Profiling dynamic RNA-protein interactions using small molecule-induced RNA editing

  1. Kyung W. Seo
  2. Ralph E. Kleiner

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Abstract

RNA binding proteins (RBPs) play an important role in biology and characterizing dynamic RNA-protein interactions in their native context is essential for understanding RBP function. Here, we develop targets of RNA-binding proteins identified by editing induced through dimerization (TRIBE-ID), a facile strategy for identifying and quantifying state-specific RNA-protein interactions based upon rapamycin-mediated chemically induced dimerization and RNA editing. We perform TRIBE-ID with G3BP1, an abundant RBP and core component of stress granules, to study transcriptome-wide G3BP1-RNA interactions during normal conditions and upon oxidative stress-induced liquid-liquid phase separation (LLPS). We quantify editing kinetics in order to infer interaction persistence and show that stress granule formation strengthens preexisting G3BP1-RNA interactions and induces new RNA-protein binding events. Further, we demonstrate that G3BP1 stabilizes its RNA clients in a dose-dependent manner, suggesting that stress granules function as RNA storage depots. Finally, we apply our method to characterize small molecule modulators of G3BP1-RNA binding. Taken together, our work provides a general approach to profile RNA-protein binding events with temporal control and illuminates the role of LLPS in organizing G3BP1-RNA interactions in the cell.

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  1. ASAPbio crowd review

    Review coordinated via ASAPbio’s crowd preprint review

    This review was completed by Ruchika Bajaj.

    This study has developed a tool to characterize small molecule modulators of RNA-protein binding events. Please see below a few points which may help strengthen the manuscript.

    • The term “temporal” is used multiple times in the paper, to facilitate clarity for readers from different disciplines, it may be useful to provide some further explanation or context for the term.
    • Introduction section, “independent datasets have failed to reach consensus”, please provide some brief explanation about those independent datasets mentioned.
    • Introduction section, last paragraph “We apply TRIBE ID to profile cytoplasmic G3BP1-RNA interactions …” - further explanation of these three processes linked together would be helpful.
    • Figure 1, please provide some further explanation for the difference between TRIBE and TRIBE-ID. Since the dimerization is forced by rapamycin, a control experiment to explain artifact binding would be helpful.
    • In the section, “Rapamycin-mediated dimerization of G3BP1-FRB and FKBP-ADAR”, recommend adding some clarification about the goal of this experiment, which could be understanding either native processes or in a rapamycin-dependent manner.
    • In section, “G3BP1 TRIBE analysis with human and Drosophila ADAR2 catalytic domains” - suggest commenting on the reasoning for ideal ADAR to possess characteristics like “high editing activity when dimerized or fused to G3BP1”. Are these characteristics important to increase signal/noise ratio in the assay? Also, an explanation of T375G mutation and control experiments with wild type ADAR for any inhibition effect for Figure 2 would be helpful.
    • In the section, “Temporally controlled G3BP1-RNA interaction analysis with TRIBE-ID”, please clarify whether the experiment described in Figure 3 provides information about the time of interaction between RNA and G3BP1.
    • A paragraph describing any limitations and other possible applications of this tool on other systems would add to the manuscript.
  2. Version 1 published on bioRxiv