Comparative analysis of DNA methylome reveals SUVH6 dependent non-CG DNA methylation and gene regulation potentially involved in Pi homeostasis in miR778-SUVH6 pathway in Arabidopsis

DNA methylation is one of the most important mechanisms for plant gene expression regulation to adapt to intra or extra environmental stimuli. Evidences indicate DNA CHG/CHH methylation and histone H3K9 methylation could reinforce each other and functionally interconnect. However, whether and how SUVH6 alone, a H3K9 methyltransferase, affects DNA methylation is not clear. Here, through comparative analysis of DNA methylomes of wildtype (WT) and SUVH6 mutant (suvh6), 478 hypo/116 hyper CHG differentially methylated regions (DMRs) and 5092 hypo/458 hyper CHH DMRs embedded in promoter, gene body and transposable element regions were identified, which indicates SUVH6 alone is required for maintaining non-CG methylation at specific regions of the Arabidopsis genome. Moreover, GO annotation reveals that, among 3299 SUVH6 potential target genes with their promoter or gene body overlapped with DMRs, 50 genes are involved in root development, 7 are associated with Pi transport, and 14 are related to phosphate (Pi) metabolism and membrane lipid remodeling. These results well coincide with the phenotype of miR778 overexpression line, which is to enhance primary root growth and increase shoot free Pi under Pi starvation. As miRNA778 targets SUVH6, the potential target genes involved in root development and Pi homeostasis identified here could be downstream of the miR778-SUVH6 pathway responsive to Pi starvation. All the above indicates that changes in DNA methylation can be applied to track SUVHs regulated gene expression.