Discovery of Domain Organization of Cancer Epigenome

• Main Authors: Yi-Chien Tsai, 蔡伊茜
• Other Authors: Ming-Ta Hsu
• Format: Others
• Language: en_US
• Published: 2010
• Online Access: http://ndltd.ncl.edu.tw/handle/79332565842835175249

碩士 === 國立陽明大學 === 生化暨分子生物研究所 === 98 === After decoding of human genome, the major work in the post-genomic era is to investigate how genes are organized in network and regulated. Formerly, epigenetic regulation studies focus on promoter region of single gene. Due to the rapidly developed array technology, we can now study the epigenetic regulation in a genome-wide context. One of the main mechanisms of tumorigenesis is the dys-function of epigenetic regulation. In this study, I explored the genome-wide differences in epigenetic regulation between normal tissues and cancer cell lines. I developed the McrBC array to study the methylome and used ChIP-on-chip to explore the global histone modifications. The array data showed that there are megabase-sized demethylation regions in cancer genomes. The tumor DNA methylome and genome-wide histone modifications were contrasted with global MNase hypersensitive sites, transcriptome, RNA polymerase II binding sites, gene density, CpG density and lamin B1 binding sites. The results showed that tumor genome is organized and regulated as large epigenetic domain units. My data provide an epigenetic organization of silenced genes with promoter methylation and demethylation in the intragenic region. The results also revealed that hypermethylated regions are highly correlated with H3K9 acetylation (H3K9A) domains, RNA polymerase II binding sites and also with highly transcribed genes. Furthermore, the hypomethylation regions match with the H3K27 trimethylation (H3K27Me3) domains and the silenced genes. 80％ of genes associated with H3K9A are located in hypermethylated regions with extensive intragenic CpG methylation and 75％ of genes associated with H3K27Me3 are located in hypomethlated regions. In addition, H3K4 acetylation, H3K9 dimethylation and HP1α were found to serve only as minor epigenetic modifications in MCF-7 genome. Analysis of H3K27Me3 modified genes showed a prevalence of brain, nerve, immune and reproductive system genes with a few exceptions which may be related to regulation of tumorigenesis. Trichostatin A (TSA) was selected to alter epigenetic modifications in MCF7 cell line in order to analyze the genome-wide changes of DNA methylation and histone modifications. TSA treatment of MCF7 cells resulted in global DNA methylation as domain units. Surprisingly, the global histone modifications of H3K9A and H3K27Me3 after TSA treatment were still organized as domain units similar to that of control MCF7. Analysis of the expression changed genes revealed a prevalence of immune genes. This may imply mechanism about how TSA act as an anti-cancer drug. Genes regulation have been studied at single gene level. In this thesis I propose a new concept that genome are organized into epigenetic domains with higher order regulation. This implies the presence of epigenetic domain boundary elements in tumor genome to regulate these domains.