作为一种重要的表观遗传学机制，DNA甲基化在动植物生长发育过程中发挥重要的生物学功能。为了深入了解水稻甲基化的格局，评估其生物学意义，最近，中国科学院昆明动物研究所遗传资源与进化国家重点实验室马普进化基因组学青年科学家小组与云南省农业科学院、深圳华大基因研究院、中国科学院植物研究所以及上海肿瘤研究所合作，构建了水稻及其野生近缘种的单碱基分辨率的DNA甲基化图谱。研究结果显示水稻基因组的甲基化水平是拟南芥的四倍。与拟南芥甲基化格局相一致的是，启动子区的甲基化抑制基因的表达，而基因内部甲基化通常与基因表达水平呈正相关。有趣的是，我们发现，甲基化在基因转录终止区（TTRS）可以显着抑制基因的表达，而且效果甚至强于启动子甲基化。通过综合分析栽培稻与野生稻的基因组、甲基化组和转录组的差异，我们发现，全基因组水平的DNA序列差异是甲基化格局差异的主要决定因素，而DNA甲基化差异仅可以解释栽培稻与野生稻之间有限的基因表达差异。此外，我们鉴定到了一批栽培稻与野生稻甲基化差异的基因。
该项研究获得的水稻单碱基分辨率甲基化谱，不仅加深了我们对植物基因组DNA甲基化机制和功能的理解，同时也为今后的水稻表观遗传学研究提供了宝贵的数据。该工作得到了973计划和云南省项目的支持，发表在BMC Genomics (2012,13: 300)上。（生物谷Bioon.com）
doi:10.1186/1471-2164-13-300
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Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
Xin Li, Jingde Zhu, Fengyi Hu, Song Ge, Mingzhi Ye, Hui Xiang, Guojie Zhang, Xiaoming Zheng, Hongyu Zhang, Shilai Zhang, Qiong Li, Ruibang Luo, Chang Yu, Jian Yu, Jingfeng Sun, Xiaoyu Zou, Xiaofeng Cao, Xianfa Xie, Jun Wang and Wen Wang
Background 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. Results 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. Conclusions 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.
