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

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. Tarafder, Jan Löwe, Bee L. Ng, Ya Guo, Jacky Guy, Miles K. Huseyin, Robert J. Klose, Matthias Merkenschlager and Amanda G. Fisher ()
Additional contact information
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

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17823-z

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