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Integrative epigenomic and transcriptomic analysis reveals the requirement of JUNB for hematopoietic fate induction

Author

Listed:
  • Xia Chen

    (Tsinghua-Peking Center for Life Sciences
    Tsinghua University)

  • Peiliang Wang

    (Tsinghua University)

  • Hui Qiu

    (Tsinghua University
    Tsinghua University)

  • Yonglin Zhu

    (Tsinghua University)

  • Xingwu Zhang

    (Tsinghua University)

  • Yaxuan Zhang

    (Tsinghua University)

  • Fuyu Duan

    (Guangzhou Women and Children’s Medical Center)

  • Shuangyuan Ding

    (Tsinghua University)

  • Jianying Guo

    (Peking University Third Hospital)

  • Yue Huang

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Jie Na

    (Tsinghua University)

Abstract

Human pluripotent stem cell differentiation towards hematopoietic progenitor cell can serve as an in vitro model for human embryonic hematopoiesis, but the dynamic change of epigenome and transcriptome remains elusive. Here, we systematically profile the chromatin accessibility, H3K4me3 and H3K27me3 modifications, and the transcriptome of intermediate progenitors during hematopoietic progenitor cell differentiation in vitro. The integrative analyses reveal sequential opening-up of regions for the binding of hematopoietic transcription factors and stepwise epigenetic reprogramming of bivalent genes. Single-cell analysis of cells undergoing the endothelial-to-hematopoietic transition and comparison with in vivo hemogenic endothelial cells reveal important features of in vitro and in vivo hematopoiesis. We find that JUNB is an essential regulator for hemogenic endothelium specialization and endothelial-to-hematopoietic transition. These studies depict an epigenomic roadmap from human pluripotent stem cells to hematopoietic progenitor cells, which may pave the way to generate hematopoietic progenitor cells with improved developmental potentials.

Suggested Citation

  • Xia Chen & Peiliang Wang & Hui Qiu & Yonglin Zhu & Xingwu Zhang & Yaxuan Zhang & Fuyu Duan & Shuangyuan Ding & Jianying Guo & Yue Huang & Jie Na, 2022. "Integrative epigenomic and transcriptomic analysis reveals the requirement of JUNB for hematopoietic fate induction," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30789-4
    DOI: 10.1038/s41467-022-30789-4
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    1. Morgan Oatley & Özge Vargel Bölükbası & Valentine Svensson & Maya Shvartsman & Kerstin Ganter & Katharina Zirngibl & Polina V. Pavlovich & Vladislava Milchevskaya & Vladimira Foteva & Kedar N. Nataraj, 2020. "Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition," Nature Communications, Nature, vol. 11(1), pages 1-18, December.
    2. Michael J. Chen & Tomomasa Yokomizo & Brandon M. Zeigler & Elaine Dzierzak & Nancy A. Speck, 2009. "Runx1 is required for the endothelial to haematopoietic cell transition but not thereafter," Nature, Nature, vol. 457(7231), pages 887-891, February.
    3. Linda T. Vo & Melissa A. Kinney & Xin Liu & Yuannyu Zhang & Jessica Barragan & Patricia M. Sousa & Deepak K. Jha & Areum Han & Marcella Cesana & Zhen Shao & Trista E. North & Stuart H. Orkin & Sergei , 2018. "Regulation of embryonic haematopoietic multipotency by EZH1," Nature, Nature, vol. 553(7689), pages 506-510, January.
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