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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
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    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. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    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.
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