IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-33246-4.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-33246-4
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-33246-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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.
    2. 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.
    3. 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.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Christoph Grohmann & Charlene M. Magtoto & Joel R. Walker & Ngee Kiat Chua & Anna Gabrielyan & Mary Hall & Simon A. Cobbold & Stephen Mieruszynski & Martin Brzozowski & Daniel S. Simpson & Hao Dong & , 2022. "Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Motoi Yamashita & Chihiro Ogawa & Baihao Zhang & Tetsuro Kobayashi & Aneela Nomura & Clive Barker & Chengcheng Zou & Satoshi Yamanaka & Ken-ichiro Hayashi & Yoichi Shinkai & Kazuyo Moro & Sidonia Farg, 2024. "Cell-type specific, inducible and acute degradation of targeted protein in mice by two degron systems," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Simone Sanzo & Katrin Spengler & Anja Leheis & Joanna M. Kirkpatrick & Theresa L. Rändler & Tim Baldensperger & Therese Dau & Christian Henning & Luca Parca & Christian Marx & Zhao-Qi Wang & Marcus A., 2021. "Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation," Nature Communications, Nature, vol. 12(1), pages 1-22, December.
    4. Henrik M. Hammarén & Eva-Maria Geissen & Clement M. Potel & Martin Beck & Mikhail M. Savitski, 2022. "Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Jacopo Gabrielli & Roberto Di Blasi & Cleo Kontoravdi & Francesca Ceroni, 2025. "Degradation bottlenecks and resource competition in transiently and stably engineered mammalian cells," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    6. Haiyan Gu & Jing Yang & Jiayu Zhang & Ying Song & Yao Zhang & Pengfei Xu & Yuanxiang Zhu & Liangliang Wang & Pengfei Zhang & Lin Li & Dahua Chen & Qinmiao Sun, 2022. "PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Varadha Balaji Venkadakrishnan & Adam G. Presser & Richa Singh & Matthew A. Booker & Nicole A. Traphagen & Kenny Weng & Nathaniel C. E. Voss & Navin R. Mahadevan & Kei Mizuno & Loredana Puca & Osasena, 2024. "Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. Ai Kiyomitsu & Toshiya Nishimura & Shiang Jyi Hwang & Satoshi Ansai & Masato T. Kanemaki & Minoru Tanaka & Tomomi Kiyomitsu, 2024. "Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    9. François Serra & Andrea Nieto-Aliseda & Lucía Fanlo-Escudero & Llorenç Rovirosa & Mónica Cabrera-Pasadas & Aleksey Lazarenkov & Blanca Urmeneta & Alvaro Alcalde-Merino & Emanuele M. Nola & Andrei L. O, 2024. "p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    10. Feng Yuan & Yi Li & Xinyue Zhou & Peiyuan Meng & Peng Zou, 2023. "Spatially resolved mapping of proteome turnover dynamics with subcellular precision," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. Yosuke Komata & Akinori Kanai & Takahiro Maeda & Toshiya Inaba & Akihiko Yokoyama, 2023. "MOZ/ENL complex is a recruiting factor of leukemic AF10 fusion proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Kosuke Yamaguchi & Xiaoying Chen & Brianna Rodgers & Fumihito Miura & Pavel Bashtrykov & Frédéric Bonhomme & Catalina Salinas-Luypaert & Deis Haxholli & Nicole Gutekunst & Bihter Özdemir Aygenli & Lau, 2024. "Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    13. Swee Y. Sharp & Marianna Martella & Sabrina D’Agostino & Christopher I. Milton & George Ward & Andrew J. Woodhead & Caroline J. Richardson & Maria G. Carr & Elisabetta Chiarparin & Benjamin D. Cons & , 2024. "Integrating fragment-based screening with targeted protein degradation and genetic rescue to explore eIF4E function," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    14. Alexander Chan & Rebecca M. Haley & Mohd Altaf Najar & David Gonzalez-Martinez & Lukasz J. Bugaj & George M. Burslem & Michael J. Mitchell & Andrew Tsourkas, 2024. "Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    15. Thao Nguyen & Eli J. Costa & Tim Deibert & Jose Reyes & Felix C. Keber & Miroslav Tomschik & Michael Stadlmeier & Meera Gupta & Chirag K. Kumar & Edward R. Cruz & Amanda Amodeo & Jesse C. Gatlin & Mar, 2022. "Differential nuclear import sets the timing of protein access to the embryonic genome," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    16. Cornelius Bergmann & Kanaan Mousaei & Silvio O. Rizzoli & Tatjana Tchumatchenko, 2025. "How energy determines spatial localisation and copy number of molecules in neurons," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    17. Courtney A. Lovejoy & Sarah R. Wessel & Rahul Bhowmick & Yuki Hatoyama & Masato T. Kanemaki & Runxiang Zhao & David Cortez, 2025. "SRBD1 facilitates chromosome segregation by promoting topoisomerase IIα localization to mitotic chromosomes," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    18. Chrysanthi Kagiou & Jose A. Cisneros & Jakob Farnung & Joanna Liwocha & Fabian Offensperger & Kevin Dong & Ka Yang & Gary Tin & Christina S. Horstmann & Matthias Hinterndorfer & Joao A. Paulo & Natali, 2024. "Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    19. Ji Min Lee & Henrik M. Hammarén & Mikhail M. Savitski & Sung Hee Baek, 2023. "Control of protein stability by post-translational modifications," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    20. Roman Vetter & Dagmar Iber, 2022. "Precision of morphogen gradients in neural tube development," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33246-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.