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| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| dc.contributor.advisor | 朱家瑩(Chia-Ying Chu) | |
| dc.contributor.author | Jo-Hsi Huang | en |
| dc.contributor.author | 黃若晞 | zh_TW |
| dc.date.accessioned | 2021-05-19T17:55:24Z | - |
| dc.date.available | 2026-07-14 | |
| dc.date.available | 2021-05-19T17:55:24Z | - |
| dc.date.copyright | 2016-08-25 | |
| dc.date.issued | 2016 | |
| dc.date.submitted | 2016-08-22 | |
| dc.identifier.citation | Chapter 1
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/7836 | - |
| dc.description.abstract | 對生物而言，受控制的基因表現是至關重要的。基因表現的控制部分有賴後轉錄(Post-transcriptional)調控者，包括DEAD-box protein 6 (DDX6)。DDX6最廣為所知的是它參與RNA代謝(RNA turnover)以及轉譯抑制(translational repression)。本研究中，我們關注DDX6在基因表現調控中所扮演的角色與其在細胞內的分佈、分佈的調控機制、及其生物意義。於第一章，我們闡述了DDX6於基因表現及其調控中的意義，並由此展開DDX6的基礎生化性質、在細胞內的功能、以及其對表型的(phenotypic)影響。第二章包括我們對於DDX6的細胞核質(nucleocytoplasmic)分佈的研究。深入地檢視現行的假說，並以分子生物以及蛋白結構的證據予以反駁。我們的結果更顯示DDX6可以藉由另外兩種並存的機制分布到細胞核與細胞質之中。第三章描述我們對於DDX6的基因表現調控的研究。我們利用整合性的功能性基因體學的方法，來探討DDX6對於核糖核酸 (RNA)及蛋白質表現的調控以及其規模與侷限。我們首先指出DDX6在細胞內能結合信使核糖核酸(messenger RNA)以及長片段非編碼核糖核酸(long noncoding RNA)。不若一般的期待，我們發現在HeLa細胞株中DDX6並不顯著地影響整體的核糖核酸及蛋白質表現量。相反地，我們觀察到DDX6調控基因表現雜訊(gene expression noise)的證據。因此，我們的實驗結果提供對於DDX6的基因表現調控的新觀點。第四章描述了我們對於DDX6的入核機制更進一步的實驗結果。這些結果或能引導未來的研究。 | zh_TW |
| dc.description.abstract | Well-tuned gene expression is essential for life and is in part secured by the post-transcriptional regulators. DEAD-box protein 6 (DDX6) is one such regulator. DDX6 is best known for its participation in RNA turnover and translational repression. In this study, we focus on the roles of DDX6 in regulating gene expression and on the subcellular localization of DDX6, and its regulation, as well as its functional implications. In the first chapter, we elaborated a logical sequence to locate the niche of DDX6 in the context of gene expression and regulation. On this basis, we further expounded the fundamental biochemical properties of DDX6, its functional roles in the cells, and their phenotypic consequences. The second chapter includes our investigation on the governing mechanism of the nucleocytoplasmic distribution of DDX6. We scrutinized the working hypothesis and refuted it with molecular and structural evidence. We further demonstrated that two parallel mechanisms direct the nucleocytoplasmic distribution of DDX6. The third chapter includes our investigation on the regulation of gene expression by DDX6. We adopted an integrative functional genomics approach to investigate the size and the extent of the DDX6-mediated regulation on RNA and protein expression. We first demonstrated that DDX6 binds both the messenger RNA and the long noncoding RNA. In contrast our original expectation, we did not observe significant regulation over the RNA or the protein expression levels by DDX6 in the HeLa cell line. Notwithstanding, we provided evidence that DDX6 regulates gene expression noise. Thus, our results provide a new perspective on the gene regulation by DDX6. The fourth chapter includes the further experimental results related to the nuclear entry mechanism of DDX6. The results described therein may guide further investigations in the future. | en |
| dc.description.provenance | Made available in DSpace on 2021-05-19T17:55:24Z (GMT). No. of bitstreams: 1 ntu-105-R02b21008-1.pdf: 16606450 bytes, checksum: fa351c7bcdb0f2545c4866868647a698 (MD5) Previous issue date: 2016 | en |
| dc.description.tableofcontents | 口試審定書 i
Acknowledgement iii 摘要 v Abstract vii I. Chapter 1 1. Abstract 1 2. Gene expression and post-transcriptional regulation 1 2.1. Gene expression 1 2.2. Post-transcriptional regulation 3 3. DEAD-box proteins 6 3.1. Basic properties of the DEAD-box proteins 6 3.2. DEAD-box proteins as RNA chaperones and RNP remodelers 9 4. DEAD-box protein 6 12 4.1. A brief introduction to the DDX6 subfamily proteins 12 4.2. Identification and characterization of the DDX6 homologs 13 4.3. DDX6 in post-transcriptional gene silencing 20 4.4. The ATPase activity of DDX6 26 4.5. The RNA binding activity of DDX6 28 4.6. The cytoplasmic localization of DDX6 35 4.7. The nuclear localization of DDX6 36 4.8. Future perspectives 41 5. Tables 45 6. References 55 II. Chapter 2 1. Abstract 74 2. Introduction 74 3. Materials and methods 76 3.1. Cell culture and transfection 76 3.2. Drug treatments for CRM1 inhibition and cell cycle synchronization 77 3.3. Plasmid sources, molecular cloning, and fusion protein construction 77 3.4. Immunofluorescence (IF) and fluorescent in situ hybridization (FISH) 78 3.5. Microscopy, image processing, and analysis 79 3.6. Whole