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Updated: Sep 10, 2025

Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules
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DEAD-Box Helicase 3 Modulates the Non-Coding RNA Pool in Ribonucleoprotein Condensates During Stress Granule

Elizaveta Korunova1, B Celia Cui1, Hao Ji1

  • 1Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, University of South Carolina Columbia, 715 Sumter St., Columbia, SC 29208, USA.

Non-Coding RNA
|August 27, 2025
PubMed
Summary
This summary is machine-generated.

The RNA helicase DDX3 influences stress granule composition. Inhibiting DDX3 with RK-33 alters non-coding RNA content, increasing circular RNAs (circRNAs) and intronic RNAs within these cellular condensates.

Keywords:
DDX3P-bodiesRK-33non-coding RNAribonucleoprotein condensatesstress granules

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • RNA Metabolism

Background:

  • Stress granules are cytoplasmic RNA-protein condensates formed during cellular stress.
  • These granules are implicated in various diseases, including cancer and neurodegeneration.
  • The DEAD-box RNA helicase DDX3 is a key component of stress granules, regulating RNA metabolism.

Purpose of the Study:

  • To investigate the role of DDX3 enzymatic activity in shaping stress granule RNA composition.
  • To determine how inhibiting DDX3 affects the non-coding RNA content of ribonucleoprotein (RNP) condensates.

Main Methods:

  • Utilized the human osteosarcoma U2OS cell line.
  • Induced stress granules using arsenite.
  • Inhibited DDX3 activity with the small molecule RK-33.
  • Purified the RNP granule fraction and performed RNA sequencing.

Main Results:

  • RK-33 treatment altered the non-coding RNA composition within RNP granules.
  • Observed a DDX3-dependent increase in circular RNA (circRNA) levels.
  • Detected alterations in granule-associated intronic RNAs.

Conclusions:

  • DDX3 enzymatic activity plays a role in regulating the cytoplasmic localization of non-coding RNAs.
  • Suggests a novel function for DDX3 in controlling circRNA and intronic RNA content in stress granules.