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Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction

Author

Listed:
  • Dounia Djeghloul

    (Hammersmith Hospital Campus)

  • Bhavik Patel

    (Hammersmith Hospital Campus)

  • Holger Kramer

    (Hammersmith Hospital Campus)

  • Andrew Dimond

    (Hammersmith Hospital Campus)

  • Chad Whilding

    (Hammersmith Hospital Campus)

  • Karen Brown

    (Hammersmith Hospital Campus)

  • Anne-Céline Kohler

    (Hammersmith Hospital Campus)

  • Amelie Feytout

    (Hammersmith Hospital Campus)

  • Nicolas Veland

    (Hammersmith Hospital Campus)

  • James Elliott

    (Hammersmith Hospital Campus)

  • Tanmay A. M. Bharat

    (University of Oxford)

  • Abul K. Tarafder

    (University of Oxford)

  • Jan Löwe

    (MRC Laboratory of Molecular Biology)

  • Bee L. Ng

    (Wellcome Genome Campus)

  • Ya Guo

    (Hammersmith Hospital Campus)

  • Jacky Guy

    (University of Edinburgh)

  • Miles K. Huseyin

    (University of Oxford)

  • Robert J. Klose

    (University of Oxford)

  • Matthias Merkenschlager

    (Hammersmith Hospital Campus)

  • Amanda G. Fisher

    (Hammersmith Hospital Campus)

Abstract

Epigenetic information is transmitted from mother to daughter cells through mitosis. Here, to identify factors that might play a role in conveying epigenetic memory through cell division, we report on the isolation of unfixed, native chromosomes from metaphase-arrested cells using flow cytometry and perform LC-MS/MS to identify chromosome-bound proteins. A quantitative proteomic comparison between metaphase-arrested cell lysates and chromosome-sorted samples reveals a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers such as PRC2 and DNA methyl-transferases, and proteins governing chromosome architecture. Deletion of PRC2, Dnmt1/3a/3b or Mecp2 in ESCs leads to an increase in the size of individual mitotic chromosomes, consistent with de-condensation. Similar results were obtained by the experimental cleavage of cohesin. Thus, we identify chromosome-bound factors in pluripotent stem cells during mitosis and reveal that PRC2, DNA methylation and Mecp2 are required to maintain chromosome compaction.

Suggested Citation

  • Dounia Djeghloul & Bhavik Patel & Holger Kramer & Andrew Dimond & Chad Whilding & Karen Brown & Anne-Céline Kohler & Amelie Feytout & Nicolas Veland & James Elliott & Tanmay A. M. Bharat & Abul K. Tar, 2020. "Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17823-z
    DOI: 10.1038/s41467-020-17823-z
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    Cited by:

    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. Rita Silvério-Alves & Ilia Kurochkin & Anna Rydström & Camila Vazquez Echegaray & Jakob Haider & Matthew Nicholls & Christina Rode & Louise Thelaus & Aida Yifter Lindgren & Alexandra Gabriela Ferreira, 2023. "GATA2 mitotic bookmarking is required for definitive haematopoiesis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Cristina Sayago & Jana Sánchez-Wandelmer & Fernando García & Begoña Hurtado & Vanesa Lafarga & Patricia Prieto & Eduardo Zarzuela & Pilar Ximénez-Embún & Sagrario Ortega & Diego Megías & Oscar Fernánd, 2023. "Decoding protein methylation function with thermal stability analysis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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