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Systematic profiling of conditional degron tag technologies for target validation studies

Author

Listed:
  • Daniel P. Bondeson

    (The Broad Institute of MIT and Harvard)

  • Zachary Mullin-Bernstein

    (The Broad Institute of MIT and Harvard)

  • Sydney Oliver

    (The Broad Institute of MIT and Harvard)

  • Thomas A. Skipper

    (The Broad Institute of MIT and Harvard)

  • Thomas C. Atack

    (The Broad Institute of MIT and Harvard)

  • Nolan Bick

    (The Broad Institute of MIT and Harvard)

  • Meilani Ching

    (The Broad Institute of MIT and Harvard)

  • Andrew A. Guirguis

    (The Broad Institute of MIT and Harvard
    Harvard Medical School
    Peter MacCallum Cancer Centre
    The University of Melbourne)

  • Jason Kwon

    (The Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Carly Langan

    (The Broad Institute of MIT and Harvard)

  • Dylan Millson

    (The Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Brenton R. Paolella

    (The Broad Institute of MIT and Harvard)

  • Kevin Tran

    (Peter MacCallum Cancer Centre
    The University of Melbourne)

  • Sarah J. Wie

    (The Broad Institute of MIT and Harvard)

  • Francisca Vazquez

    (The Broad Institute of MIT and Harvard)

  • Zuzana Tothova

    (The Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Todd R. Golub

    (The Broad Institute of MIT and Harvard
    Harvard Medical School)

  • William R. Sellers

    (The Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Alessandra Ianari

    (The Broad Institute of MIT and Harvard)

Abstract

Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the generalizability of genetic manipulation. However, successful design of a CDT fusion protein often requires a prolonged, ad hoc cycle of construct design, failure, and re-design. To address this limitation, we report here a system to rapidly compare the activity of five unique CDTs: AID/AID2, IKZF3d, dTAG, HaloTag, and SMASh. We demonstrate the utility of this system against 16 unique protein targets. We find that expression and degradation are highly dependent on the specific CDT, the construct design, and the target. None of the CDTs leads to efficient expression and/or degradation across all targets; however, our systematic approach enables the identification of at least one optimal CDT fusion for each target. To enable the adoption of CDT strategies more broadly, we have made these reagents, and a detailed protocol, available as a community resource.

Suggested Citation

  • Daniel P. Bondeson & Zachary Mullin-Bernstein & Sydney Oliver & Thomas A. Skipper & Thomas C. Atack & Nolan Bick & Meilani Ching & Andrew A. Guirguis & Jason Kwon & Carly Langan & Dylan Millson & Bren, 2022. "Systematic profiling of conditional degron tag technologies for target validation studies," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33246-4
    DOI: 10.1038/s41467-022-33246-4
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    References listed on IDEAS

    as
    1. Michael A. Erb & Thomas G. Scott & Bin E. Li & Huafeng Xie & Joshiawa Paulk & Hyuk-Soo Seo & Amanda Souza & Justin M. Roberts & Shiva Dastjerdi & Dennis L. Buckley & Neville E. Sanjana & Ophir Shalem , 2017. "Transcription control by the ENL YEATS domain in acute leukaemia," Nature, Nature, vol. 543(7644), pages 270-274, March.
    2. Behnam Nabet & Fleur M. Ferguson & Bo Kyung A. Seong & Miljan Kuljanin & Alan L. Leggett & Mikaela L. Mohardt & Amanda Robichaud & Amy S. Conway & Dennis L. Buckley & Joseph D. Mancias & James E. Brad, 2020. "Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
    3. Aisha Yesbolatova & Yuichiro Saito & Naomi Kitamoto & Hatsune Makino-Itou & Rieko Ajima & Risako Nakano & Hirofumi Nakaoka & Kosuke Fukui & Kanae Gamo & Yusuke Tominari & Haruki Takeuchi & Yumiko Saga, 2020. "The auxin-inducible degron 2 technology provides sharp degradation control in yeast, mammalian cells, and mice," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    4. Toby Mathieson & Holger Franken & Jan Kosinski & Nils Kurzawa & Nico Zinn & Gavain Sweetman & Daniel Poeckel & Vikram S. Ratnu & Maike Schramm & Isabelle Becher & Michael Steidel & Kyung-Min Noh & Gio, 2018. "Systematic analysis of protein turnover in primary cells," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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