PT  - JOURNAL ARTICLE
AU  - Trendel, Jakob
AU  - Schwarzl, Thomas
AU  - Prakash, Ananth
AU  - Bateman, Alex
AU  - Hentze, Matthias W
AU  - Krijgsveld, Jeroen
TI  - The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
AID  - 10.1101/329995
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 329995
4099  - http://biorxiv.org/content/early/2018/05/30/329995.short
4100  - http://biorxiv.org/content/early/2018/05/30/329995.full
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.