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24 results for “proteomics”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.

    Nature communications · 2024 · 15(1): 10796

    Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal …

    PMID 39737952 DOI ↗

  6. LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.

    RNA (New York, N.Y.) · 2024 · 30(3): 223-239

    Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified …

    PMID 38164626 DOI ↗

  7. Remodeling oncogenic transcriptomes by small molecules targeting NONO.

    Nature chemical biology · 2023 · 19(7): 825-836

    Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants …

    PMID 36864190 DOI ↗

  8. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.

    Molecular cell · 2023 · 83(14): 2595-2611.e11

    RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier …

    PMID 37421941 DOI ↗

  9. 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 ↗

  10. Proteomic discovery of chemical probes that perturb protein complexes in human cells.

    Molecular cell · 2023 · 83(10): 1725-1742.e12

    Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" …

    PMID 37084731 DOI ↗

  11. Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.

    Nature communications · 2023 · 14(1): 551

    Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it …

    PMID 36759613 DOI ↗

  12. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.

    Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53

    Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …

    PMID 35378331 DOI ↗

  13. Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2463: 67-80

    Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …

    PMID 35344168 DOI ↗

  14. APEX Proximity Labeling of Stress Granule Proteins.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2428: 381-399

    Ascorbate peroxidase (APEX)-catalyzed proximity labeling has been recently established as a robust approach to uncover localized protein environments and transient protein-protein interactions occurring across mammalian cells. This molecular tool enables improved identification of individual proteins localized to and involved in …

    PMID 35171492 DOI ↗

  15. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.

    Nature communications · 2022 · 13(1): 7506

    Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains …

    PMID 36473869 DOI ↗

  16. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.

    Nature communications · 2022 · 13(1): 3833

    Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival. Here, we demonstrate that upregulation of the splicing factor, RBM17 preferentially marks and sustains LSCs and …

    PMID 35781533 DOI ↗

  17. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.

    Cell reports · 2022 · 38(10): 110481

    Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this …

    PMID 35263585 DOI ↗

  18. A multi-scale map of cell structure fusing protein images and interactions.

    Nature · 2021 · 600(7889): 536-542

    The cell is a multi-scale structure with modular organization across at least four orders of magnitude<sup>1</sup>. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are …

    PMID 34819669 DOI ↗

  19. Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.

    Cell reports · 2021 · 36(10): 109685

    Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). …

    PMID 34496257 DOI ↗

  20. Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics.

    Cell reports · 2019 · 27(5): 1356-1363.e3

    Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological …

    PMID 31042464 DOI ↗

  21. Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.

    Cell reports · 2019 · 27(4): 1244-1253.e4

    A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …

    PMID 31018137 DOI ↗

  22. Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules.

    Cell · 2018 · 172(3): 590-604.e13

    Stress granules (SGs) are transient ribonucleoprotein (RNP) aggregates that form during cellular stress and are increasingly implicated in human neurodegeneration. To study the proteome and compositional diversity of SGs in different cell types and in the context of neurodegeneration-linked mutations, …

    PMID 29373831 DOI ↗

  23. From Protein-RNA Predictions toward a Peptide-RNA Code.

    Molecular cell · 2016 · 64(3): 437-438

    The RNA field is undergoing a renaissance, with a deluge of proteins being identified to bind RNA. Two reports now introduce proteome-wide approaches that identify the peptides that are crosslinked to RNA (Castello et al., 2016; He et al., 2016).

    PMID 27814488 DOI ↗

  24. Alternative splicing in stem cell self-renewal and diferentiation.

    Advances in experimental medicine and biology · 2010 · 695: 92-104

    This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …

    PMID 21222201 DOI ↗

Datasets 3

GSE198212 GSE · GEO

Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO

Homo sapiens · GPL24676

GSE193134 GSE · GEO

LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function

Homo sapiens · GPL20301

GSE157467 GSE · GEO

Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress

Homo sapiens · GPL20301

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