Chromatin modification induced by DNA damage and repair.DNA methylation induced by DNA damage and repair causes stochastic variations of gene expression

We report the changes in chromatin structure and gene expression after homology-directed repair (HR) of a DNA double-strand break (DSB). The histone code at the DSB site undergoes transient changes following DNA damage, and is stably modified after repair. Chromatin changes are associated with modification in DNA methylation and local chromatin structure, which determine the rate of transcription of the repaired gene. During repair discrete DNA loops form that connect the 5' and the 3' ends of the repaired GFP gene. Some of these loops are sensitive to RNaseH, suggesting that they are stabilized by RNA:DNA hybrids. BER-NER enzymes recruited to the DSB influence the final methylation status of the repaired gene, as does transcription of the gene during the three weeks following repair. The changes in methylation patterns are permanent, and can be used to detect the damagerepair events. We provide three examples of this, comparing the qualitative methylation profiles of two suppressor genes, frequently methylated in cancer, and of a neutral gene, GFP. These data demonstrate that somatic DNA methylation induced by DNA damage and HR stably modifies local chromatin structure and is a source of permanent stochastic variation of gene expression in somatic cells.