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

Asuka Higo,Rie Terada,Toshinori Kinoshita,Yoshiaki Tarutani,Noriko Saihara,Megumi Yamada,Tomoaki Sakamoto,Hiroyuki Tsuji,Fumihito Miura,Tetsuji Kakutani,Tetsuya Kurata,Takashi Ito,Ko Shimamoto,Satoru Moritoh,Shojiro Tamaki,Tasuku Ito,Yoko Higashi,Yoichiro Fukao,Masayuki Fujiwara

doi:10.1038/s41467-020-17963-2

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.

Highlights

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
For the CG and CHG contexts, methylated cytosines were enriched in the pericentromeric regions in vegetative and reproductive shoot apical meristem (SAM) and mature leaves, and the methylation levels of these cytosines were generally comparable among the tested organs
The CHH context was globally changed: CHH methylation levels were higher in the vegetative SAM than in mature leaves, and global CHH hypermethylation occurred during the vegetative-to-reproductive transition in the SAM

Summary

Introduction

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. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs. DNA methylation is an epigenetic modification in which cytosine residues are methylated in three sequence contexts (CG, CHG, and CHH, where H is a nucleotide other than G). To reveal features of DNA methylation in the SAM and its mechanism of regulation, we generated single-base-resolution maps of cytosine methylation by whole-genome bisulfite sequencing (BS-seq), and performed RNA-seq, small RNA-seq (smRNA-seq), and proteome analysis of the SAMs in the vegetative and reproductive stages and in mature leaf blades (Supplementary Fig. 1b and Supplementary Table 1). We further propose that two rounds of DNA methylation occur during plant reproduction: first, reconfiguration at the edges of TEs in the SAM, and second, reprogramming in the bodies and at the edges of TEs during germ cell differentiation

Methods

Results

Conclusion