Sensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry

The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induced cross-links. Here we demonstrate protocol optimizations, and apply the enhanced protocol to a set of model protein-RNA complexes to better characterize the properties of UV-induced protein-RNA cross-links. We use these insights to study a non-canonical protein-RNA interaction between SF3A1 of the U2 snRNP and stem-loop 4 of the U1 snRNP, demonstrating that UV cross-linking and mass spectrometry is a reliable standalone data type for low resolution structural characterizations of protein-RNA interactions.