Abstract
SummaryThe compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA-interactome capture (RIC). However, it remained unknown if the complement of RBPs changes in response to environmental perturbations and whether these rearrangements are important. To answer these questions, we developed “comparative RIC” and applied it to cells challenged with an RNA virus called sindbis (SINV). Over 200 RBPs display differential interaction with RNA upon SINV infection. These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. RBPs stimulated by the infection redistribute to viral replication factories and regulate the capacity of the virus to infect. For example, ablation of XRN1 causes cells to be refractory to SINV, while GEMIN5 moonlights as a regulator of SINV gene expression. In summary, RNA availability controls RBP localization and function in SINV-infected cells.
Highlights
RNA-binding proteins (RBPs) assemble with RNA forming ribonucleoproteins (RNPs) that dictate RNA fate (Glisovic et al, 2008)
We developed a ‘‘comparative RNA-interactome capture (RIC)’’ approach to profile with high accuracy RBP dynamics in cells infected with sindbis virus (SINV) (Figures 1A and 1B)
Applying RIC to Cells Infected with SINV To study the dynamics of cellular RBPs in response to physiological cues, we challenged cells with a cytoplasmic RNA virus and applied RIC
Summary
RNA-binding proteins (RBPs) assemble with RNA forming ribonucleoproteins (RNPs) that dictate RNA fate (Glisovic et al, 2008). A system-wide approach termed RNA-interactome capture (RIC) has greatly expanded the compendium of RBPs (RBPome) (Hentze et al, 2018). Several RBPs did not follow this trend, displaying protein-level independent changes in RNA binding and raising the question of whether physiological perturbations can induce such responsive behavior more widely. To address this possibility, we developed a ‘‘comparative RIC’’ (cRIC) approach to profile with high accuracy RBP dynamics in cells infected with sindbis virus (SINV) (Figures 1A and 1B)
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