ArticleNature methods2020
An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- A nucleic acid labeling chemistry reveals surface DNA on exosomes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- The nascent RNA labelling compound 5-ethynyl uridine (EU) integrates into DNA in some animals.BMC molecular and cell biology · 2025Article
- A nucleic acid labeling chemistry reveals surface DNA on exosomes.bioRxiv : the preprint server for biology · 2025Article
- mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase.Cell reports · 2025Article
- RNA Decay Assay: 5-Ethynyl-Uridine Labeling and Chasing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- B-Cell Epigenetic Modulation of IgA Response by 5-Azacytidine and IgA Nephropathy.Journal of the American Society of Nephrology : JASN · 2024Article
- Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analogues.Nucleic acids research · 2024Article
- Exploring the Mutated Kinases for Chemoenzymatic Synthesis ofMolecules (Basel, Switzerland) · 2024Article
- 3D convolutional neural networks predict cellular metabolic pathway use from fluorescence lifetime decay data.APL bioengineering · 2024Article
- satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect.Genome biology · 2023Article
- An Optimized Enzyme-Nucleobase Pair EnablesBiochemistry · 2022Article
- Robust synthesis of 2'-azido modified RNA from 2'-amino precursors by diazotransfer reaction.Organic & biomolecular chemistry · 2022Article
- Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides.Journal of the American Chemical Society · 2022Article
- Labeling and sequencing nucleic acid modifications using bio-orthogonal tools.RSC chemical biology · 2022Review
- Exploiting Endogenous Enzymes for Cancer-Cell Selective Metabolic Labeling of RNA in Vivo.Journal of the American Chemical Society · 2022Article
- Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling.RSC chemical biology · 2022Article
- Interrogating the transcriptome with metabolically incorporated ribonucleosides.Molecular omics · 2021Review
- New approaches to target RNA binding proteins.Current opinion in chemical biology · 2021Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Tissues and organs are composed of diverse cell types, which poses a major challenge for cell-type-specific profiling of gene expression. Current metabolic labeling methods rely on exogenous pyrimidine analogs that are only incorporated into RNA in cells expressing an exogenous enzyme. This approach assumes that off-target cells cannot incorporate these analogs. We disprove this assumption and identify and characterize the enzymatic pathways responsible for high background incorporation. We demonstrate that mammalian cells can incorporate uracil analogs and characterize the enzymatic pathways responsible for high background incorporation. To overcome these limitations, we developed a new small molecule-enzyme pair consisting of uridine/cytidine kinase 2 and 2'-azidouridine. We demonstrate that 2'-azidouridine is only incorporated in cells expressing uridine/cytidine kinase 2 and characterize selectivity mechanisms using molecular dynamics and X-ray crystallography. Furthermore, this pair can be used to purify and track RNA from specific cellular populations, making it ideal for high-resolution cell-specific RNA labeling. Overall, these results reveal new aspects of mammalian salvage pathways and serve as a new benchmark for designing, characterizing and evaluating methodologies for cell-specific labeling of biomolecules.
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