Comparison of co-regulation of DNA methylation and smallRNA expression between Arabidopsis infected with RNA and DNA virus

In plants, which are particularly sensitive to changes of environmental conditions, modulation of DNA methylation is a crucial mechanism of regulation of gene expression in response to abiotic and biotic stresses. Monitoring plant's immune system in response to bacterial pathogen infection demonstrated that also dynamic DNA methylation changes, and not only gene imprinting, have regulatory effect in plant pathogen defense. Critical elements for epigenetic modifications of plant genomes are non-coding smallRNA e same RNA family is also a hallmark of plant reaction to virus infection. Interestingly, sRNA have a central role in both plant genome methylation and resistance upon virus infection, however, the interaction between sRNA expression and DNA methylation regulating the immune system in response to virus infection has not been investigated so far. To correlate dynamic DNA methylation and differential sRNA expression in response to virus infection, we have performed genome-wide methylation and sRNA expression profiling on Arabidopsis leaves systemically infected with either the DNA-genome virus Caulifower mosaic virus or the RNA virus Cucumber mosaic virus. We developed a software package to analyze the sRNA expression and the DNA methylation profile and deploy a genome wide comparison of control and infected samples to search regions significantly different either in the methylation profile or in the sRNA expression, or in both. In the regions where we observe significant correlation of methylation (mainly CHH methylation) and sRNA expression modifications, we found that both hypo- and hypermethylation correlated with downregulation of 21/24nt sRNAs. These regions mostly comprised transposons and few of them contained promoter or coding sequences of genes involved, according to gene ontology, in DNA-binding and DNA-dependent regulation of transcription and response to abiotic or biotic stimulus. This confirms virus-induced infection regulation of sRNA and DNA methylation. We are presently still in the process of data analysis and more details about correlation of virus-induced modification of sRNA and DNA methylation levelswill be reported.