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Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation

Author

Listed:
  • Satoyo Oya

    (The University of Tokyo)

  • Mayumi Takahashi

    (National Institute of Genetics)

  • Kazuya Takashima

    (National Institute of Genetics)

  • Tetsuji Kakutani

    (The University of Tokyo
    National Institute of Genetics)

  • Soichi Inagaki

    (The University of Tokyo
    PRESTO, Japan Science and Technology Agency)

Abstract

Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.

Suggested Citation

  • Satoyo Oya & Mayumi Takahashi & Kazuya Takashima & Tetsuji Kakutani & Soichi Inagaki, 2022. "Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32165-8
    DOI: 10.1038/s41467-022-32165-8
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    References listed on IDEAS

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    3. Hiroya Ishihara & Kaoru Sugimoto & Paul T. Tarr & Haruka Temman & Satoshi Kadokura & Yayoi Inui & Takuya Sakamoto & Taku Sasaki & Mitsuhiro Aida & Takamasa Suzuki & Soichi Inagaki & Kengo Morohashi & , 2019. "Primed histone demethylation regulates shoot regenerative competency," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
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    1. Xiaozhen Zhao & Yiming Wang & Bingqin Yuan & Hanxi Zhao & Yujie Wang & Zheng Tan & Zhiyuan Wang & Huijun Wu & Gang Li & Wei Song & Ravi Gupta & Kenichi Tsuda & Zhonghua Ma & Xuewen Gao & Qin Gu, 2024. "Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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