Journal
NATURE COMMUNICATIONS
Volume 13, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-022-30284-w
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Funding
- ETH Scientific Equipment program
- European Union [FP7-JTI 115766]
- Strategic Focus Area for the ETH Domain Personalized Health and Related Technologies (TechTransfer Project) [PHRT-503]
- European Research Council [670821]
- NCCR RNA and Disease of the SNSF [51NF40-182880]
- ETH Zurich [ETH-24-16-2]
- Sinergia grant of the SNSF [CRSII3_127454]
- Swiss National Science Foundation (SNF) [CRSII3_127454, 51NF40-182880] Funding Source: Swiss National Science Foundation (SNF)
- European Research Council (ERC) [670821] Funding Source: European Research Council (ERC)
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This study reveals the crucial role of pi-stacking interactions between nucleobases and aromatic amino acids in UV-induced cross-linking of RNA-protein complexes. These findings can contribute to the interpretation of cross-linking data in structural studies and genome-wide datasets.
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 pi-stacked to phenylalanines. Notably, this pi-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 pi-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. Although UV-induced cross-linking is a widely used method to study RNA-protein complexes, the cross-linking reactions are poorly understood. Here, the authors show that pi-stacking interactions between nucleobases and aromatic amino acids play a key role in the cross-linking process.
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