作為一種重要的表觀遺傳學(xué)機(jī)制,，DNA甲基化在動(dòng)植物生長(zhǎng)發(fā)育過(guò)程中發(fā)揮重要的生物學(xué)功能,。為了深入了解水稻甲基化的格局,，評(píng)估其生物學(xué)意義,，最近,，中國(guó)科學(xué)院昆明動(dòng)物研究所遺傳資源與進(jìn)化國(guó)家重點(diǎn)實(shí)驗(yàn)室馬普進(jìn)化基因組學(xué)青年科學(xué)家小組與云南省農(nóng)業(yè)科學(xué)院,、深圳華大基因研究院,、中國(guó)科學(xué)院植物研究所以及上海腫瘤研究所合作，構(gòu)建了水稻及其野生近緣種的單堿基分辨率的DNA甲基化圖譜,。研究結(jié)果顯示水稻基因組的甲基化水平是擬南芥的四倍,。與擬南芥甲基化格局相一致的是，啟動(dòng)子區(qū)的甲基化抑制基因的表達(dá),，而基因內(nèi)部甲基化通常與基因表達(dá)水平呈正相關(guān),。有趣的是，我們發(fā)現(xiàn),，甲基化在基因轉(zhuǎn)錄終止區(qū)（TTRS）可以顯著抑制基因的表達(dá),，而且效果甚至強(qiáng)于啟動(dòng)子甲基化。通過(guò)綜合分析栽培稻與野生稻的基因組,、甲基化組和轉(zhuǎn)錄組的差異,，我們發(fā)現(xiàn),，全基因組水平的DNA序列差異是甲基化格局差異的主要決定因素，而DNA甲基化差異僅可以解釋栽培稻與野生稻之間有限的基因表達(dá)差異,。此外,，我們鑒定到了一批栽培稻與野生稻甲基化差異的基因。
該項(xiàng)研究獲得的水稻單堿基分辨率甲基化譜,，不僅加深了我們對(duì)植物基因組DNA甲基化機(jī)制和功能的理解,，同時(shí)也為今后的水稻表觀遺傳學(xué)研究提供了寶貴的數(shù)據(jù)。該工作得到了973計(jì)劃和云南省項(xiàng)目的支持,，發(fā)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.
