IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-50144-z.html
   My bibliography  Save this article

Cell fate decision by a morphogen-transcription factor-chromatin modifier axis

Author

Listed:
  • Jin Ming

    (Westlake University
    Westlake Institute for Advanced Study
    Chinese Academy of Sciences)

  • Lihui Lin

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jiajun Li

    (Westlake University
    Westlake Institute for Advanced Study)

  • Linlin Wu

    (Westlake University
    Westlake Institute for Advanced Study)

  • Shicai Fang

    (Chinese Academy of Sciences)

  • Tao Huang

    (Westlake University
    Westlake Institute for Advanced Study)

  • Yu Fu

    (Westlake University
    Westlake Institute for Advanced Study)

  • Dong Liu

    (Westlake University
    Westlake Institute for Advanced Study)

  • Wenhui Zhang

    (Westlake University
    Westlake Institute for Advanced Study)

  • Chen Li

    (Chinese Academy of Sciences)

  • Yongzheng Yang

    (Chinese Academy of Sciences)

  • Yi Huang

    (Chinese Academy of Sciences)

  • Yue Qin

    (Westlake University
    Westlake Institute for Advanced Study)

  • Junqi Kuang

    (Westlake University
    Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Xingnan Huang

    (Westlake University
    Westlake Institute for Advanced Study)

  • Liman Guo

    (Chinese Academy of Sciences)

  • Xiaofei Zhang

    (Chinese Academy of Sciences)

  • Jing Liu

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jiekai Chen

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Chengchen Zhao

    (Westlake University)

  • Bo Wang

    (Westlake University
    School of Information and Electronic Engineering
    Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province)

  • Duanqing Pei

    (Westlake University
    Westlake Laboratory of Life Sciences and Biomedicine)

Abstract

Cell fate decisions remain poorly understood at the molecular level. Embryogenesis provides a unique opportunity to analyze molecular details associated with cell fate decisions. Works based on model organisms have provided a conceptual framework of genes that specify cell fate control, for example, transcription factors (TFs) controlling processes from pluripotency to immunity1. How TFs specify cell fate remains poorly understood. Here we report that SALL4 relies on NuRD (nucleosome-remodeling and deacetylase complex) to interpret BMP4 signal and decide cell fate in a well-controlled in vitro system. While NuRD complex cooperates with SALL4 to convert mouse embryonic fibroblasts or MEFs to pluripotency, BMP4 diverts the same process to an alternative fate, PrE (primitive endoderm). Mechanistically, BMP4 signals the dissociation of SALL4 from NuRD physically to establish a gene regulatory network for PrE. Our results provide a conceptual framework to explore the rich landscapes of cell fate choices intrinsic to development in higher organisms involving morphogen-TF-chromatin modifier pathways.

