RT Journal Article
SR Electronic
T1 The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 329995
DO 10.1101/329995
A1 Trendel, Jakob
A1 Schwarzl, Thomas
A1 Prakash, Ananth
A1 Bateman, Alex
A1 Hentze, Matthias W
A1 Krijgsveld, Jeroen
YR 2018
UL http://biorxiv.org/content/early/2018/05/30/329995.abstract
AB 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-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B 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.