Differential regulation of DNA methylation of Arabidopsis in response to RNA and DNA virus infection

The establishment and maintenance of DNA methylation are relatively well understood in developmental processes whereas little is known about their dynamics and biological relevance in innate immunity. In plants, which are sessile and cannot escape the environmental conditions in which they live, modulation of DNA methylation might be effective in regulating gene expression in response to abiotic and biotic stresses. Non-coding smallRNAs are a hallmark of plants virus infections but are as much critical for epigenetic modifications of plant genomes; however, the involvement of DNA methylation in regulation of plant immune system in response to virus infection was not investigated before. We have examined the effect of virus infection on host DNA methylation and the correlation with smallRNA and gene expression regulation on a genomic scale. To investigate the possibility that DNA methylation dynamically responds to virus infection, we have performed genome-wide methylation profiling on Arabidopsis leaves systemically infected with either the DNA-genome virus Cauliflower mosaic virus (CaMV-Arabidopsis) or the RNA virus Cucumber mosaic virus (CMV-Arabidopsis). Single-base resolution methylomes analysis revealed increase of methylated sites in CMV-Arabidopsis and demethylation in CaMV-Arabidopsis. We also found different methylation patterns for the three sequence contexts (CG, CHG, CHH) with significant preponderance of the CHH-context. While 60% of the 2700 differentially methylated regions (DMR, 250nt in length) in CMV-Arabidopsis showed an increase of methylation in the CHH-context, 4000 of the 5600 DMRs found after infection with CaMV were demethylated. Furthermore, we tested CMV infection effects in A. thaliana mutants depleted in DNA methylation functions by elimination of CG methylation (met1-3 mutant) or non-CG methylation (mutations in drm1, drm2, cmt2 and cmt3 - ddcc mutants). Both mutants showed increased susceptibility to CMV. We observed a 20-fold increment of CMV RNA accumulation in ddcc and met1-3 mutants vs. wt Arabidopsis plants. Taken together our results indicate that RNA- and DNA-genome virus infections induce different regulation of DNA methylation, and unveil methylation-dependent antiviral immune responses in Arabidopsis.