Trendel, J. et al. Cell 176, 391–403 (2019).

Current methods for studying protein–RNA interactions focus mainly on either one protein, such as in CLIP-seq, or interactome capture involving only poly(A) RNAs, neither of which offers a full picture of how proteins interact with RNAs. Trendel et al. introduce a generic purification method for extracting global protein–RNA complexes, called XRNAX. They find that UV-cross-linked protein–RNA complexes are insoluble in the interphase of TRIZOL, a chemical solution that is widely used in RNA extraction. The complexes extracted from the interphase contain all major RNA biotypes and are enriched with RNA-binding proteins. To explore the RNA-bound proteome, one can carry out additional steps, including tryptic digest and silica column enrichment, to prepare the XRNAX extracts for mass spectrometry. The researchers applied XRNAX on three human cell lines (MCF7, HeLa, and HEK293), and identified over 700 proteins that interact with non-poly(A) RNAs. Moreover, XRNAX combined with CLIP-seq allows for further RNA sequencing to identify protein-binding RNAs.