The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest
2018
Authors: Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J
CellNetworks People: Hentze Matthias, Krijgsveld Jeroen
Journal: Cell. 2018 Dec 1. pii: S0092-8674(18)31463-6. doi: 10.1016/j.cell.2018.11.004

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-related changes in the total proteome. In addition, we combine XRNAX with crosslinking immunoprecipitation sequencing (CLIP-seq) to validate the interaction of ncRNA with lamin B1 and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.