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Acute and rapid degradation of endogenous proteins by Trim-Away

Nature Protocols volume 13, pages 2149–2175 (2018)Cite this article

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A Publisher Correction to this article was published on 30 November 2018

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Abstract

Protein depletion is a key approach to understanding the functions of a protein in a biological system. We recently developed the Trim-Away approach in order to rapidly degrade endogenous proteins without prior modification. Trim-Away is based on the ubiquitin ligase and Fc receptor TRIM21, which recognizes antibody-bound proteins and targets them for degradation by the proteasome. In a typical Trim-Away experiment, protein degradation is achieved in three steps: first, introduction of an antibody against the target protein; second, recruitment of endogenous or exogenous/overexpressed TRIM21 to the antibody–bound target protein; and third, proteasome-mediated degradation of the target protein, antibody and TRIM21 complex. Protein degradation by Trim-Away is acute and rapid, with half-lives of ~10–20 min. The major advantages of Trim-Away over other protein degradation methods are that it can be applied to any endogenous protein without prior modification; that it uses conventional antibodies that are widely available; and that it can be applied to a wide range of cell types, including nondividing primary human cells, for which other loss-of-function assays are challenging. In this protocol, we describe the detailed procedures for antibody preparation and delivery in mouse oocytes and cultured cells via microinjection and electroporation. In addition, we provide recommendations for antibody selection and validation, and for the generation of TRIM21-overexpressing cell lines for cases in which endogenous TRIM21 is limited. A typical Trim-Away experiment takes just a few hours.

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Fig. 1
Fig. 2
Fig. 3: Schematic of Trim-Away experiments in mouse oocytes.
Fig. 4: Trim-Away in mouse oocytes.

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Change history

  • 30 November 2018

    In the version of this paper originally published, the present address of W.A. McEwan was accidentally omitted. This address (UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK) has now been added as affiliation 3, and the equal-contributions note has been updated to affiliation 4. These changes are reflected in the PDF and HTML versions of the protocol.

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Acknowledgements

We thank A. Musacchio and S. Maffini for advice on protein electroporation, and members of the Schuh lab and the James lab for helpful discussions. The research leading to these results received financial support from the Medical Research Council (MC_U105192711 and MC_U105181010), the Max Planck Society, the European Community’s Seventh Framework Programme (FP7/2007–2013) under grant agreement no. 241548, European Research Council (ERC) Starting Grant no. 337415 and a Wellcome Trust Investigator Award.

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Author notes

  1. William A. McEwan

    Present address: UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK

  2. These authors contributed equally: Dean Clift, Chun So.

Authors and Affiliations

  1. Laboratory of Molecular Biology, Medical Research Council, Cambridge, UK

    Dean Clift, William A. McEwan, Leo C. James & Melina Schuh

  2. Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

    Chun So & Melina Schuh

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Contributions

D.C. and M.S. conceived and designed the study. D.C. carried out all experiments, with the following exceptions: C.S. simplified and optimized the methods for conducting Trim-Away experiments in mouse oocytes and early embryos, and optimized the peptide-binding assay. W.A.M. and D.C. optimized antibody electroporation. W.A.M. generated and characterized stable cell lines. D.C. and L.C.J. purified recombinant TRIM21 protein. C.S. and D.C. prepared figures. L.C.J. wrote the section on antibody purification; W.A.M. wrote the section on generating stable cell lines; and C.S., D.C. and M.S. wrote all other sections of the manuscript. All authors edited the manuscript. M.S. supervised the study.

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Correspondence to Dean Clift, Leo C. James or Melina Schuh.

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Key reference using this protocol

1. Clift, D. et al. Cell 171, 1692–1706.e18 (2017) https://doi.org/10.1016/j.cell.2017.10.033

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Clift, D., So, C., McEwan, W.A. et al. Acute and rapid degradation of endogenous proteins by Trim-Away. Nat Protoc 13, 2149–2175 (2018). https://doi.org/10.1038/s41596-018-0028-3

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