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系統識別號 U0026-3007201315083800
論文名稱(中文) 基於酵母菌全基因組分析之表觀遺傳學研究
論文名稱(英文) Epigenetic Analysis for Genome-wide Profiles of Saccharomyces cerevisiae
校院名稱 成功大學
系所名稱(中) 資訊工程學系碩博士班
系所名稱(英) Institute of Computer Science and Information Engineering
學年度 101
學期 2
出版年 102
研究生(中文) 林展賢
研究生(英文) Chan-Hsien Lin
學號 P78961346
學位類別 博士
語文別 英文
論文頁數 90頁
口試委員 指導教授-蔣榮先
口試委員-蔡少正
口試委員-詹世煌
口試委員-吳華林
口試委員-王大為
口試委員-歐陽彥正
口試委員-黃憲達
口試委員-陳中明
中文關鍵字 生物資訊  表觀遺傳  核小體  組蛋白變異  酵母菌基因組分析  序列分析 
英文關鍵字 Bioinformatics  epigenetics  nucleosome  histone variant  genome analysis  sequence analysis 
學科別分類
中文摘要 表觀遺傳學意指在基因序列在未受改變的情況下,基因功能具有可逆或可遺傳性的改變,其主要的機制是經由調控染色質來達成。染色質的組成包含脫氧核糖核酸與核小體,而核小體是纏繞脫氧核糖核酸的基本單元,主要由四對組織蛋白所構成;核小體在脫氧核糖核酸上的分佈並非均等纏繞,其位置的變化可直接影響周邊的基因表現,因此核小體的相關研究在基因調控上至為重要。
近年來隨著生物技術的進步,針對全基因組的實驗,其成本逐漸降低且準確度提高,而本研究則藉由酵母菌全基因組的資料,以資料分析的角度研究以核小體為主體的表觀遺傳現象,分析結果揭露了在基因組上的生物特徵。分析層面主要有二:一則結合多筆核小體位置的資訊,量化核小體穩定度的程度,並探討其序列偏好對於穩定性的影響;一則以組織蛋白為主體,分別探討其在脂肪酸代謝、與端粒基因沉默所扮演的角色,進一步探討相關調控的細節。
本研究以酵母菌作為模式生物,經由全基因組的資料的分析,以二層次的探討提供了核小體在表觀遺傳現象調控的概觀,而相關的分析結果與生物特徵,更可作為未來全面探討核小體調控的基礎。
英文摘要 In molecular biology, the study of gene expression plays an important role because the amount of gene expression reflects the amount of functional proteins, and there are many factors that can affect gene expression. In epigenetics, the research focuses on the factors rather than just changes in the underlying nucleotide sequence, and refers to relevant modifications to the genome that do not involve a change in DNA sequence. Gene expression can be controlled through epigenetic regulation such as chromatin remodeling or histone modification.
In this dissertation, multiple genome-wide profiles of epigenetic target in Saccharomyces cerevisiae were used for analysis on the chromatin regulation. For profiles of nucleosome positioning, we quantified the nucleosome stability by incorporating mass sequencing data, and provided a significant flanking pattern of sequence preference around nucleosomal DNA for a stable nucleosome. For profiles of histone-related proteins, the gene expression coupling with binding sites provide a framework to study the function of the histone variant in response to oleate, and to study the function of histone chaperone on the gene silencing at telomere-proximal regions.
Our analysis on epigenetics revealed the function of the histone-related proteins, and also provided a reliable measure for nucleosome stability. Both studies contribute to the field of epigenetic regulation, and relevant results can extend to further researches regarding the mechanism of chromatin remodeling.
論文目次 摘 要 i
ABSTRACT ii
ACKNOWLEDGEMENT iii
CONTENTS iv
LIST OF TABLES vii
LIST OF FIGURES viii
Chapter 1. Introduction 1
1.1 Overview 1
1.2 Objective 3
1.3 Organization of dissertation 4
Chapter 2. Related Genome-wide Profiling Biotechnologies 6
2.1 Microarray 6
2.2 ChIP-on-chip 6
2.3 High-throughput next generation sequencing 8
2.4 MNase-seq 10
Chapter 3. Epigenetic Analysis on Nucleosome Stability 12
3.1 Background 12
3.2 Materials and Method 13
3.2.1 Datasets 13
3.2.2 Detection of nucleosome positions from sequencing data 15
3.2.3 Calculation of NCS of each base pair 19
3.2.4 Application of NCS for data of nucleosomes 20
3.2.5 Evaluation of the relationship of nucleosome score with dinucleotide frequency 22
3.2.6 Using fold change of dinucleotide certainty to partition nucleosomal region 24
3.3 Results and Discussion 26
3.3.1 NCS shows clear discrimination of A/T-based dinucleotide frequencies 26
3.3.2 NCS reveals the flanking pattern on the preference of A/T-based dinucleotides 31
3.3.3 The negative relationship between NCS and poly(dA:dT) 34
3.3.4 The opposite tendency between NCS and NCP/noise 35
3.3.5 Further analysis on Broggard’s score 39
3.4 Summery 44
Chapter 4. Epigenetic Analysis on Histone-related Proteins 47
4.1 Background 47
4.2 Materials and Method 50
4.2.1 Using transcript DNA microarray for the analysis of gene function 50
4.2.2 Using ChIP-on-chip data for the analysis of protein binding sites 51
4.2.3 Nucleosome detection using ChIP-on-chip data 54
4.3 Results and Discussion 56
4.3.1 Htz1p is required for a subset of oleic acid-responsive genes 56
4.3.2 Htz1p shows different preference on the oleate conditions 59
4.3.3 Chz1p, Gcn5p, and Swr1p are associated with Htz1p in oleate-response 62
4.3.4 Htz1p and Chz1p regulates transcription of telomere-proximal genes 64
4.3.5 Htz1p association with subtelomeric DNA is independent of Chz1p 68
4.3.6 Nucleosome detection on telomere regions 71
4.4 Summery 74
Chapter 5. Conclusion and Future Works 75
5.1 Conclusion Remarks 75
5.2 Future Works 76
5.2.1 Nucleosome dynamics caused from Sequence-based factors 77
5.2.2 Nucleosome dynamics caused from Protein-based factors 78
5.2.3 Nucleosome dynamics caused from DNA-chromosome factors 79
5.2.4 System approaches to determine the relationship between factors 79
REFERENCES 81
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