Confirmation of no Causal Relationship between Genome-wide DNA Methylation and Transcriptome Changes after Gamma Irradiation

Genome-wide DNA methylation change is one of the major epigenetic regulation mechanisms involved in DNA damage response (DDR) and genome stability. Whole-genome bisulfite sequencing analysis demonstrated genomic DNA hypomethylation in all Arabidopsis genomes after gamma irradiation, but preferentially at non-CG sites of nuclear chromosomes. Chloroplastic or mitochondrial genome was the most resistant or the most sensitive to DNA hypomethylation induced by gamma irradiation, respectively. The methylation changes of those genomes displayed no difference between CG and non-CG sites. In contrast, the genomic DNA hypomethylation of nuclear chromosomes slightly differed depending on the gene regions or genomic features. The number of differentially methylated regions (DMRs) with decreased DNA methylation was much more than that of DMRs with increased DNA methylation in accordance with the overall DNA hypomethylaton of the whole genomes. Thirty-four DMRs were identified to be associated with transcriptome changes after gamma irradiation, but none of them were correlated with transcriptional induction of DDR genes. These results suggest that the genome-wide DNA hypomethylation would play a role in indirect DDR mechanisms rather than in direct transcriptional activation for DDR genes.