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研究生:徐千惠
研究生(外文):Chien-Hui Hsu
論文名稱:FGF9基因3’UTR序列對調控FGF9蛋白質表現之研究
論文名稱(外文):The post-transcriptional regulation of human FGF9 3’ untranslated region (3’UTR) on FGF9 protein expression
指導教授:孫孝芳孫孝芳引用關係
指導教授(外文):Hsiao-Fang Sunny Sun
學位類別:碩士
校院名稱:國立成功大學
系所名稱:分子醫學研究所
學門:醫藥衛生學門
學類:醫學學類
論文種類:學術論文
論文出版年:2005
畢業學年度:93
語文別:英文
論文頁數:83
中文關鍵詞:第九纖維母細胞生長因子三端非轉譯序列
外文關鍵詞:3'UTRAREFGF9MS
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  細胞中的後轉錄調控是經由調節核醣核酸穩定度、轉譯效率、訊息核醣核酸的運輸與位移以及多聚腺核苷酸的選擇與長度來調節基因的表現量。主要是藉由非轉譯序列和其特定之調控蛋白交互作用來調控。其中,三端非轉譯的區域已在先前的研究中被指出,是決定發育時期細胞不同蛋白質表現分佈的重要調控序列。第九纖維母細胞生長因子在先前的動物研究中被發現是一個對胚胎發育、器官形成、性別發育和維持生命機能都十分重要的內分泌物質;然而目前對於人類第九纖維母細胞生長因子基因調控的研究所知有限。本實驗室先前之研究指出此基因的三端非轉譯序列上之微衛星序列具有調控基因表現的能力;進一步的生物資訊分析發現,此區域有富含腺核苷酸及尿核苷酸的序列存在,可能參與基因調控,並在表達序列標籤資料庫中,亦發現此基因有數種不同長度的三端非轉譯序列。這些結果都指出人類第九纖維母細胞生長因子的三端非轉譯序列研究之重要性。因此,這個實驗的主要目的在於找出此區域中具調控功能的序列及相互作用之蛋白質。我們利用快速放大基因末端片段的方法,發現在人類胚胎腎細胞株(HEK293)中有五種不同的三端非轉譯序列存在。此五種不同的片段包含微衛星序列及富含腺核苷酸及尿核苷酸序列之各種組合。進而利用冷光報導基因系統來研究此兩種調控序列和不同的三端非轉譯片段對此生長因子表現的調控,實驗結果顯示此兩種調控序列的突變皆會增加蛋白質的表現量,而不同的三端非轉譯片段也有不同的調控能力。進一步的實驗也發現,此兩種調控序列是經由與特定調控蛋白的結合來增加核醣核酸的不穩定度。綜合以上結果顯示,在人類第九纖維母細胞生長因子的三端非轉譯序列上,微衛星序列及富含腺核苷酸及尿核苷酸序列,可經由讓核醣核酸較不穩定的負調控方式來改變人類第九纖維母細胞生長因子在細胞中的表現程度。
 Post-transcriptional control, which includes determining transcript stability, level of translation, mRNA targeting, poly (A) shortening and alternative polyadenylation, has been shown to regulate protein expression via interaction of untranslated regions (5’ and 3’UTR) with regulatory proteins. Recent studies reveal the power of 3’UTR in controlling cell–fate determination, location and timing of cell division, and shaping the expression pattern during development. Fibroblast growth factor 9 (FGF9) is an autocrine/paracrine growth factor that plays important roles in embryonic development, organ development, sexual development and physiologic maintenances. Limited studies have reported the expression control of human FGF9. Our previous study has demonstrated the microsatellite (MS) motif of FGF9 3’UTR can influence gene expression in a reporter gene system. Additional sequence analysis using bioinformatics tools suggested the AU-rich element (ARE) of FGF9 3’UTR may also participate in regulating FGF9 mRNAs. Furthermore, information from searching EST database showed several FGF9 transcripts with different length in 3’UTR. These data suggested the potential regulatory role of FGF9 3’UTR on FGF9 protein expression. This study aims to identify all possible functional cis-elements of FGF9 3’UTR and its associated proteins. We have identified five FGF9 transcripts with different lengths in 3’end by 3’RACE in HEK293 cells. The varied lengths of 614-, 549-, 194-, 73-, and 50-bp from the stop codon of FGF9 transcript are containing both MS and ARE motifs, MS motif only, or none of the motifs. The role of each element and varied FGF9 transcripts in regulating FGF9 protein expression is investigated using luciferase assay. The data showed either a point mutation within the AUUUA motif or deletion of FGF9 3’UTR MS motif significantly increased reporter gene activity in HEK293 cells, besides; the different FGF9 transcripts have various expression level of reporter gene. Additional mRNA turnover and RNA-protein interaction studies suggested both ARE and MS motif of FGF9 3’UTR may destabilize FGF9 mRNA through the interactions and RNA-binding proteins. In conclusion, results from this study indicate ARE and MS motifs of FGF9 3’UTR can modulate FGF9 protein expression by destabilizing FGF9 mRNA stability.
