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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 張典顯 | |
dc.contributor.author | Hsuan-Kai Wang | en |
dc.contributor.author | 王宣凱 | zh_TW |
dc.date.accessioned | 2021-06-17T00:30:58Z | - |
dc.date.available | 2023-02-17 | |
dc.date.copyright | 2020-02-17 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2020-02-10 | |
dc.identifier.citation | 1 Madhani, H. D. & Guthrie, C. Dynamic RNA-RNA interactions in the spliceosome. Annual review of genetics 28, 1-26, doi:10.1146/annurev.ge.28.120194.000245 (1994).
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Function of conserved domains of hnRNP A1 and other hnRNP A/B proteins. The EMBO journal 13, 5483-5495 (1994). 14 Zhu, J., Mayeda, A. & Krainer, A. R. Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Molecular cell 8, 1351-1361 (2001). 15 Del Gatto-Konczak, F., Olive, M., Gesnel, M. C. & Breathnach, R. hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Molecular and cellular biology 19, 251-260 (1999). 16 Gallego, M. E., Gattoni, R., Stevenin, J., Marie, J. & Expert-Bezancon, A. The SR splicing factors ASF/SF2 and SC35 have antagonistic effects on intronic enhancer-dependent splicing of the beta-tropomyosin alternative exon 6A. The EMBO journal 16, 1772-1784, doi:10.1093/emboj/16.7.1772 (1997). 17 Ghigna, C. et al. Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. 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Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism. Rna 8, 969-980 (2002). 43 Pleiss, J. A., Whitworth, G. B., Bergkessel, M. & Guthrie, C. Rapid, transcript-specific changes in splicing in response to environmental stress. Molecular cell 27, 928-937, doi:10.1016/j.molcel.2007.07.018 (2007). 44 Morgan, J. T., Fink, G. R. & Bartel, D. P. Excised linear introns regulate growth in yeast. Nature 565, 606-+, doi:10.1038/s41586-018-0828-1 (2019). 45 Edwards, S. R. & Johnson, T. L. Intron RNA sequences help yeast cells to survive starvation. Nature 565, 578-579, doi:10.1038/d41586-019-00088-y (2019). 46 Black, D. L. Mechanisms of alternative pre-messenger RNA splicing. Annual review of biochemistry 72, 291-336, doi:10.1146/annurev.biochem.72.121801.161720 (2003). 47 Qiu, Z. R., Schwer, B. & Shuman, S. Determinants of Nam8-dependent splicing of meiotic pre-mRNAs. 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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/66338 | - |
dc.description.abstract | 剪接內含子是普遍存在的非編碼核糖核酸序列,通常注定要從新合成的核糖核酸中去除並迅速降解。但是,最近的研究表明,當營養缺乏時,積累的內含子可以幫助酵母細胞存活。在這裡,我們描述了一個指數,簡稱為IA,可用以評估內含子積累水平和剪接效率。通過使用IA指數的篩選準則,可以在各種生長條件下鑑定出新的內含子和信使核糖核酸前驅物積累事件。令人驚訝的是,在所有檢查的生長條件下,其中包括在營養培養基中指數生長期間,都發現了許多信使核糖核酸前驅物積累事件。內含子水平的提高是由於這些轉錄物不能被有效剪接和/或這些內含子不能被降解導致的。此外,在不同生長條件下,轉錄物的剪接效率會隨之變動,這表示剪接是響應於環境而專門進行調節的。順式信息分析表明,剪接效率低下的轉錄本內含子短,啟動子弱。剪接效率會隨轉錄加強而增加。為了確定反式因子與剪接事件之間的相互作用,我們開發了細胞內調節子的高通量篩選技術(CHRES),並且套用於約4,300種不同單基因缺失的酵母菌珠中。有趣的是,剪接較差的轉錄本的調節子與標準剪接的轉錄本幾乎不同。我們發現Ras / PKA信號傳遞路徑參與了低效率剪接轉錄本(KIN28)的調控。當將飢餓的細胞轉移到含有葡萄糖的豐富培養基中時,它可使KIN28轉錄物迅速被剪接,而當葡萄糖受到限制時,KIN28轉錄物則不能被有效剪接,這有助於細胞在需要呼吸作用時生長。因此,本篇研究展示了我們鑑定新型內含子積累事件及其調控機制的有效方法。同時展示了具有轉錄物特定性的調控網絡,其中包括營養刺激物的感知和信號傳遞讓剪接開始進行,使細胞得以快速適應新環境。 | zh_TW |
dc.description.abstract | Spliceosomal introns are ubiquitous non-coding RNA sequences that typically destined for removing from newly synthesized RNAs and rapidly degrading. However, recent studies suggest that accumulated introns help yeast cells survive when nutrients were scarc. Here, we describe an index, IA, to evaluate intron accumulation level and splicing efficiency. By using IA criteria, novel intron and pre-mRNA accumulation events were identified in various growth conditions. Surprisingly, lots of pre-mRNA accumulation events were found in all examined growth conditions including during exponential growth in rich medium. Increased levels of intron result from failures of these transcripts to be efficiently spliced and/or of these introns to be degraded. In