博碩士論文 962211001 詳細資訊

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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)
★ 大腸癌細胞株之 EGFR—K-ras 訊號路徑的基因微陣列實驗 與化學基因體學分析★ 小鼠胚胎幹細胞株之建立及人類誘導多能性幹細胞之培養技術
★ 由神經生長因子誘導之細胞內訊號路徑活化的化學基因體學分析★ 利用健保資料庫探討常見複雜疾病之中草藥處方研究
★ 細胞週期蛋白D1 mRNA在小鼠胚胎及成體幹細胞和腫瘤細胞中的表現及其受多能性相關因子影響之探討★ 主觀影響療癒的案例與主觀在醫療重要性的探討
★ 精神分裂症病患與正常人之DNA甲基化網絡的差異★ 躁鬱症病患的精子之DNA 甲基化的網路分析
★ 運用時間序列微陣列資料來預測調控基因★ 以大鼠嗜鉻性瘤細胞株建立神經訊號傳遞之細胞分子生物學模型
★ Cloud-R:以R軟體與雲端技術為基礎的生物統計應用網站★ 中草藥藥性與中草藥遺傳演化樹之關係
★ 運用高通量基因微矩陣列方法解析由嗜鉻 細胞分化成神經細胞之全基因體的調控★ 神經生長因子在神經分化中轉錄因子活性及基因調控機制之橫觀
★ 利用階層式叢集及不同分類方法分析人類正常組織特異性基因★ 由ENCODE計畫分析脫氧核醣核酸酶I與組蛋白修飾
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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
Chapter 2 Materials and Methods 15
2-2 METHODS 18
Chapter 3 Results 35
3-7 VALIDATION ON B_1_554331 49
Chapter 4 Discussion 50
Chapter 5 Conclusion 54
References: 55
參考文獻 . "Affymetrix Data Resource Center." from http://www.affymetrix.com/index.affx.
. "http://www.genome.jp/kegg/." from http://www.genome.jp/kegg/.
Agullo, G., L. Gamet-Payrastre, et al. (1997). "Relationship between flavonoid structure and inhibition of phosphatidylinositol 3-kinase: a comparison with tyrosine kinase and protein kinase C inhibition." Biochem Pharmacol 53(11): 1649-57.
Ahmad, K. and S. Henikoff (2002). "Epigenetic consequences of nucleosome dynamics." Cell 111(3): 281-4.
Aparicio, O. A. O., Geisberg JV, Struhl K (2004). Current Protocols in Cell Biology. University of Southern California, Los Angeles, California, USA, John Wiley & Sons, Inc.
Arango, D., A. J. Wilson, et al. (2004). "Molecular mechanisms of action and prediction of response to oxaliplatin in colorectal cancer cells." Br J Cancer 91(11): 1931-46.
Birney, E., J. A. Stamatoyannopoulos, et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature 447(7146): 799-816.
Bondos, S. E. and X. X. Tan (2001). "Combinatorial transcriptional regulation: the interaction of transcription factors and cell signaling molecules with homeodomain proteins in Drosophila development." Crit Rev Eukaryot Gene Expr 11(1-3): 145-71.
Boulikas, A. P., Evagelos Bellis, and Petros Christofis (2007). "Designing platinum compounds in cancer: structures and mechanisms." Cancer Therapy 5: 537-583.
Boyer, J., W. L. Allen, et al. (2006). "Pharmacogenomic identification of novel determinants of response to chemotherapy in colon cancer." Cancer Res 66(5): 2765-77.
Boyle, A. P., S. Davis, et al. (2008). "High-resolution mapping and characterization of open chromatin across the genome." Cell 132(2): 311-22.
Cartwright, I. L. and S. C. Elgin (1986). "Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster." Mol Cell Biol 6(3): 779-91.
Collins, F. S., M. Morgan, et al. (2003). "The Human Genome Project: lessons from large-scale biology." Science 300(5617): 286-90.
Crawford, G. E., S. Davis, et al. (2006). "DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays." Nat Methods 3(7): 503-9.
Crawford, G. E., I. E. Holt, et al. (2004). "Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites." Proc Natl Acad Sci U S A 101(4): 992-7.
Dekker, J., K. Rippe, et al. (2002). "Capturing chromosome conformation." Science 295(5558): 1306-11.
Diehl, A. D., J. A. Lee, et al. (2007). "Ontology development for biological systems: immunology." Bioinformatics 23(7): 913-5.
Dingwall, C., G. P. Lomonossoff, et al. (1981). "High sequence specificity of micrococcal nuclease." Nucleic Acids Res 9(12): 2659-73.
Elgin, S. C. (1988). "The formation and function of DNase I hypersensitive sites in the process of gene activation." J Biol Chem 263(36): 19259-62.
