To study the associations between endogenous DNA double-strand breaks, DNA methylation, and cell cycle

Abstract

This study aimed to evaluate the association between global hypomethylation and endogenous DSBs (EDSBs). Global hypomethylation is one of the most common molecular events in the multistep carcinogenesis. This process leads to genomic instability. EDSBs could account for a substantial fraction of oncogenic events in human carcinomas If EDSBs do not arise uniformly or are not processed at equal rates across the genome; mutation hot spots should be present. Therefore, genome wide methylation depletion may cause genomic instability if DNA methylation influences EDSB processes. In this thesis, we first developed a set of novel techniques to analyze the extent and methylation level of genomic EDSBs. The first is L1-EDSB-LMPCR and COBRA-L1-EDSB to quantitate level and methylation of EDSBs. The other is chromatin immunoprecipitating γ-H2AX, one of the earliest DSB repair responses. Then we evaluated the relation between quantity and methylation of EDSBs and the cellular DSB repair response. Our study discovered first endogenous DNA breakages are universally detectable and are hypermethylated. Second, the levels of EDSBs and γ-H2AX-bound DNA are cell type specific and inversely related. Whereas WBCs possessed more L1-EDSB-LMPCR than did epithelial cells, epithelial had more γ-H2AX-bound L1s than WBCs. Finally, the EDSBs are concealed in heterochromatin, which obstructs the early cellular DSB repair response. Trichostatin A treatment, which inhibits histone deacetylase and disrupts heterochromatin, released methylated EDSBs and increased the quantity and methylation level of γ-H2AX-bound DNA. DNA hypomethylation can therefore be linked to a high mutation rate if the early repair response of unmethylated EDSBs is error prone.