Suggested Citation

  • Jin Ming & Lihui Lin & Jiajun Li & Linlin Wu & Shicai Fang & Tao Huang & Yu Fu & Dong Liu & Wenhui Zhang & Chen Li & Yongzheng Yang & Yi Huang & Yue Qin & Junqi Kuang & Xingnan Huang & Liman Guo & Xia, 2024. "Cell fate decision by a morphogen-transcription factor-chromatin modifier axis," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50144-z
    DOI: 10.1038/s41467-024-50144-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-50144-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-50144-z?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. Anastasiia Lozovska & Artemis G. Korovesi & André Dias & Alexandre Lopes & Donald A. Fowler & Gabriel G. Martins & Ana Nóvoa & Moisés Mallo, 2024. "Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Shengyong Yu & Chunhua Zhou & Jiangping He & Zhaokai Yao & Xingnan Huang & Bowen Rong & Hong Zhu & Shijie Wang & Shuyan Chen & Xialian Wang & Baomei Cai & Guoqing Zhao & Yuhan Chen & Lizhan Xiao & He , 2022. "BMP4 drives primed to naïve transition through PGC-like state," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Monique Pedroza & Seher Ipek Gassaloglu & Nicolas Dias & Liangwen Zhong & Tien-Chi Jason Hou & Helene Kretzmer & Zachary D. Smith & Berna Sozen, 2023. "Self-patterning of human stem cells into post-implantation lineages," Nature, Nature, vol. 622(7983), pages 574-583, October.
    4. Abed AlFatah Mansour & Ohad Gafni & Leehee Weinberger & Asaf Zviran & Muneef Ayyash & Yoach Rais & Vladislav Krupalnik & Mirie Zerbib & Daniela Amann-Zalcenstein & Itay Maza & Shay Geula & Sergey Viuk, 2012. "The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming," Nature, Nature, vol. 488(7411), pages 409-413, August.
    5. 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.
    6. Bo Wang & Chen Li & Jin Ming & Linlin Wu & Shicai Fang & Yi Huang & Lihui Lin & He Liu & Junqi Kuang & Chengchen Zhao & Xingnan Huang & Huijian Feng & Jing Guo & Xuejie Yang & Liman Guo & Xiaofei Zhan, 2023. "The NuRD complex cooperates with SALL4 to orchestrate reprogramming," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Mona S. Spector & Serge Desnoyers & Daniel J. Hoeppner & Michael O. Hengartner, 1997. "Interaction between the C. elegans cell-death regulators CED-9 and CED-4," Nature, Nature, vol. 385(6617), pages 653-656, February.
    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. Luke Simpson & Andrew Strange & Doris Klisch & Sophie Kraunsoe & Takuya Azami & Daniel Goszczynski & Triet Minh & Benjamin Planells & Nadine Holmes & Fei Sang & Sonal Henson & Matthew Loose & Jennifer, 2024. "A single-cell atlas of pig gastrulation as a resource for comparative embryology," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Yueli Yang & Wenqi Jia & Zhiwei Luo & Yunpan Li & Hao Liu & Lixin Fu & Jinxiu Li & Yu Jiang & Junjian Lai & Haiwei Li & Babangida Jabir Saeed & Yi Zou & Yuan Lv & Liang Wu & Ting Zhou & Yongli Shan & , 2024. "VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Allen W. Lynch & Myles Brown & Clifford A. Meyer, 2023. "Multi-batch single-cell comparative atlas construction by deep learning disentanglement," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    4. Karin D. Prummel & Helena L. Crowell & Susan Nieuwenhuize & Eline C. Brombacher & Stephan Daetwyler & Charlotte Soneson & Jelena Kresoja-Rakic & Agnese Kocere & Manuel Ronner & Alexander Ernst & Zahra, 2022. "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    5. Daniel F. Kaemena & Masahito Yoshihara & Meryam Beniazza & James Ashmore & Suling Zhao & Mårten Bertenstam & Victor Olariu & Shintaro Katayama & Keisuke Okita & Simon R. Tomlinson & Kosuke Yusa & Keis, 2023. "B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    6. Nimrod Rappoport & Elad Chomsky & Takashi Nagano & Charlie Seibert & Yaniv Lubling & Yael Baran & Aviezer Lifshitz & Wing Leung & Zohar Mukamel & Ron Shamir & Peter Fraser & Amos Tanay, 2023. "Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. 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.
    8. Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt, 2016. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-39, July.
    9. D. M. Jeziorska & E. A. J. Tunnacliffe & J. M. Brown & H. Ayyub & J. Sloane-Stanley & J. A. Sharpe & B. C. Lagerholm & C. Babbs & A. J. H. Smith & V. J. Buckle & D. R. Higgs, 2022. "On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    10. Shengyong Yu & Chunhua Zhou & Jiangping He & Zhaokai Yao & Xingnan Huang & Bowen Rong & Hong Zhu & Shijie Wang & Shuyan Chen & Xialian Wang & Baomei Cai & Guoqing Zhao & Yuhan Chen & Lizhan Xiao & He , 2022. "BMP4 drives primed to naïve transition through PGC-like state," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    11. Geethika Arekatla & Stavroula Skylaki & David Corredor Suarez & Hartland Jackson & Denis Schapiro & Stefanie Engler & Markus Auler & German Camargo Ortega & Simon Hastreiter & Andreas Reimann & Dirk L, 2024. "Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Yi-Cheng Chang & Jan Manent & Jan Schroeder & Siew Fen Lisa Wong & Gabriel M. Hauswirth & Natalia A. Shylo & Emma L. Moore & Annita Achilleos & Victoria Garside & Jose M. Polo & Paul Trainor & Edwina , 2022. "Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    13. Andreas Fønss Møller & Jesper Grud Skat Madsen, 2023. "JOINTLY: interpretable joint clustering of single-cell transcriptomes," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    14. 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.
    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. 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.
    17. 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.
    18. Ajita Shree & Musale Krushna Pavan & Hamim Zafar, 2023. "scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    19. Tao Huang & Dong Liu & Xiaomin Wang & Junqi Kuang & Manqi Wu & Beibei Wang & Zechuan Liang & Yixin Fan & Bo Chen & Zhaoyi Ma & Yu Fu & Wenhui Zhang & Jin Ming & Yue Qin & Chengchen Zhao & Bo Wang & Du, 2024. "Engineering mouse cell fate controller by rational design," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    20. Mingze Gao & Chen Qiao & Yuanhua Huang, 2022. "UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference," Nature Communications, Nature, vol. 13(1), pages 1-11, 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:15:y:2024:i:1:d:10.1038_s41467-024-50144-z. 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.