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Setd2 supports GATA3+ST2+ thymic-derived Treg cells and suppresses intestinal inflammation

Author

Listed:
  • Zhaoyun Ding

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences)

  • Ting Cai

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences
    Guangdong Academy of Medical Sciences)

  • Jupei Tang

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences)

  • Hanxiao Sun

    (Shanghai Jiao Tong University School of Medicine)

  • Xinyi Qi

    (Shanghai Jiao Tong University School of Medicine (SJTUSM))

  • Yunpeng Zhang

    (Shanghai Jiao Tong University School of Medicine)

  • Yan Ji

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences)

  • Liyun Yuan

    (University of Chinese Academy of Sciences, Chinese Academy of Science)

  • Huidan Chang

    (University of Chinese Academy of Sciences, Chinese Academy of Science)

  • Yanhui Ma

    (Shanghai Jiao Tong University School of Medicine)

  • Hong Zhou

    (Anhui Medical University)

  • Li Li

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Huiming Sheng

    (Shanghai Jiao Tong University School of Medicine)

  • Ju Qiu

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences)

Abstract

Treg cells acquire distinct transcriptional properties to suppress specific inflammatory responses. Transcription characteristics of Treg cells are regulated by epigenetic modifications, the mechanism of which remains obscure. Here, we report that Setd2, a histone H3K36 methyltransferase, is important for the survival and suppressive function of Treg cells, especially those from the intestine. Setd2 supports GATA3+ST2+ intestinal thymic-derived Treg (tTreg) cells by facilitating the expression and reciprocal relationship of GATA3 and ST2 in tTreg cells. IL-33 preferentially boosts Th2 cells rather than GATA3+ Treg cells in Foxp3Cre-YFPSetd2 flox/flox mice, corroborating the constraint of Th2 responses by Setd2 expression in Treg cells. SETD2 sustains GATA3 expression in human Treg cells, and SETD2 expression is increased in Treg cells from human colorectal cancer tissues. Epigenetically, Setd2 regulates the transcription of target genes (including Il1rl1) by modulating the activity of promoters and intragenic enhancers where H3K36me3 is typically deposited. Our findings provide mechanistic insights into the regulation of Treg cells and intestinal immunity by Setd2.

Suggested Citation

  • Zhaoyun Ding & Ting Cai & Jupei Tang & Hanxiao Sun & Xinyi Qi & Yunpeng Zhang & Yan Ji & Liyun Yuan & Huidan Chang & Yanhui Ma & Hong Zhou & Li Li & Huiming Sheng & Ju Qiu, 2022. "Setd2 supports GATA3+ST2+ thymic-derived Treg cells and suppresses intestinal inflammation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35250-0
    DOI: 10.1038/s41467-022-35250-0
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    1. Zhongzhong Ji & Yaru Sheng & Juju Miao & Xiaoxia Li & Huifang Zhao & Jinming Wang & Chaping Cheng & Xue Wang & Kaiyuan Liu & Kai Zhang & Longmei Xu & Jufang Yao & Lijing Shen & Jian Hou & Wenhao Zhou , 2019. "The histone methyltransferase Setd2 is indispensable for V(D)J recombination," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    2. Jason Ernst & Pouya Kheradpour & Tarjei S. Mikkelsen & Noam Shoresh & Lucas D. Ward & Charles B. Epstein & Xiaolan Zhang & Li Wang & Robbyn Issner & Michael Coyne & Manching Ku & Timothy Durham & Mano, 2011. "Mapping and analysis of chromatin state dynamics in nine human cell types," Nature, Nature, vol. 473(7345), pages 43-49, May.
    3. Mo Xu & Maria Pokrovskii & Yi Ding & Ren Yi & Christy Au & Oliver J. Harrison & Carolina Galan & Yasmine Belkaid & Richard Bonneau & Dan R. Littman, 2018. "c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont," Nature, Nature, vol. 554(7692), pages 373-377, February.
    4. Francesco Neri & Stefania Rapelli & Anna Krepelova & Danny Incarnato & Caterina Parlato & Giulia Basile & Mara Maldotti & Francesca Anselmi & Salvatore Oliviero, 2017. "Intragenic DNA methylation prevents spurious transcription initiation," Nature, Nature, vol. 543(7643), pages 72-77, March.
    5. Chris Schiering & Thomas Krausgruber & Agnieszka Chomka & Anja Fröhlich & Krista Adelmann & Elizabeth A. Wohlfert & Johanna Pott & Thibault Griseri & Julia Bollrath & Ahmed N. Hegazy & Oliver J. Harri, 2014. "The alarmin IL-33 promotes regulatory T-cell function in the intestine," Nature, Nature, vol. 513(7519), pages 564-568, September.
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