title: Characterization of non-CG genomic hypomethylation associated with gamma-ray-induced suppression of CMT3 transcription in Arabidopsis thaliana.
abstract: Ionizing radiation causes various epigenetic changes, as well as a variety of DNA lesions such as strand breaks, cross-links, oxidative damages, etc., in genomes. However, radiation-induced epigenetic changes have rarely been substantiated in plant genomes. The current study investigates whether DNA methylation of Arabidopsis thaliana genome is altered by gamma rays. We found that genomic DNA methylation decreased in wild-type plants with increasing doses of gamma rays (5, 50 and 200 Gy). Irradiation with 200 Gy significantly increased the expression of transcriptionally inactive centromeric 180-bp (CEN) and transcriptionally silent information (TSI) repeats. This increase suggested that there was a substantial release of transcriptional gene silencing by gamma rays, probably by induction of DNA hypomethylation. High expression of the DNA demethylase ROS1 and low expression of the DNA methyltransferase CMT3 supported this hypothesis. Moreover, Southern blot analysis following digestion of genomic DNA with methylation-sensitive enzymes revealed that the DNA hypomethylation occured preferentially at CHG or CHH sites rather than CG sites, depending on the radiation dose. Unlike CEN and TSI repeats, the number of Ta3, AtSN1 and FWA repeats decreased in transcription but increased in non-CG methylation. In addition, the cmt3-11 mutant showed neither DNA hypomethylation nor transcriptional activation of silenced repeats upon gamma irradiation. Furthermore, profiles of genome-wide transcriptomes in response to gamma rays differed between the wild-type and cmt3-11 mutant. These results suggest that gamma irradiation induced DNA hypomethylation preferentially at non-CG sites of transcriptionally inactive repeats in a locus-specific manner, which depends on CMT3 activity.
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Genmgu-gil, Jeongeup-si, Jeollabuk-do 580-185, Republic of Korea.
authors.forename: Ji Eun
authors.initials: JE
authors.lastname: Kim
authors.forename: Min Hee
authors.initials: MH
authors.lastname: Lee
authors.forename: Eun Ju
authors.initials: EJ
authors.lastname: Cho
authors.forename: Ji Hong
authors.initials: JH
authors.lastname: Kim
authors.forename: Byung Yeoup
authors.initials: BY
authors.lastname: Chung
authors.forename: Jin-Hong
authors.initials: JH
authors.lastname: Kim
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000528:radiation effects; D029681:Arabidopsis Proteins / Q000235:genetics*; D019175:DNA Methylation / Q000528:radiation effects*; D015257:DNA-Cytosine Methylases / Q000235:genetics*; D004307:Dose-Response Relationship, Radiation; D005720:Gamma Rays / Q000009:adverse effects*; D020868:Gene Silencing / Q000528:radiation effects*; D018745:Genome, Plant / Q000235:genetics*; D009154:Mutation; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics / Q000528:radiation effects; D014158:Transcription, Genetic / Q000235:genetics / Q000528:radiation effects*
chemical_list: D029681:Arabidopsis Proteins; D015257:DNA-Cytosine Methylases; C429766:CMT3 protein, Arabidopsis