IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-57537-8.html
   My bibliography  Save this article

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells

Author

Listed:
  • Camilla Rega

    (The Institute of Cancer Research)

  • Ifigenia Tsitsa

    (The Institute of Cancer Research)

  • Theodoros I. Roumeliotis

    (The Institute of Cancer Research)

  • Izabella Krystkowiak

    (The Institute of Cancer Research)

  • Maria Portillo

    (The Institute of Cancer Research)

  • Lu Yu

    (The Institute of Cancer Research)

  • Julia Vorhauser

    (The Institute of Cancer Research)

  • Jonathon Pines

    (The Institute of Cancer Research)

  • Jörg Mansfeld

    (The Institute of Cancer Research)

  • Jyoti Choudhary

    (The Institute of Cancer Research)

  • Norman E. Davey

    (The Institute of Cancer Research)

Abstract

The cell cycle governs a precise series of molecular events, regulated by coordinated changes in protein and phosphorylation abundance, that culminates in the generation of two daughter cells. Here, we present a proteomic and phosphoproteomic analysis of the human cell cycle in hTERT-RPE-1 cells using deep quantitative mass spectrometry by isobaric labelling. By analysing non-transformed cells and improving the temporal resolution and coverage of key cell cycle regulators, we present a dataset of cell cycle-dependent protein and phosphorylation site oscillation that offers a foundational reference for investigating cell cycle regulation. These data reveal regulatory intricacies including proteins and phosphorylation sites exhibiting cell cycle-dependent oscillation, and proteins targeted for degradation during mitotic exit. Integrated with complementary resources, our data link cycle-dependent abundance dynamics to functional changes and are accessible through the Cell Cycle database (CCdb), an interactive web-based resource for the cell cycle community.

Suggested Citation

  • Camilla Rega & Ifigenia Tsitsa & Theodoros I. Roumeliotis & Izabella Krystkowiak & Maria Portillo & Lu Yu & Julia Vorhauser & Jonathon Pines & Jörg Mansfeld & Jyoti Choudhary & Norman E. Davey, 2025. "High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57537-8
    DOI: 10.1038/s41467-025-57537-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-57537-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-57537-8?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. David Walter & Saskia Hoffmann & Eirini-Stavroula Komseli & Juri Rappsilber & Vassilis Gorgoulis & Claus Storgaard Sørensen, 2016. "SCFCyclin F-dependent degradation of CDC6 suppresses DNA re-replication," Nature Communications, Nature, vol. 7(1), pages 1-10, April.
    2. Diana Mahdessian & Anthony J. Cesnik & Christian Gnann & Frida Danielsson & Lovisa Stenström & Muhammad Arif & Cheng Zhang & Trang Le & Fredric Johansson & Rutger Schutten & Anna Bäckström & Ulrika Ax, 2021. "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics," Nature, Nature, vol. 590(7847), pages 649-654, February.
    3. Paul Adrian Ginno & Lukas Burger & Jan Seebacher & Vytautas Iesmantavicius & Dirk Schübeler, 2018. "Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape," Nature Communications, Nature, vol. 9(1), pages 1-12, 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. Rebecca J. Harris & Maninder Heer & Mark D. Levasseur & Tyrell N. Cartwright & Bethany Weston & Jennifer L. Mitchell & Jonathan M. Coxhead & Luke Gaughan & Lisa Prendergast & Daniel Rico & Jonathan M., 2023. "Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Daniel Dimitrov & Dénes Türei & Martin Garrido-Rodriguez & Paul L. Burmedi & James S. Nagai & Charlotte Boys & Ricardo O. Ramirez Flores & Hyojin Kim & Bence Szalai & Ivan G. Costa & Alberto Valdeoliv, 2022. "Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Ana Martinez-Val & Dorte B. Bekker-Jensen & Sophia Steigerwald & Claire Koenig & Ole Østergaard & Adi Mehta & Trung Tran & Krzysztof Sikorski & Estefanía Torres-Vega & Ewa Kwasniewicz & Sólveig Hlín B, 2021. "Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    4. Juan Manuel Valverde & Geronimo Dubra & Michael Phillips & Austin Haider & Carlos Elena-Real & Aurélie Fournet & Emile Alghoul & Dhanvantri Chahar & Nuria Andrés-Sanchez & Matteo Paloni & Pau Bernadó , 2023. "A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation," Nature Communications, Nature, vol. 14(1), pages 1-23, 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:16:y:2025:i:1:d:10.1038_s41467-025-57537-8. 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.