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DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem

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Listed:
  • Asuka Higo

    (Yokohama City University)

  • Noriko Saihara

    (Yokohama City University
    Nara Institute of Science and Technology, Ikoma)

  • Fumihito Miura

    (Kyushu University Graduate School of Medical Sciences, Fukuoka
    Japan Science and Technology Agency (JST))

  • Yoko Higashi

    (Nara Institute of Science and Technology, Ikoma)

  • Megumi Yamada

    (Nara Institute of Science and Technology, Ikoma)

  • Shojiro Tamaki

    (Nara Institute of Science and Technology, Ikoma)

  • Tasuku Ito

    (National Institute of Genetics
    The Graduate University for Advanced Studies (SOKENDAI)
    Norwich Research Park)

  • Yoshiaki Tarutani

    (National Institute of Genetics)

  • Tomoaki Sakamoto

    (Nara Institute of Science and Technology, Ikoma
    Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku)

  • Masayuki Fujiwara

    (Nara Institute of Science and Technology, Ikoma
    YANMAR HOLDINGS Co. Ltd.)

  • Tetsuya Kurata

    (Nara Institute of Science and Technology, Ikoma
    EditForce Inc.)

  • Yoichiro Fukao

    (Nara Institute of Science and Technology, Ikoma
    Ritsumeikan University, Kusatsu)

  • Satoru Moritoh

    (National Institute for Physiological Sciences
    Ritsumeikan University, Kusatsu)

  • Rie Terada

    (Meijo University)

  • Toshinori Kinoshita

    (Nagoya University)

  • Takashi Ito

    (Kyushu University Graduate School of Medical Sciences, Fukuoka)

  • Tetsuji Kakutani

    (National Institute of Genetics
    The Graduate University for Advanced Studies (SOKENDAI)
    The University of Tokyo, Bunkyo-ku)

  • Ko Shimamoto

    (Nara Institute of Science and Technology, Ikoma)

  • Hiroyuki Tsuji

    (Yokohama City University)

Abstract

DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we show that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also show that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.

Suggested Citation

  • Asuka Higo & Noriko Saihara & Fumihito Miura & Yoko Higashi & Megumi Yamada & Shojiro Tamaki & Tasuku Ito & Yoshiaki Tarutani & Tomoaki Sakamoto & Masayuki Fujiwara & Tetsuya Kurata & Yoichiro Fukao &, 2020. "DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17963-2
    DOI: 10.1038/s41467-020-17963-2
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    Cited by:

    1. Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Jian Zeng & Xin’Ai Zhao & Zhe Liang & Inés Hidalgo & Michael Gebert & Pengfei Fan & Christian Wenzl & Sebastian G. Gornik & Jan U. Lohmann, 2023. "Nitric oxide controls shoot meristem activity via regulation of DNA methylation," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Li He & Huan Huang & Mariem Bradai & Cheng Zhao & Yin You & Jun Ma & Lun Zhao & Rosa Lozano-Durán & Jian-Kang Zhu, 2022. "DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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