Global RNA-Protein Interactome purification screening identifies RRP1 in IL-1-stimulated BMDM cells

An “unbiased” approach that holds promise for isolating total protein-RNA complexes from whole cell samples without any labeling and identifying RBPs that lack classical RNA-binding domains (RBDs) or that bind different RNA classes is greatly needed. On the other hand, due to the scarcity of primary cells and the difficulty of RNA labeling, few studies have utilized these techniques to identify RBPs in primary cells, resulting in a shortage of information on the role of RBP-RNA interactions and their function in regulating pathogenesis. In recent years, an unbiased “Phase Separation-based RNA-protein complex-capture” approach has been proposed to analyze whole cell RNA-RBP interactions. This approach is based on the concept that crosslinked global protein-RNA complexes in total cell samples will separate into the insoluble interphase during RNA extraction with acid guanidinium thiocyanate-phenol-chloroform. Based on this approach, here we first developed a modified RNA-protein complex-capture method (GRPIp) in primary bone marrow derived macrophages (BMDMs), and then we utilized GRPIp to profile the dynamic landscape of RNA-binding proteome in BMDMs upon IL-1β stimulation.