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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

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Listed:
  • Jiangping He

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL)
    University of Chinese Academy of Sciences)

  • Xiuling Fu

    (Southern University of Science and Technology)

  • Meng Zhang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL)
    University of Chinese Academy of Sciences)

  • Fangfang He

    (Southern University of Science and Technology)

  • Wenjuan Li

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Mazid Md. Abdul

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL)
    University of Chinese Academy of Sciences)

  • Jianguo Zhou

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL)
    Chinese Academy of Sciences)

  • Li Sun

    (Southern University of Science and Technology)

  • Chen Chang

    (Southern University of Science and Technology)

  • Yuhao Li

    (Southern University of Science and Technology)

  • He Liu

    (Chinese Academy of Sciences)

  • Kaixin Wu

    (Chinese Academy of Sciences)

  • Isaac A. Babarinde

    (Southern University of Science and Technology)

  • Qiang Zhuang

    (Southern University of Science and Technology
    Nankai University)

  • Yuin-Han Loh

    (A*STAR Institute of Molecular and Cell Biology
    National University of Singapore)

  • Jiekai Chen

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL))

  • Miguel A. Esteban

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL)
    Chinese Academy of Sciences)

  • Andrew P. Hutchins

    (Southern University of Science and Technology)

Abstract

The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability and are carefully regulated by the epigenetic system. However, the full complexity of this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that TEs are suppressed by heterochromatic marks like H3K9me3, and are also labelled by all major types of chromatin modification in complex patterns, including bivalent activatory and repressive marks. We identified 29 epigenetic modifiers that significantly deregulated at least one type of TE. The loss of Setdb1, Ncor2, Rnf2, Kat5, Prmt5, Uhrf1, and Rrp8 caused widespread changes in TE expression and chromatin accessibility. These effects were context-specific, with different chromatin modifiers regulating the expression and chromatin accessibility of specific subsets of TEs. Our work reveals the complex patterns of epigenetic regulation of TEs.

Suggested Citation

  • Jiangping He & Xiuling Fu & Meng Zhang & Fangfang He & Wenjuan Li & Mazid Md. Abdul & Jianguo Zhou & Li Sun & Chen Chang & Yuhao Li & He Liu & Kaixin Wu & Isaac A. Babarinde & Qiang Zhuang & Yuin-Han , 2019. "Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-08006-y
    DOI: 10.1038/s41467-018-08006-y
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    Cited by:

    1. Mujahid Ali & Lubna Younas & Jing Liu & Huangyi He & Xinpei Zhang & Qi Zhou, 2024. "Development and evolution of Drosophila chromatin landscape in a 3D genome context," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Chunhong Yu & Xiaoyun Lei & Fang Chen & Song Mao & Lu Lv & Honglu Liu & Xueying Hu & Runhan Wang & Licong Shen & Na Zhang & Yang Meng & Yunfan Shen & Jiale Chen & Pishun Li & Shi Huang & Changwei Lin , 2022. "ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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