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. 2019 Jan 10;176(1-2):391-403.e19.
doi: 10.1016/j.cell.2018.11.004. Epub 2018 Dec 6.

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Jakob Trendel  1 , Thomas Schwarzl  2 , Rastislav Horos  2 , Ananth Prakash  3 , Alex Bateman  3 , Matthias W Hentze  2 , Jeroen Krijgsveld  4
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Free article

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Jakob Trendel et al. Cell. .
Free article

Abstract

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.

Keywords: RNA-binding domain; Trizol; UV-crosslinking; autophagy; mRNA; mass spectrometry; ncRNA; protein-RNA interactions; proteomics; ribophagy.

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