ArticleNature methods2024
TREX reveals proteins that bind to specific RNA regions in living cells.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 32 citations in OpenAlex.
- Progress and challenges in traceless ligand-directed labelling chemistry.Communications chemistry · 2026Review
- Elucidating structure-function relationships in the mammalian nucleolus.Nature reviews. Molecular cell biology · 2026Review
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- RiboScreenBiomedicines · 2026Review
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- Accelerating Resistance Breeding: Emerging Methods to Identify and Validate Plant Immunity Genes.Plants (Basel, Switzerland) · 2026Review
- Distinct steps of nuclear maturation of human pre-60S complexes require the activity of GTPases including GNL3L.Nucleic acids research · 2026Article
- An intrinsically disordered region mediates RNA-binding selectivity and cellular activities of LARP6.Nature communications · 2026Article
- HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution.Nucleic acids research · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Long noncoding RNA regulation of immunity.Nature immunology · 2026Review
- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
- Enhanced hybridization-proximity labeling discovers protein interactomes of single RNA molecules.Nature communications · 2025Article
- A molecular cartographer's toolkit for mapping RNA's uncharted realms.Cell reports · 2025Review
- Orchestrating Nutrient Homeostasis: RNA-Binding Proteins as Molecular Conductors in Metabolic Disease Pathogenesis.Nutrients · 2025Review
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Decoding RNA-Protein Interactions: Methodological Advances and Emerging Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Ribosome heterogeneity and specialization.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- lncRNA NORAD modulates STAT3/STAT1 balance and innate immune responses in human cells via interaction with STAT3.Nature communications · 2025Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.