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

Kyung W. Seo, Ralph E. Kleiner

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

RNA-binding proteins (RBPs) play an important role in biology, and characterizing dynamic RNA–protein interactions is essential for understanding RBP function. In this study, we developed targets of RBPs identified by editing induced through dimerization (TRIBE-ID), a facile strategy for quantifying state-specific RNA–protein interactions upon rapamycin-mediated chemically induced dimerization and RNA editing. We performed TRIBE-ID with G3BP1 and YBX1 to study RNA–protein interactions during normal conditions and upon oxidative stress-induced biomolecular condensate formation. We quantified editing kinetics to infer interaction persistence and show that stress granule formation strengthens pre-existing RNA–protein interactions and induces new RNA–protein binding events. Furthermore, we demonstrate that G3BP1 stabilizes its targets under normal and oxidative stress conditions independent of stress granule formation. Finally, we apply our method to characterize small-molecule modulators of G3BP1–RNA binding. Taken together, our work provides a general approach to profile dynamic RNA–protein interactions in cellular contexts with temporal control. [Figure not available: see fulltext.]

Original languageEnglish (US)
Pages (from-to)1361-1371
Number of pages11
JournalNature Chemical Biology
Volume19
Issue number11
DOIs
StatePublished - Nov 2023

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology

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