The human RNA-binding proteome and its dynamics during translational arrest

• Verfasst von: Trendel, Jakob [VerfasserIn]
• Verfasst von: Hentze, Matthias W. [VerfasserIn]
• Verfasst von: Krijgsveld, Jeroen [VerfasserIn]
• Titel: The human RNA-binding proteome and its dynamics during translational arrest
• Verf.angabe: Jakob Trendel, Thomas Schwarzl, Rastislav Horos, Ananth Prakash, Alex Bateman, Matthias W. Hentze, and Jeroen Krijgsveld
• Jahr: 2019
• Jahr des Originals: 2018
• Umfang: 32 S.
• Fussnoten: Published: December 6, 2018 ; Gesehen am 03.05.2019
• Titel Quelle: Enthalten in: Cell
• Ort Quelle: [Cambridge, Mass.] : Cell Press, 1974
• Jahr Quelle: 2019
• Band/Heft Quelle: 176(2019), 1, Seite 391-403
• ISSN Quelle: 1097-4172
• DOI: doi:10.1016/j.cell.2018.11.004
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: autophagy
• Sach-SW: mass spectrometry
• Sach-SW: mRNA
• Sach-SW: ncRNA
• Sach-SW: protein-RNA interactions
• Sach-SW: proteomics
• Sach-SW: ribophagy
• Sach-SW: RNA-binding domain
• Sach-SW: Trizol
• Sach-SW: UV-crosslinking
• K10plus-PPN: 1664538488

Abstract

Summary - 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.