cell, nuclear, and cytoplasmic protein extraction 80 3.7. RNA co-immunoprecipitation (RIP) 81 3.8. Western blot (WB) 82 3.9. RNA extraction, reverse transcription, and quantitative real-time PCR (qPCR) 82 3.10. Quantitative mass spectrometry (MS) and data analysis 83 3.11. Protein structures and NLS prediction 83 4. Results 84 4.1. DDX6 is present in the human cell nuclei 84 4.2. DDX6 binds the nuclear lncRNA MALAT1 85 4.3. DDX6 is insensitive to the LMB treatment 85 4.4. The putative NES of DDX6 is structurally inaccessible to CRM1 86 4.5. The putative NLS, miRISC, and MALAT1 are dispensable for the nuclear entry of DDX6 88 4.6. The CTD of DDX6 drives nuclear localization 89 4.7. The CTD of DDX6 binds to the condensed chromosomes during mitosis 91 4.8. The CTD of DDX6 facilitates nuclear entry by hitchhiking on the condensed chromosomes during mitosis 92 4.9. 4E-T can mediate piggyback shuttling of DDX6 92 5. Discussion 94 5.1. The widespread nuclear localization of DDX6 94 5.2. On the nucleocytoplasmic shuttling model of DDX6 96 5.3. The alternative mechanisms for the nucleocytoplasmic distribution of DDX6: A new synthesis 97 6. Figures 100 7. References 132 III. Chapter 3 1. Abstract 138 2. Introduction 138 3. Materials and methods 140 3.1. Cell culture and siRNA transfection 140 3.2. RNA co-immunoprecipitation (RIP) 141 3.3. RNA extraction, reverse transcription, and quantitative real-time PCR (qPCR) 141 3.4. Protein extraction and Western blot (WB) 142 3.5. Polysome fractionation and profiling 142 3.6. RIP-seq and RNA-seq sample preparation and data acquisition 143 3.7. RIP-seq and RNA-seq data analysis 144 3.8. Quantitative MS sample preparation and data acquisition 145 3.9. MS data analysis 146 4. Results 146 4.1. DDX6 binds both the mRNA and the lncRNA in human cell lines 146 4.2. DDX6 binds the RNA localized in different subcellular compartments 147 4.3. DDX6 has limited effect on the overall RNA expression level 149 4.4. DDX6 regulates the expression noise of its target RNA 151 4.5. DDX6 has limited effect on the overall protein expression level 152 4.6. DDX6 regulates the protein expression noise of its bound mRNA 154 4.7. DDX6 has limited effect on the polysome occupancy 155 4.8. DDX6-regulated RNA and protein expression are weakly coupled 155 5. Discussions 156 5.1. A generalization of the concept of the DDX6’s RNA binding activity 156 5.2. On the role of DDX6 in regulating RNA and protein expression 158 5.3. On the role of DDX6 in cell fate maintenance, specifications, and responses to stimuli: Under the “cell fate attractor” theory 162 6. Figures 165 7. References 205 IV. Chapter 4 1. Abstract 213 2. Introduction 213 3. Materials and methods 214 3.1. Molecular cloning 214 3.2. Cell culture and plasmid transfection 214 3.3. Sample preparation and microscopy 214 3.4. Image analysis 215 3.5. Protein sequence and structural analysis 216 4. Results 217 4.1. A semi-automatic workflow for the imaging-based analysis of the nucleocytoplasmic distribution 217 4.2. Time-dependent phenotypic shift in the cells expressing YFP-PKM-DDX6 CTD 218 4.3. The nucleocytoplasmic localization of the DDX6 homologs CTD 219 4.4. Mutational analysis of the DDX6 CTD motifs 220 5. Discussion 220 6. Figures 223 7. References 236 V. Appendices 1. List of quantitative PCR primer sets 238 2. List of small interfering RNA oligonucleotides 239 3. List of antibodies for Western blot 240 4. List of antibodies for immunofluorescence 241 5. List of antibodies for immunoprecipitation 242 6. List of expression vectors and constructs 243 | |
| dc.language.iso | en | |
| dc.title | DEAD-box Protein 6的分子生物學探討 | zh_TW |
| dc.title | Molecular Interrogation of DEAD-box Protein 6 | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 104-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 張典顯(Tien-Hsien Chang),黃怡萱(Yi-Shuian Huang) | |
| dc.subject.keyword | 基因表現,後轉錄調控,基因靜默,DEAD-box protein,DDX6,核質分布,入核信號,出核信號,信使核糖核酸,長片段非編碼核糖核酸,基因表現雜訊, | zh_TW |
| dc.subject.keyword | Gene expression,post-transcriptional regulation,DEAD-box proteins,DDX6,nucleocytoplasmic distribution,nuclear localization signal,nuclear export signal,messenger RNA,long noncoding RNA,gene expression noise, | en |
| dc.relation.page | 244 | |
| dc.identifier.doi | 10.6342/NTU201603271 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2016-08-22 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生命科學系 | zh_TW |
| dc.date.embargo-lift | 2026-07-14 | - |
| Appears in Collections: | 生命科學系 | |
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| ntu-105-1.pdf Until 2026-07-14 | 16.22 MB | Adobe PDF |
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