Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
文献类型：期刊论文
| 作者 | Li X1,2; Zhu JD3,4; Hu FY5; Ge S6; Ye MZ2; Xiang H1; Zhang GJ1,2; Zheng XM6; Zhang HY3; Zhang SL5 |
| 刊名 | BMC GENOMICS
 |
| 出版日期 | 2012 |
| 卷号 | 13期号:X页码:e300 |
| 关键词 | Cultivated and wild rice Methylomes Transcriptional termination regions (TTRs) Gene expression |
| 通讯作者 | xxie@vsu.edu ; wangj@genomics.org.cn ; wwang@mail.kiz.ac.cn |
| 合作状况 | 其它 |
| 英文摘要 | 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. |
| 收录类别 | SCI |
| 资助信息 | This work was supported by the Chinese 973 program (2007CB815700, 2005CB121000, 2009CB825606 and 2009CB825607), the Provincial Key Grant of Yunnan Province (2008CC017; 2008GA002), the National Natural Science Foundation of China (U0836605, 30921140312 and 30872963), the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Ole Rømer grant from the Danish Natural Science Research Council, a CAS-Max Planck Society Fellowship, the 100 talent program of CAS, a Shanghai Science Foundation grant (07DJ14074), and a European 6th program grant (LSHB-CT-2005- 019067) to WW, JW, SG or JZ. |
| 语种 | 英语 |
| 公开日期 | 2013-09-17 |
| 源URL | [http://159.226.149.42:8088/handle/152453/7647]  |
| 专题 | 昆明动物研究所_基因起源组 昆明动物研究所_遗传资源与进化国家重点实验室 |
| 作者单位 | 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 |
| 推荐引用方式 GB/T 7714 | Li X,Zhu JD,Hu FY,et al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression[J]. BMC GENOMICS,2012,13(X):e300. |
| APA | Li X.,Zhu JD.,Hu FY.,Ge S.,Ye MZ.,...&Wang W[*].(2012).Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.BMC GENOMICS,13(X),e300. |
| MLA | Li X,et al."Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression".BMC GENOMICS 13.X(2012):e300. |
入库方式： OAI收割
来源：昆明动物研究所
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