長期以來基因表現的調節機制已被認知到在生理功能及演化方面扮演了很重要的角色，如胚胎發育、種內及種間演化的差異性。而種內及種間基因表現的差異性對基因調節的演化提供了很好的基本研究材料，而且可以應用在許多不同的物種。先前對種內基因調節演化的研究，在不同物種的研究結果有相當高的一致性，都指出外因子(trans factors)是影響種內基因表現差異的主要因素，但在種間基因表現差異的研究則結論出幾個不同的演化模式。因此在本計畫中，我們將運用最先進的高通量研究法-第二代基因定序(Second Generation Sequencing-Solexa)，來研究酵母菌種間基因調節的演化。由於我們的初期結果與前人酵母菌的研究結果不太一致，因此我們更進一步利用基因工程方法置換內因子(cis-element or promoter region)及利用基因架構在質體(plasmid)內來探討研究分析中推論的正確性及可能影響的因子機制。藉此，相信也能使我們對種間基因調節演化有更深入的了解。在本計畫中我們試圖回答下列問題：(1)在種間的演化內因子(cis-factors)及外因子(trans-factors)各扮演了什麼樣的角色？(2)是否所推斷出的純內因子(cis-only)調節的基因是完全不受外因子的影響？(3)是否基因表現只受到基因間區間(intergenetic region,包含啟動區(promoter))的影響？(4)是否相鄰基因影響基因的表現？ Gene regulations of the genome-wide gene expressions have long been recognized playing a significant role in physiological functions and evolution. Intra- and interspecific gene expression differencs have formed a framework of fundamental knowledge of gene regulations. Previous studies have outlined a consist evolution pattern of gene regulation at the intraspecific level, however no consensus can be made at the interspecific level. In this study, we apply a most modern high-through-put technology, the Second Generation Sequencing, to attain the interspecific evolutionary patterns of gene regulations in yeast. Since our preliminary results do not consist with previous yeast studies, we make a step further to obtain some additional evidence with genetic engineering to manipulate those cis-elements and trans conditions, like promoter swapping and plasmid applications. These results should provide us a better insight of interspecific evolutionary contents. Here, we try to address the following questions: (1) What are the evolutionary roles of cis and trans factors in interspecific gene regulations? (2) Whether those determined “cis-only” regulatory genes are really only affected by promoter elements? (3) Whether those “cis-only” gene expressions affected by chromatin folding? (4) Whether those “cis-only” gene expressions affected by neighbor genes? 研究期間：10008 ~ 10107
