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

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.

Mobile small RNAs regulate genome-wide DNA methylation

“…Base-resolution methylomes are being actively generated in multiple species, including crops and nonmodel plants (38,(57)(58)(59). Clear diversity in the epigenomes of closely related subspecies and accessions has been observed from these data (38,57). With our demonstration that site-specific transmission of epiallelic states from one accession to another can be achieved by grafting and by de novo methylation of unmethylated DNA, it is likely that at least some effects of grafting are due to the movement of RNA.…”

“…We have demonstrated that mobile sRNAs regulate patterns of DNA methylation genome-wide, and that expression of specific genes exhibits mobile regulation. Base-resolution methylomes are being actively generated in multiple species, including crops and nonmodel plants (38,(57)(58)(59). Clear diversity in the epigenomes of closely related subspecies and accessions has been observed from these data (38,57).…”

The Birth of a Black Rice Gene and Its Local Spread by Introgression

“…These results suggest that alteration of the DNA methylation status in these genes can change the activities of the anthocyanin biosynthetic pathway. Furthermore, genome-wide methylome analysis in maize and rice has suggested that the DNA methylation in the promoter region often represses gene expression, whereas moderate gene-body methylation has a positive effect on the gene expression (Li et al, 2012;Regulski et al, 2013). Therefore, DNA methylation status may affect gene expression.…”

DNA methylation polymorphism and stability in Chinese indica hybrid rice

“…Recently developed methods, such as bisulfate-based sequencing and MeDIP-seq, have a higher resolution of 1 [24,25] to 35 [26] base pairs. Furthermore, they can be used to profile all forms of single methylation polymorphisms (SMPs).…”

“…A recent study revealed that epigenetic variations are widespread within natural A. thaliana lines [27]. DNA methylation polymorphisms have also been observed between wild and cultivated rice [25], and between the indica and japonica subspecies of rice [23].…”