Sequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif

Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in isolation, and in broader context with components of the U1 snRNP. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.