ArticleAnalytical chemistry2021
Single Nucleotide Resolution RNA-Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow.
Article in Analytical chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Review
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Article
- pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.Life science alliance · 2024Article
- Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome.Journal of proteome research · 2024Article
- Removal ofScience (New York, N.Y.) · 2024Article
- Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.Nature communications · 2024Article
- Specific protein-RNA interactions are mostly preserved in biomolecular condensates.Science advances · 2024Article
- A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2.Nucleic acids research · 2023Article
- Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes.Nature communications · 2022Article
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Authors and funding
8 authors.
Funding
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Abstract
RNA-protein interactions mediate many intracellular processes. CLIR-MS (cross-linking of isotope-labeled RNA and tandem mass spectrometry) allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a single experiment. Using isotopically labeled RNA segments for UV-light-induced cross-linking generates characteristic isotope patterns that constrain the sequence database searches, increasing spatial resolution. Whereas the use of segmentally isotopically labeled RNA is effective, it is technically involved and not applicable in some settings, e.g., in cell or tissue samples. Here we introduce an extension of the CLIR-MS workflow that uses unlabeled RNA during cross-linking and subsequently adds an isotopic label during sample preparation for MS analysis. After RNase and protease digests of a cross-linked complex, the nucleic acid part of a peptide-RNA conjugate is labeled using the enzyme T4 polynucleotide kinase and a 1:1 mixture of heavy
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