TABLE OF CONTENTS

ABSTRACT IN CHINESE I
ABSTRACT IN ENGLISH II
ACKNOWLEDGEMENT IV
TABLE OF CONTENTS VI
LIST OF TABLES IX
LIST OF FIGURES X

1 INTRODUCTION 1
1.1 Fibroblast growth factor 9 (FGF9) 1
1.1.1 Molecular property of human FGF9 1
1.1.2 The biological functions of FGF9 1
1.1.3 The pathogenic role of FGF9 3
1.2 Controls of gene expression in Eukaryotes 4
1.2.1 Controls of gene expression 4
1.2.2 Post-transcriptional regulation 4
1.2.3 mRNA decay pathways in mammalian cells 6
1.3 The role of 3’UTR mediated mRNA stability 7
1.3.1 Cis-acting elements determinant in mRNA stability 7
1.3.2 Trans-factors that bind the 3’UTR cis-acting determinants 11
1.4 Objective of this study 12
2 MATERIALS AND METHODS 14
2.1 Cell culture 14
2.1.1 Routine maintenance and subculture 14
2.1.2 Cell stock 14
2.2 Total RNA isolation and reverse transcriptional polymerase chain reaction (RT-PCR) 15
2.2.1 Total RNA isolation 15
2.2.2 DNase treatment 15
2.2.3 Reverse transcription 16
2.2.4 Polymerase Chain Reaction (PCR) 17
2.3 Plasmid DNA preparation and DNA purification 17
2.3.1 Minipreparation of plasmid DNA 17
2.3.2 Midipreparation of plasmid DNA 18
2.3.3 Gel extraction 19
2.4 Rapid amplification of cDNA 3’ends (3’RACE) 20
2.4.1 Primer design for 3’RACE 20
2.4.2 First-strand cDNA synthesis and RACE-PCR 20
2.4.3 Cloning human FGF9 3’UTR transcripts by TA cloning 21
2.4.4 Rapid colony screening 22
2.5 Construction of reporter plasmid with human FGF9 3’UTR and mutation constructs 22
2.5.1 Vectors 22
2.5.2 Full length and deletion constructs 23
2.5.3 Mutation constructs 25
2.6 Transient transfection and luciferase assay 26
2.6.1 Transient transfection 26
2.6.2 Luciferase assay 27
2.6.3 Protein assay 28
2.6.4 Statistical analysis 28
2.7 mRNA turnover study 28
2.7.1 Time point and dosage for Actinomycin D (Act D) treatment 28
2.7.2 RT-PCR for mRNA turnover study 29
2.7.3 Real-time TaqMan relative-quantitative PCR 29
2.7.4 Luciferase assay with Act D treatment 31
2.8 RNA-electrophoretic mobility shift assay (RNA-EMSA) 31
2.8.1 Design biotin-labeled RNA oligos 31
2.8.2 Prepare the total cell extracts 32
2.8.3 Perform binding reaction and electrophoresis 32
2.8.4 Electrophoretic transfer of binding reactions to nylon membrane 33
2.8.5 Detect biotin-labeled RNA by Chemiluminescence 33
2.9 Computational analysis 35
2.9.1 Restriction enzyme site prediction 35
2.9.2 Primer design 35
2.9.3 RNA secondary structure prediction 35
2.9.4 Potential regulatory elements prediction 35
2.9.5 AU-rich element search 36
2.9.6 EST database search 36
2.9.7 Multiple sequence alignment 36
3 RESULTS 38
3.1 Bioinformatics prediction 38
3.2 Cloning and sequencing of the 3′-ends of the human FGF9 gene 39
3.3 The ARE and MS motif of the human FGF9 3’UTR is a cis-acting element in HEK293 40
3.4 Effect of the ARE sequence and MS motifs of human FGF9 3’UTR on mRNA stability 41
3.5 Pattern of interaction between the FGF9 3’UTR and RNA-binging proteins 42
4 DISCUSSIONS 44
4.1 Identification of post-transcriptional regulation of FGF9 44
4.2 The regulation of FGF9 gene expression by 3’UTR 48
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