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

Asuka Higo, Noriko Saihara, Fumihito Miura, Yoko Higashi, Megumi Yamada, Shojiro Tamaki, Tasuku Ito, Yoshiaki Tarutani, Tomoaki Sakamoto, Masayuki Fujiwara, Tetsuya Kurata, Yoichiro Fukao, Satoru Moritoh, Rie Terada, Toshinori Kinoshita, Takashi Ito, Tetsuji Kakutani, Ko Shimamoto and Hiroyuki Tsuji ()
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Asuka Higo: Yokohama City University
Noriko Saihara: Yokohama City University
Fumihito Miura: Kyushu University Graduate School of Medical Sciences, Fukuoka
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
Yoshiaki Tarutani: National Institute of Genetics
Tomoaki Sakamoto: Nara Institute of Science and Technology, Ikoma
Masayuki Fujiwara: Nara Institute of Science and Technology, Ikoma
Tetsuya Kurata: Nara Institute of Science and Technology, Ikoma
Yoichiro Fukao: Nara Institute of Science and Technology, Ikoma
Satoru Moritoh: National Institute for Physiological Sciences
Rie Terada: Meijo University
Toshinori Kinoshita: Nagoya University
Takashi Ito: Kyushu University Graduate School of Medical Sciences, Fukuoka
Tetsuji Kakutani: National Institute of Genetics
Ko Shimamoto: Nara Institute of Science and Technology, Ikoma
Hiroyuki Tsuji: Yokohama City University

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17963-2

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