由ENCODE計畫分析脫氧核醣核酸酶I與組蛋白修飾

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姓名

紀旻秀(Min-Xiu Ji) 查詢紙本館藏

畢業系所

系統生物與生物資訊研究所

論文名稱

由ENCODE計畫分析脫氧核醣核酸酶I與組蛋白修飾
(Analysis of DNase I hypersensitivity sites and Histone modifications data from ENCODE project)

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摘要(中)

近年來，表觀基因體學的文獻發表有成長的趨勢，許多的文獻都著重於表觀基因體與影響基因的表現狀況。此篇論文，我們則提出了與以往不同的角度來分析表觀基因體與脫氧核醣核酸酶I高敏感位點之關聯性。
於組蛋白修飾的部分，我們能從文獻中得知，某些組蛋白修飾會引起基因高表現或低表現。此次我們的研究在脫氧核醣核酸酶I高敏感位點與六種組蛋白修飾中，我們觀察到這六種組蛋白修飾與open chromatin有相關性。例如：從脫氧核醣核酸酶I高敏感位點與H3K4me3共同存在的頻率會比脫氧核醣核酸酶I高敏感位點與H3K27me3共同存在的頻率還要高。H3K4me3與open chromatin有正相關；反之，H3K27me3則與open chromatin呈負相關性。
另外，我們也分析在不同細胞株的H3K4me3與H3K27me3共同調控的基因中，他們各自的功能，此結果與之前文獻亦有相同之處。例如：癌症細胞中，我們發現與代謝相關基因，它們存在於H3K4me3與H3K27me3重疊的地方。

摘要(英)

In recent years, publications of papers on epigenetics have increased. Many papers concerned epigenetics and gene expression. This thesis analyzed the association between epigenetics and DNase I hypersensitive sites.
We focus on histone modification part of epigenetics. Previous studies indicated that some histone modifications might affect gene expression. This thesis analyzed the association between six types of histone modifications and DNase I hypersensitive sites, and we found correlations between histone modifications and open chromatin. Specifically, From our research, H3K4me3 and DNase I Hypersensitive sites overlap more frequently then H3K27me3 and DNase I Hypersensitive sites frequency. H3K4me3 is positively correlated with open chromatin, and H3K27me3 is negatively correlated with open chromatin.
Besides, we also analyzed, across cell lines, the functions of genes where H3K4me3 and H3K27me3 overlap, and the result is similar to the previous studies. For example, in cancer cells are found metabolism-related genes with overlapping H3K4me3 and H3K27me3.

關鍵字(中)

★ 表觀基因體學
★ 組蛋白修飾
★ 脫氧核醣核酸酶I高敏感位點

關鍵字(英)

★ Epigenetic
★ histone modification
★ DNase I Hypersensitive sites

論文目次

目錄
中文摘要 i
Abstract ii
致謝 iii
目錄 iv
圖目錄 vii
表目錄 ix
第一章緒論 1
1-1 基因體學與表觀遺傳學 1
1-2 DNA甲基化 2
1-3 組蛋白修飾 4
1-4 表觀基因體與疾病 7
1-5 研究動機 9
第二章研究方法 10
2-1 數據來源 10
2-2 分析平台 11
2-3 不同的chromosome上 promoter、gene body 和 intergenic 的比例 11
2-4 DNase I 或 histone modification在 chr1~chrY 的比例 13
2-5 組蛋白修飾和DNase I Hypersensitivity分別在promoter、gene body和Intergenic之分析方法 14
2-6 H3K4me3和H3K27me3在全基因組與Promoter、Gene body和Intergenic上之分析方法 15
2-7 Gene Ontology enrichment分析：使用GOrilla 15
第三章結果 18
3-1 Promoter、gene body和intergenic在chromosome上的分布狀況 18
3-2 DNase I或histone modification在chromosome和細胞株上的分布情形 21
3-3 不同細胞株的DNase I和histone modification在promoter、gene body或intergenic的關係 26
3-4 不同細胞株上H3K4me3和H3K27me3在whole genome、promoter、gene body或intergenic的關係 32
3-5 Gene Ontology分析不同細胞株上H3K4me3和H3K27me3在promoter和gene body的分析結果 35
第四章討論 48
第五章結論 49
第六章參考文獻 51
附錄一 54
附錄二 58
附錄三 60
附錄四 61
附錄五 73
附錄六 79

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指導教授

王孫崇(Sun-Chong Wang)

審核日期

2013-6-11

推文