| 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 ZmDDM1 are abundantly expressed in embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development.We found that ZmDDM1 is critical for DNA methylation at CHG sites and to a lesser extent at CG sites in heterochromatic regions,and unexpectedly,required for the formation of mCHH islands.In addition,ZmDDM1 is indispensable for the presence of 24-nt siRNA,suggesting its involvement in the RdDM pathway.We found that ZmDDM1 is associated with AGO4 in planta.Mutation of ZmDDM1 cause thousands genes mys-regulation and activation of large TE family.Our results provide novel insight into the role of ZmDDM1 in regulating the formation of mCHH islands via the RdDM pathway maize,suggesting that in comparison to Arabidopsis,maize may have adopted distinct mechanisms for regulating mCHH.In addition,we perfomed ChIP-seq experiment to investigate the target site of ZmDDM1.We identified that ZmDDM1 mainly located at loci with high GC content,low DNA methylation and open chromatin.Moreover,small RNA and CHH methylation is abundant near the target sites of ZmDDM1,further corroborating that DDM1 is required for the formation of mCHH island.Interestingly,DDM1 primarily occupied at the transcription start site of protein coding genes,which exhibited higher level of transcription than genes that are not targeted by ZmDDM1,suggesting that ZmDDM1 occupancy is positively associated with active transcription.Furthermore,we performed ChIP-seq analysis using ZmAGO4 antibodies,and the results found that most of ZmDDM1 occupancy sites are overlapped with those targeted by ZmAGO4.As one of my side project,we identified that distinct pattern of H3K4me2 and H3K4me3 may have a impact on the recruitment of methionine chain-elongate pathway from leucine biosynthesis.In sum my study in this thesis demonstrated that in maize,DDM1 participate in RdDM pathway via association with ZmAGO4,which greatly enhance our understanding about the mechanism of ZmDDM1 regulate DNA methylation in plant. |
