Decrease in DNA methylation 1(DDM1) is required for the formation of ~mCHH islands in maize

DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize.Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of Zm DDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that Zm DDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, inheterochromatic regions, and unexpectedly, it is required for the formation ofmCHH islands. In addition, Zm DDM1 is indispensable for the presence of 24-nt si RNA, suggesting its involvement in the Rd DM pathway. Our results provide novel insight into the role of Zm DDM1 in regulating the formation of mCHH islands, via the Rd DM pathway maize, suggesting that,in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating ~mCHH.