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G1/S restriction point coordinates phasic gene expression and cell differentiation

Author

Listed:
  • Brian DeVeale

    (University of California San Francisco
    University of California San Francisco)

  • Leqian Liu

    (University of California San Francisco
    University of California San Francisco)

  • Ryan Boileau

    (University of California San Francisco
    University of California San Francisco)

  • Jennifer Swindlehurst-Chan

    (University of California San Francisco
    University of California San Francisco)

  • Bryan Marsh

    (University of California San Francisco
    University of California San Francisco)

  • Jacob W. Freimer

    (University of California San Francisco
    University of California San Francisco)

  • Adam Abate

    (University of California San Francisco
    University of California San Francisco
    Chan Zuckerberg Biohub)

  • Robert Blelloch

    (University of California San Francisco
    University of California San Francisco)

Abstract

Pluripotent embryonic stem cells have a unique cell cycle structure with a suppressed G1/S restriction point and little differential expression across the cell cycle phases. Here, we evaluate the link between G1/S restriction point activation, phasic gene expression, and cellular differentiation. Expression analysis reveals a gain in phasic gene expression across lineages between embryonic days E7.5 and E9.5. Genetic manipulation of the G1/S restriction point regulators miR-302 and P27 respectively accelerates or delays the onset of phasic gene expression in mouse embryos. Loss of miR-302-mediated p21 or p27 suppression expedites embryonic stem cell differentiation, while a constitutive Cyclin E mutant blocks it. Together, these findings uncover a causal relationship between emergence of the G1/S restriction point with a gain in phasic gene expression and cellular differentiation.

Suggested Citation

  • Brian DeVeale & Leqian Liu & Ryan Boileau & Jennifer Swindlehurst-Chan & Bryan Marsh & Jacob W. Freimer & Adam Abate & Robert Blelloch, 2022. "G1/S restriction point coordinates phasic gene expression and cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31101-0
    DOI: 10.1038/s41467-022-31101-0
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    References listed on IDEAS

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    1. Andrew McDavid & Lucas Dennis & Patrick Danaher & Greg Finak & Michael Krouse & Alice Wang & Philippa Webster & Joseph Beechem & Raphael Gottardo, 2014. "Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-10, July.
    2. Jenny Hsu & Julia Arand & Andrea Chaikovsky & Nancie A. Mooney & Janos Demeter & Caileen M. Brison & Romane Oliverio & Hannes Vogel & Seth M. Rubin & Peter K. Jackson & Julien Sage, 2019. "E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    3. Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
    4. Blanca Pijuan-Sala & Jonathan A. Griffiths & Carolina Guibentif & Tom W. Hiscock & Wajid Jawaid & Fernando J. Calero-Nieto & Carla Mulas & Ximena Ibarra-Soria & Richard C. V. Tyser & Debbie Lee Lian H, 2019. "A single-cell molecular map of mouse gastrulation and early organogenesis," Nature, Nature, vol. 566(7745), pages 490-495, February.
    5. Gennaro Gambardella & Annamaria Carissimo & Amy Chen & Luisa Cutillo & Tomasz J. Nowakowski & Diego di Bernardo & Robert Blelloch, 2017. "The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
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