Photocatalytic Chemical Crosslinking for Profiling RNA-Protein Interactions in Living Cells

The dynamic interactions between RNAs and proteins play crucial roles in regulating diverse cellular processes. Proteome-wide characterization of these interactions in their native cellular context remains desirable but challenging. Herein, we developed a photocatalytic crosslinking (PhotoCAX) strategy coupled with mass spectrometry (PhotoCAX-MS) and RNA sequencing (PhotoCAX-seq) for the study of the composition and dynamics of protein-RNA interactions. By integrating the blue light-triggered photocatalyst with a dual-functional RNA-protein crosslinker (RP-linker) and the phase separation-based enrichment strategy, PhotoCAX-MS revealed a total of 2044 RBPs in human HEK293 cells. We further employed PhotoCAX to investigate the dynamic change of RBPome in macrophage cells upon LPS-stimulation, as well as the identification of RBPs interacting directly with the 5 ' untranslated regions of SARS-CoV-2 RNA.

Automated summary

The interactions between RNA and proteins are crucial for cellular processes. This study developed a photocatalytic crosslinking strategy combined with mass spectrometry and RNA sequencing to study the composition and dynamics of protein-RNA interactions. The approach identified numerous RNA binding proteins in human cells and investigated the dynamic changes of RBPs in macrophage cells and their interactions with SARS-CoV-2 RNA.