Fambrough, D., K. McClure, et al. (1999). "Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes." Cell 97(6): 727-41.
Greenberg, M. E., E. B. Ziff, et al. (1986). "Stimulation of neuronal acetylcholine receptors induces rapid gene transcription." Science 234(4772): 80-3.
Gross, D. S. and W. T. Garrard (1988). "Nuclease hypersensitive sites in chromatin." Annu Rev Biochem 57: 159-97.
Hara, S., M. Oya, et al. (2005). "Akt activation in renal cell carcinoma: contribution of a decreased PTEN expression and the induction of apoptosis by an Akt inhibitor." Ann Oncol 16(6): 928-33.
Harris, M. A., J. Clark, et al. (2004). "The Gene Ontology (GO) database and informatics resource." Nucleic Acids Res 32(Database issue): D258-61.
Huang D.W., S. B. T., Lempicki R.A. (2009). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources." Nature Protocols(4): 14.
Hutchison, N. and H. Weintraub (1985). "Localization of DNAase I-sensitive sequences to specific regions of interphase nuclei." Cell 43(2 Pt 1): 471-82.
Jongstra, J., T. L. Reudelhuber, et al. (1984). "Induction of altered chromatin structures by simian virus 40 enhancer and promoter elements." Nature 307(5953): 708-14.
Jung, T., B. Catalgol, et al. (2009). "The proteasomal system." Mol Aspects Med.
King, C. R., J. Yu, et al. (2005). "Interethnic variability of ERCC2 polymorphisms." Pharmacogenomics J 5(1): 54-9.
Lee, Y.-C. G. (2007). "Expertise Pathway Open Software." 2009, from http://bio.tmu.edu.tw:8080/expose/index.htm.
Lewin, B. (2004). Genes VIII. P. Region, Pearson Prentice Hall.
LoPiccolo, J., G. M. Blumenthal, et al. (2008). "Targeting the PI3K/Akt/mTOR pathway: effective combinations and clinical considerations." Drug Resist Updat 11(1-2): 32-50.
Midgley, R. and D. Kerr (1999). "Colorectal cancer." Lancet 353(9150): 391-9.
Moss, T. (2001). DNA-protein interactions: principles and protocols, Humana Press.
Paez, J. and W. R. Sellers (2003). "PI3K/PTEN/AKT pathway. A critical mediator of oncogenic signaling." Cancer Treat Res 115: 145-67.
Pang, S. K., C. W. Yu, et al. (2008). "Impact of oxaliplatin and a novel DACH-platinum complex in the gene expression of HCT116 colon cancer cells." Oncol Rep 20(5): 1269-76.
Plasencia, C., E. Martinez-Balibrea, et al. (2006). "Expression analysis of genes involved in oxaliplatin response and development of oxaliplatin-resistant HT29 colon cancer cells." Int J Oncol 29(1): 225-35.
Pollack, J. R. (2009). Microarray Analysis of the Physical Genome, Humana Press.
Prioleau, M. N., P. Nony, et al. (1999). "An insulator element and condensed chromatin region separate the chicken beta-globin locus from an independently regulated erythroid-specific folate receptor gene." EMBO J 18(14): 4035-48.
Raymond, E., S. Faivre, et al. (2002). "Cellular and molecular pharmacology of oxaliplatin." Mol Cancer Ther 1(3): 227-35.
Ren, B., F. Robert, et al. (2000). "Genome-wide location and function of DNA binding proteins." Science 290(5500): 2306-9.
Ruan, Y., P. Le Ber, et al. (2004). "Interrogating the transcriptome." Trends Biotechnol 22(1): 23-30.
Segal, E., Y. Fondufe-Mittendorf, et al. (2006). "A genomic code for nucleosome positioning." Nature 442(7104): 772-8.
Shannon, P., A. Markiel, et al. (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks." Genome Res 13(11): 2498-504.
Simon, M. A. (2000). "Receptor tyrosine kinases: specific outcomes from general signals." Cell 103(1): 13-5.
Tan, P. B. and S. K. Kim (1999). "Signaling specificity: the RTK/RAS/MAP kinase pathway in metazoans." Trends Genet 15(4): 145-9.
Teletchéa, S. K., J.-M. Teuben, M.-A. Elizondo-Riojas, J. Reedijk, J. Kozelka (2006). "A new pyrazole-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding." Chem. Eur. J. 12.
Tollefsbol, T. O. (2004). Epigenetics protocols, Humana Press.
van Noort, V., B. Snel, et al. (2004). "The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model." EMBO Rep 5(3): 280-4.
Woynarowski, J. M., W. G. Chapman, et al. (1998). "Sequence- and region-specificity of oxaliplatin adducts in naked and cellular DNA." Mol Pharmacol 54(5): 770-7.
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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