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A new rapid-degradation system combined with super-resolution microscopy

Nature Reviews Molecular Cell Biology (2025)Cite this article

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The nucleus of eukaryotic cells is compartmentalized into different membraneless organelles (MLOs) with important functions. Nuclear speckles are enriched in RNA-binding proteins (RBPs) and splicing factors with mixed-charge domains, whereas paraspeckles contain RBPs with prion-like domains that are spatially organized by the scaffold RNA NEAT1. Both MLOs coordinate the nuclear stress response and are found in close proximity to each other, but have not been found to fuse.

Acute depletion is crucial for studying RBPs, which are long-lived, are highly abundant and compensate for each other’s function. However, existing depletion tools cannot be successfully applied to proteins within nuclear MLOs. hGRAD consists of a ‘one-fits-all’ plasmid that can be stably integrated into any cell line. After doxycycline induction, a GFP nanobody fused to the F-box domain of the human E3 ubiquitin ligase FBXW11 is expressed and targets endogenous GFP-tagged proteins for rapid proteasomal degradation within 2 hours, enabling us to track the effect of specific RBPs on MLO architecture.

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References

Original article

  • Okuda, E. K. et al. Rapid depletion and super-resolution microscopy reveal dual roles of SRSF5 in coordinating nuclear speckle–paraspeckle crosstalk during cellular stress. Nucleic Acids Res. 53, gkaf713 (2025)

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Related article

  • Arnold, B. et al. hGRAD: A versatile “one-fits-all” system to acutely deplete RNA binding proteins from condensates. J. Cell Biol. 223, e202304030 (2024)

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank M. Müller-McNicoll and M. Heilemann for feedback and mentorship. The authors thank SCALE-it and IMPRS for financial support.

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Authors and Affiliations

  1. Institute for Molecular Bioscience, Goethe-Universität, Frankfurt am Main, Germany

    Ellen Kazumi Okuda

  2. IMPRS for Cellular Biophysics, Frankfurt am Main, Germany

    Ellen Kazumi Okuda

  3. Institute of Physical and Theoretical Chemistry, Goethe-Universität, Frankfurt am Main, Germany

    Laurell Fridolin Kessler

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  1. Ellen Kazumi Okuda
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  2. Laurell Fridolin Kessler
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Correspondence to Ellen Kazumi Okuda or Laurell Fridolin Kessler.

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Okuda, E.K., Kessler, L.F. A new rapid-degradation system combined with super-resolution microscopy. Nat Rev Mol Cell Biol (2025). https://doi.org/10.1038/s41580-025-00908-2

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  • DOI: https://doi.org/10.1038/s41580-025-00908-2

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