Abstract
BackgroundDNA 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.ResultsThe 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.ConclusionsThe 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.
Highlights
DNA methylation plays important biological roles in plants and animals
Methylation landscapes in rice To investigate the general methylation patterns of rice as well as the DNA methylation divergence between cultivated and wild rice, we included in our samples both subspecies of Asian cultivated rice, Oryza sativa spp. japonica and indica (IR64, from the International Rice Research Institute, IRRI), and their wild relatives, Oryza rufipogon (Accession 105327, originally collected from Sri Lanka and provided by IRRI) and Oryza nivara (Accession 105426, originally collected from India and provided by IRRI)
Using these values we conducted binomial tests with false positive rate below 5% to exclude those methylated cytosine (mC) that may be the results of non-conversion of cytosines during our bisulfite treatment or T to C sequencing errors during the base calling process
Summary
DNA methylation plays important biological roles in plants and animals. It has been proposed to be an alternative inheritance system playing an important role in evolution [2,3], as many case studies in plants and animals have. Pioneer studies of epigenetic modifications in rice, including DNA and histone methylation, using traditional methylated DNA enrichment method suggested possible functional roles of DNA methylation in rice [16,17], but this approach is difficult to discriminate major genomic elements including promoters, gene bodies, transposons, and repeats. To what extent and how the cultivated rice has evolved divergent DNA methylation pattern from its wild relative species still need to be addressed
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