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。

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.

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