IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31101-0.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31101-0
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-31101-0?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. 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.
    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. Ran Wang & Xianfa Yang & Jiehui Chen & Lin Zhang & Jonathan A. Griffiths & Guizhong Cui & Yingying Chen & Yun Qian & Guangdun Peng & Jinsong Li & Liantang Wang & John C. Marioni & Patrick P. L. Tam & , 2023. "Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Monika Graf & Marta Interlandi & Natalia Moreno & Dörthe Holdhof & Carolin Göbel & Viktoria Melcher & Julius Mertins & Thomas K. Albert & Dennis Kastrati & Amelie Alfert & Till Holsten & Flavia de Far, 2022. "Single-cell transcriptomics identifies potential cells of origin of MYC rhabdoid tumors," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    3. Francisco X. Galdos & Sidra Xu & William R. Goodyer & Lauren Duan & Yuhsin V. Huang & Soah Lee & Han Zhu & Carissa Lee & Nicholas Wei & Daniel Lee & Sean M. Wu, 2022. "devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    4. Sivakamasundari Vijayakumar & Roberta Sala & Gugene Kang & Angela Chen & Michelle Ann Pablo & Abidemi Ismail Adebayo & Andrea Cipriano & Jonas L. Fowler & Danielle L. Gomes & Lay Teng Ang & Kyle M. Lo, 2023. "Monolayer platform to generate and purify primordial germ-like cells in vitro provides insights into human germline specification," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    5. Yasuaki Uehara & Yusuke Tanaka & Shuyang Zhao & Nikolaos M. Nikolaidis & Lori B. Pitstick & Huixing Wu & Jane J. Yu & Erik Zhang & Yoshihiro Hasegawa & John G. Noel & Jason C. Gardner & Elizabeth J. K, 2023. "Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    6. J. McClatchy & R. Strogantsev & E. Wolfe & H. Y. Lin & M. Mohammadhosseini & B. A. Davis & C. Eden & D. Goldman & W. H. Fleming & P. Conley & G. Wu & L. Cimmino & H. Mohammed & A. Agarwal, 2023. "Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Ci Fu & Xiang Zhang & Amanda O. Veri & Kali R. Iyer & Emma Lash & Alice Xue & Huijuan Yan & Nicole M. Revie & Cassandra Wong & Zhen-Yuan Lin & Elizabeth J. Polvi & Sean D. Liston & Benjamin VanderSlui, 2021. "Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    8. Junyi Chen & Xiaoying Wang & Anjun Ma & Qi-En Wang & Bingqiang Liu & Lang Li & Dong Xu & Qin Ma, 2022. "Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Kotaro Shimizu & Junichi Kikuta & Yumi Ohta & Yutaka Uchida & Yu Miyamoto & Akito Morimoto & Shinya Yari & Takashi Sato & Takefumi Kamakura & Kazuo Oshima & Ryusuke Imai & Yu-Chen Liu & Daisuke Okuzak, 2023. "Single-cell transcriptomics of human cholesteatoma identifies an activin A-producing osteoclastogenic fibroblast subset inducing bone destruction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    10. Young Hee Lee & Yu-Been Kim & Kyu Sik Kim & Mirae Jang & Ha Young Song & Sang-Ho Jung & Dong-Soo Ha & Joon Seok Park & Jaegeon Lee & Kyung Min Kim & Deok-Hyeon Cheon & Inhyeok Baek & Min-Gi Shin & Eun, 2023. "Lateral hypothalamic leptin receptor neurons drive hunger-gated food-seeking and consummatory behaviours in male mice," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Sandra Curras-Alonso & Juliette Soulier & Thomas Defard & Christian Weber & Sophie Heinrich & Hugo Laporte & Sophie Leboucher & Sonia Lameiras & Marie Dutreix & Vincent Favaudon & Florian Massip & Tho, 2023. "An interactive murine single-cell atlas of the lung responses to radiation injury," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Seung-Hyun Jung & Byung-Hee Hwang & Sun Shin & Eun-Hye Park & Sin-Hee Park & Chan Woo Kim & Eunmin Kim & Eunho Choo & Ik Jun Choi & Filip K. Swirski & Kiyuk Chang & Yeun-Jun Chung, 2022. "Spatiotemporal dynamics of macrophage heterogeneity and a potential function of Trem2hi macrophages in infarcted hearts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    13. Zhou Tang & Zhangsheng Yu & Cheng Wang, 2020. "A fast iterative algorithm for high-dimensional differential network," Computational Statistics, Springer, vol. 35(1), pages 95-109, March.
    14. Hailun Zhu & Sihai Dave Zhao & Alokananda Ray & Yu Zhang & Xin Li, 2022. "A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    15. Javier Rodríguez-Ubreva & Anna Arutyunyan & Marc Jan Bonder & Lucía Del Pino-Molina & Stephen J. Clark & Carlos de la Calle-Fabregat & Luz Garcia-Alonso & Louis-François Handfield & Laura Ciudad & Edu, 2022. "Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    16. Hannah Drew Rickner & Lulu Jiang & Rui Hong & Nicholas K. O’Neill & Chromewell A. Mojica & Benjamin J. Snyder & Lushuang Zhang & Dipan Shaw & Maria Medalla & Benjamin Wolozin & Christine S. Cheng, 2022. "Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    17. Jeremy Lotto & Rebecca Cullum & Sibyl Drissler & Martin Arostegui & Victoria C. Garside & Bettina M. Fuglerud & Makenna Clement-Ranney & Avinash Thakur & T. Michael Underhill & Pamela A. Hoodless, 2023. "Cell diversity and plasticity during atrioventricular heart valve EMTs," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    18. Kensuke Miyake & Junya Ito & Jun Nakabayashi & Shigeyuki Shichino & Kenji Ishiwata & Hajime Karasuyama, 2023. "Single cell transcriptomics clarifies the basophil differentiation trajectory and identifies pre-basophils upstream of mature basophils," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    19. Ryan G. Lim & Osama Al-Dalahmah & Jie Wu & Maxwell P. Gold & Jack C. Reidling & Guomei Tang & Miriam Adam & David K. Dansu & Hye-Jin Park & Patrizia Casaccia & Ricardo Miramontes & Andrea M. Reyes-Ort, 2022. "Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    20. Qian-Yue Zhang & Xiao-Ping Ye & Zheng Zhou & Chen-Fang Zhu & Rui Li & Ya Fang & Rui-Jia Zhang & Lu Li & Wei Liu & Zheng Wang & Shi-Yang Song & Sang-Yu Lu & Shuang-Xia Zhao & Jian-Nan Lin & Huai-Dong S, 2022. "Lymphocyte infiltration and thyrocyte destruction are driven by stromal and immune cell components in Hashimoto’s thyroiditis," Nature Communications, Nature, vol. 13(1), pages 1-18, 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_s41467-022-31101-0. 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.