發展酵素非限制性全基因體調控因子解析方法

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姓名

柯怡安(Yi-An Ko) 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

發展酵素非限制性全基因體調控因子解析方法
(Development of a Non-Restricted Functional Elements Assay Method for Identifying Genome-Wide Regulatory Elements)

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摘要(中)

後基因組學的研究分析目前面臨的一個重大挑戰，即整合基因、調控元件和染色質結構的全基因組規模之研究。染色質結構之於基因表現有很大的影響，尤其是調控元件透過被不同蛋白質或調控因子結合，能扮演各種不同的角色。因此我們開發出一種新的方法，利用全基因組元件經由非限制型酵素降解未被蛋白質結合之片段，來詮釋經過刺激後結合狀態產生變化的調控元件，並進行更全面HCT- 116大腸癌細胞株經含有鉑金屬之化療藥物處理後基因組的變化。我們實驗的目的是通過使用高分辨率的啟動子貼磚微陣列晶片和外顯子微陣列晶片，將樣品經已優化濃度的DNA酶一處理，並以一個商業軟件包Partek，和成對高斯合併方法作數據分析。在我們的實驗數據中，我們從啟動子晶片得到12,117個基因的啟動子有變化，3,043基因有差異性表現量於外顯子陣列。通過整合的兩種數據，我們發現，61 ％的基因表達其上游的啟動子區域也出現變化。此結果表明，這些區域可能參與調節轉錄後鉑金屬藥物刺激。我們的研究可能提供一種新方法的研究全基因組調控元件。

摘要(英)

A major challenge for post-genomics research is the integration gene expressions with their corresponding regulatory elements and chromatin architectures on a genome-wide scale. Regulatory elements exert diverse mechanisms to regulate the expression of genes through protein-protein or protein-DNA interactions, while chromatin structures act in the upstream of the regulatory cascade and have a broad effect on the expression of multiple genes. Here, we developed a novel method, denoted as genome-wide non-restricted functional elements assay (NOFEE), to identify changes of regulatory elements and to pursue a more comprehensive characterization of the gene expression profile of HCT-116 colorectal cancer cell line in response to the treatment of a Pt-based compound. Our experiments integrate high-resolution promoter tiling arrays and exon arrays on samples that were treated with optimized concentration of DNase I. Data were subsequently analyzed with ‘Partek’ software package, which is a commercial product based on pair-wise Gaussian merging method. A total of 12,117 regions in the promoter array and 3,043 differentially expressed genes in the exon array were used in our experiment. By integrating these datasets, we show that 61% of the exon expression profile can be associated with promoter regulatory regions suggesting that promoters in these regions may be directly involved in the transcriptional regulation of in response to Pt-compound treatment. Our results also suggest that the NOFEE approach can be a powerful method for genome-wide investigations of cis-acting regulatory elements.

關鍵字(中)

★ 啟動子晶片
★ 成對高斯配對法
★ 大腸直腸癌
★ 脱氧核糖核酸酶

關鍵字(英)

★ DNase
★ Colorectal Cancer
★ Pair-wise Gaussian
★ Promoter Array

論文目次

Abstract i
摘要 ii
Chapter 1 Introduction 1
1-1 CURRENT STUDIES OF GENE REGULATORY ELEMENTS 1
1-2 DNASE-CHIP 4
1-3 CHIP-CHIP 7
1-4 NOFEE-CHIP 9
1-5 ANALYSIS 11
1-6 COLORECTAL CANCER AND OXALIPLATIN－THE PT-BASED COMPOUND 12
Chapter 2 Materials and Methods 15
2-1 MATERIALS 15
2-2 METHODS 18
Chapter 3 Results 35
3-1 EXPERIMENTAL RESULTS 35
3-2 PARTEK ANALYSIS 37
3-3 INTEGRATION OF PROMOTER ARRAY AND EXON ARRAY 39
3-4 GENE ONTOLOGY BY DAVID 41
3-5 PATHWAY MAPPINGS 44
3-6 NETWORK ANALYSIS 47
3-7 VALIDATION ON B_1_554331 49
Chapter 4 Discussion 50
Chapter 5 Conclusion 54
References: 55

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指導教授

凌慶東、王孫崇
(Qing-Dong Ling、Sun-Chong Wang)

審核日期

2009-7-30

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