族群中個體的差異來自於遺傳物質的變異，其中可能為DNA序列上蛋白質編碼區段的改變或是DNA序列上造成基因調控機制的不同所造成的。近來研究指出轉錄調控的變異也可能是導致物種演化的主因，但轉錄調控機制的改變在演化上還有很多是不明瞭的。本研究將探討酵母菌在逆境壓力下，特別是熱休克(heat shock)情況下，基因調控機制的演化，尤其是同序列調控因子變異性(cis regulatory variation)及外部調控因子變異性(trans regulatory variation)對酵母菌在熱休克壓力下對基因調控的影響。酵母菌在熱休克逆境下大約有324個基因表現會被誘發兩倍以上，以及約有484個基因的表現被抑制兩倍以上。本研究特別針對酵母菌中基因表現量會受高溫刺激而增加的基因，因為這些基因可能與酵母菌適應高溫環境有關。本研究從324個基因中隨機挑選65個具BY-RM基因多型性(polymorphism)的基因，利用焦磷酸定序定量分析技術檢測BY-RM對偶基因的相對表現量以推論同序列調控因子變異性，及外部調控因子變異性對BY-RM基因表現量差異的相對貢獻程度。本研究的結果顯示，BY和RM品系酵母菌不管是在一般環境下或是在熱休克壓力反應下，BY和RM對偶基因表現量的差異主要還是由外部調控因子變異性(trans major effect [trans variation effect alone + major trans variation effect])所造成的，其受外部調控因子變異性的基因比例分別是76.9% 和64.6%。然而在熱休克壓力反應下外部調控因子變異性效應則有減弱的現象，顯示同序列調控因子變異性對影響酵母菌族群在熱休克壓力的適應性上扮演了重要的角色。這65個熱休克反應基因在經歷熱休克壓力後，有46.2% (30/65)的基因其影響BY和RM對偶基因表現量差異的因素(同序列調控因子變異性或外部調控因子變異性)並不因熱休克刺激而改變、30.8% (20/65)的基因其影響BY和RM對偶基因表現量差異的因素則因熱休克刺激而使外部調控因子變異性的效應減弱以及23.1% (15/65)的基因其影響BY和RM對偶基因表現量差異的因素則因熱休克刺激而使外部調控因子變異性的效應增加。經過分析後外部調控因子變異性效應改變可能與基因本身上游轉錄因子個數多寡、熱休克相關轉錄因子種類的不同、TATA box調控元件的有無、基因所在染色體上的位置(左臂或右臂)、基因在染色體的排列位置及方向(華生、克里克股)及基因功能有關。

Phenotypic variation among individuals in a population can be due to DNA sequence variation expecially in protein coding regions or in gene regulatory elements. Recently, many reserch have pointed out that mutations in transcriptional regulation may have been a principal cause for phenotypic evolution. However, the mechanisms and the causes for evolutionary changes in transcriptional regulation are still poorly understood. In this thesis, I studied the relative evolutionary roles of cis and/or trans regulatory variation for yeast cells to cope with environmental changes, specifically focusing on the heat shock response. It has been shown that the expression of about 324 genes were induced at least two fold and about 484 genes whose expression was repressed at least two fold in response to heat shock in Saccharomyces cerevisiae. I especailly focus on the genes which were induced by at least two fold upon heat stress because these genes might be responsible for yeast to adapt for heat stress. In this study, I randomly select 65 genes which show polymorphism(s) in BY and RM strains from the 324 induced by at least two-fold genes upon heat stress for further pyrosequencing analysis to explore the relative contributions of cis and trans regulatory variations to expression divergence between BY and RM. My results indicated that the expression divergence of BY and RM were mainly due to trans regulatory variations in both normal condition and in heat stress condition, 76.9% and 64.6% of the genes were affected by the trans major regulatory variations, respectively. However, the effect of trans regulatory variation was decarase after heat shock stress. These results indicated that the cis regulatory variation may play an important role on the adaption to the heat stress environment. My results showed that 46.2% (30/65) of genes showed the same trend of cis or trans variation effect even after heat shock stress, 30.8% (20/65) of genes showed decrease of trans variation effect and 23.1% (15/65) of genes showed increase of trans variation effect after heat shock stress. Further analysis showed that the number of upstream transcription factors of the gene, TATA box regulatory elements, the location of genes on chromosomes left or right arm, the direction of genes at Watson or Crick strand and gene fuction may correlate with the increase or decarase in trans variation effect after heat shock. More detail analysis is presented in the main text.

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