title: Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.
abstract: 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.
authors: 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.
authors: Xin
authors: X
authors: Li
authors: Jingde
authors: J
authors: Zhu
authors: Fengyi
authors: F
authors: Hu
authors: Song
authors: S
authors: Ge
authors: Mingzhi
authors: M
authors: Ye
authors: Hui
authors: H
authors: Xiang
authors: Guojie
authors: G
authors: Zhang
authors: Xiaoming
authors: X
authors: Zheng
authors: Hongyu
authors: H
authors: Zhang
authors: Shilai
authors: S
authors: Zhang
authors: Qiong
authors: Q
authors: Li
authors: Ruibang
authors: R
authors: Luo
authors: Chang
authors: C
authors: Yu
authors: Jian
authors: J
authors: Yu
authors: Jingfeng
authors: J
authors: Sun
authors: Xiaoyu
authors: X
authors: Zou
authors: Xiaofeng
authors: X
authors: Cao
authors: Xianfa
authors: X
authors: Xie
authors: Jun
authors: J
authors: Wang
authors: Wen
authors: W
authors: Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D016000:Cluster Analysis; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics*; D059828:Plant Cells / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic
chemical_list: D003596:Cytosine