Abstract
DNA methylation is important for controlling gene expression in all eukaryotes. Microarray analysis of mutant and chemically-treated Arabidopsis thaliana seedlings with reduced DNA methylation revealed an altered gene expression profile after treatment with the DNA methylation inhibitor 5-aza-2′ deoxycytidine (5-AC), which included the upregulation of expression of many transposable elements. DNA damage-response genes were also coordinately upregulated by 5-AC treatment. In the ddm1 mutant, more specific changes in gene expression were observed, in particular for genes predicted to encode transposable elements in centromeric and pericentromeric locations. These results confirm that DDM1 has a very specific role in maintaining transcriptional silence of transposable elements, while chemical inhibitors of DNA methylation can affect gene expression at a global level.
Highlights
DNA cytosine methylation, at CG dinucleotides plays a role in maintaining gene silencing and in gene imprinting
A reduction in CG methylation was observed for 5-aza-29 deoxycytidine (5-AC) treatment on a per-sample basis, six CG sites in the sequenced region are methylated in 90–100% of control samples, these were found to be no more than 80% methylated after 5-AC treatment and no more than 30% methylated at any CG site in the ddm1 plants
CNG/CNN methylation requiring DRM1, DRM2 and CMT3, which is not inhibited by 5-AC, affects a different subset of genes located in euchromatin which have a variety of developmental functions, and their expression is largely unaffected by the ddm1 mutation (Figures S7 and S8) [30,31]. These results indicate that use of inhibitors of cytosine methylation can directly or indirectly influence the expression of genes throughout the genome, but that the loss of DDM1 has little effect on the expression of genes that are influenced by DNA methylation but are located in the euchromatic chromosome arms
Summary
DNA cytosine methylation, at CG dinucleotides plays a role in maintaining gene silencing and in gene imprinting. In Arabidopsis, CG methylation is maintained by the methyltransferase MET1 [1], while CHROMOMETHYLASE3 (CMT3) and the DOMAINS REARRANGED METHYLASEs (DRM1 and DRM2) are involved in the maintenance of CNG and CNN methylation respectively [2,3,4,5,6]. DNA cytosine methylation is typically associated with transcriptional silence in plants [8]. Cytosine methylation has been shown to be required for maintaining transcriptional silence of transposable elements through an RNAi-dependent pathway, and has been shown to be required for parent-of-origin specific expression of the FWA gene in Arabidopsis endosperm [9,10]
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