>Chimalliviridae</i> family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, …

    PMID 37790334 DOI ↗

Datasets 1

GSE247544 GSE · GEO

Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner

GPL24247

Analyses 1

GSE247544 scRNA-seq Data Processing

GSE247544 · 3 steps · scRNA-seq · geo_data_processing

Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner. (2025)