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

Abstract

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 the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is 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. 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.

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

“…Next, we set to validate the causative role of DNA methylation on gene expression by using methylome mutants. We took advantage of the RNA-seq data from kernel tissue of the ddm1 double mutant which disturbs DNA methylome dramatically [37]. We assessed whether the genes detected as exhibiting natural variation for DNA methylation linked to DMRs in our population would also show changes in expression in the ddm1 mutant.…”

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

“…Once established, CG methylation in Arabidopsis is maintained by MET1, which is homologous to mammalian DNMT1 and recognizes hemi‐methylated me CG/GC generated by DNA replication and methylates the unmodified cytosine; meanwhile, CHG methylation is maintained by the plant specific methyltransferase CMT3 or CMT2. Maintenance of the asymmetric CHH methylation in plants is achieved by constant de novo methylation, either through the RdDM pathway or through an alternative maintenance pathway that depends on the methyltransferase CMT2 and the chromatin remodeling factor DDM1 (Zemach et al ; Fu et al ; Long et al ; Tan et al ).…”

EXPORTIN 1A prevents transgene silencing in Arabidopsis by modulating nucleo‐cytoplasmic partitioning of HDA6

“…In addition to DNA methylation, histone posttranslational modifications (PTMs) and chromatin remodeling play vital roles in epigenetic regulation (Liu et al ): the DDM1 protein (an SNF2 family nucleosome remodeler) functions in DNA methylation regulation in all cytosine contexts (Long et al ), and the interplay between histone modification and DNA methylation is important for transcriptional regulation (Cedar and Bergman ; Saze et al ; Du et al ). The coordinated roles of the Su(var)3‐9 class of histone H3K9 methyltransferase KYP and CMT3 methyltransferase is one example of this relationship: KYP binds methylated CHG and recruits the CMT3 methyltransferase to enhance CHG methylation (Jackson et al ; Jasencakova et al ).…”