Open Access Highly Accessed Research article

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

Xin Li12, Jingde Zhu34, Fengyi Hu5, Song Ge6, Mingzhi Ye2, Hui Xiang1, Guojie Zhang12, Xiaoming Zheng6, Hongyu Zhang3, Shilai Zhang5, Qiong Li5, Ruibang Luo27, Chang Yu2, Jian Yu3, Jingfeng Sun3, Xiaoyu Zou3, Xiaofeng Cao8, Xianfa Xie9*, Jun Wang102* and Wen Wang1*

Author Affiliations

1 CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China

2 BGI-Shenzhen, Shenzhen, 518083, China

3 Shanghai Cancer Institute, Renji Hospital affiliated to School of Medicine, Shanghai Jiaotong University, LN 2200/25, Xietu Road, Shanghai, 200032, China

4 Center for Basic and Translational Epigenetic Research of Diseases, School of Life Science, Anhui Medical University, Hefei, 230032, China

5 Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China

6 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, 100093, China

7 School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510641, China

8 The State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

9 Department of Biology, Virginia State University, Petersburg, VA, 23806, USA

10 Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark

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BMC Genomics 2012, 13:300  doi:10.1186/1471-2164-13-300

Published: 2 July 2012



DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara.


The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice.


The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.

Cultivated and wild rice; Methylomes; Transcriptional termination regions (TTRs); Gene expression