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

DNA methylation plays important biological roles in plants and animals. To comprehensively reveal rice genomic methylation patterns and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. 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 promote 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 DNA sequence divergence may be the major determinant of methylational differences at the whole genome level while DNA methylational difference can only account for limited gene expression variation between cultivated and wild rice. We also identified a number of genes with significant difference in methylation level between the wild and cultivated rice.