ArticleNature communications2022
Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- RNA-induced PRC2 inhibition depends on the sequence of bound RNA.Nature communications · 2026Article
- Dissecting the RNA-binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport.Nucleic acids research · 2026Article
- RNA-induced PRC2 inhibition depends on the sequence of bound RNA.Research square · 2025Article
- Expanding Epitranscriptomics to Non-Enzymatic RNA Modifications.Trends in chemistry · 2025Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Current perspectives in drug targeting intrinsically disordered proteins and biomolecular condensates.BMC biology · 2025Review
- Article
- pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.Life science alliance · 2024Article
- Neurotransmitter metabolites in milk ferments ofHeliyon · 2024Article
- Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome.Journal of proteome research · 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
- Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila.BMC biology · 2023Article
- Article
- Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.Molecular microbiology · 2023Review
- Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics.Nature communications · 2023Article
- Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association.The Plant cell · 2023Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Photo-induced cross-linking is a mainstay technique to characterize RNA-protein interactions. However, UV-induced cross-linking between RNA and proteins at "zero-distance" is poorly understood. Here, we investigate cross-linking of the RBFOX alternative splicing factor with its hepta-ribonucleotide binding element as a model system. We examine the influence of nucleobase, nucleotide position and amino acid composition using CLIR-MS technology (crosslinking-of-isotope-labelled-RNA-and-tandem-mass-spectrometry), that locates cross-links on RNA and protein with site-specific resolution. Surprisingly, cross-linking occurs only at nucleotides that are π-stacked to phenylalanines. Notably, this π-stacking interaction is also necessary for the amino-acids flanking phenylalanines to partake in UV-cross-linking. We confirmed these observations in several published datasets where cross-linking sites could be mapped to a high resolution structure. We hypothesize that π-stacking to aromatic amino acids activates cross-linking in RNA-protein complexes, whereafter nucleotide and peptide radicals recombine. These findings will facilitate interpretation of cross-linking data from structural studies and from genome-wide datasets generated using CLIP (cross-linking-and-immunoprecipitation) methods.
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