addition, the splicing efficiency of transcripts varies with different growth conditions that suggest splicing is specifically regulated in response to environments. Cis-information analysis demonstrated the inefficiently spliced transcripts have short intron and weak promoters. Splicing efficiency increases with increased transcription. To identify interactions between trans-factors and splicing events, we developed a cell-based high-throughput regulator screening (CHRES) and implemented in the background of ~4,300 different gene deletions. Interestingly, regulators of the poorly spliced transcripts are distinct from the canonically spliced transcript. The Ras/PKA signaling transduction was found to involve in the regulation of inefficiently spliced transcript KIN28. It enables KIN28 transcript to be rapidly spliced when shifting starved cells to rich medium containing glucose but to be inefficiently spliced when glucose is limited, that help cell in respiratory growth. Thus, our work demonstrates the capacity of our approach to identifying novel intron accumulation events and their regulatory mechanisms. It exhibited transcript-specific regulatory networks that include sensing and signaling of the nutrient stimuli to activate splicing, allowing cells to quickly adapt to the new environments. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T00:30:58Z (GMT). No. of bitstreams: 1 ntu-109-D00b48008-1.pdf: 6583712 bytes, checksum: c153e4b56a2c080a433d7780340203e2 (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 口試委員會審定書 i
誌謝 ii 中文摘要 iv ABSTRACT v CONTENTS vii LIST OF FIGURES x LIST OF TABLES xiv Chapter 1 Introduction 1 1.1 Splicing is an essential step in eukaryotes 1 1.2 Difficulties in the characterization of splicing regulation in higher eukaryotic cells 2 1.3 Budding yeast is a potential model organism for studying splicing regulation 3 1.4 Regulated splicing in budding yeast 5 1.5 Additional splicing factors remain to identify in yeast 8 1.6 The network of splicing regulators and target transcripts 9 Chapter 2 Results 10 2.1 An index which evaluated intron and pre-mRNA accumulation level 10 2.2 Identify intron and pre-mRNA accumulation events in various growth conditions 31 2.3 Pre-mRNA accumulation events during exponential growth mainly result from inefficient splicing 51 2.4 Un-spliced but polyadenylated RNAs validate inefficient splicing occurred during exponential growth 55 2.5 Distinct splicing regulation in response to environments 59 2.6 Splicing efficiency increased with transcription rate 63 2.7 Screening for regulator involved in inefficient splicing 73 2.8 Networks and GO analysis showed distinct regulation between two transcripts 83 2.9 RAS/PKA signaling pathway regulated KIN28 splicing 96 2.10 Rapidly increased splicing efficiency of KIN28 in response to glucose 104 Chapter 3 Discussion 114 3.1 Intron accumulation index 114 3.2 Mechanisms and function of inefficient splicing regulation 115 3.3 Substrate-specific transcription and splicing regulation 116 3.4 Connecting the spliceosome to cellular environment 117 3.5 Implications 121 Chapter 4 Materials and Methods 122 4.1 RNA-sequence analysis 122 4.2 Yeast strains and growth conditions 124 4.3 RT-PCR gel electrophoresis 124 4.4 In vivo splicing reporter assays 129 4.5 Cell-based high-throughput regulator screening (CHRES) 129 4.5.1 Array construction for screening 129 4.5.2 Data acquisition from high-throughput flow cytometry 130 4.5.3 FACS data pre-processing 130 4.5.4 Identification of candidates 131 4.6 Analysis of splicing efficiency by RT-qPCR 131 4.7 Go enrichment analysis 133 4.8 Networks analysis 133 4.9 Overexpression of activated Ras2p 134 4.10 Competitive-fitness assay 134 4.11 Regression between the IA index and features of i-genes 135 4.12 Random forest model to determine features that influence splicing 136 4.13 Microscopic imaging of GFP-tagged strains 137 4.14 Read coverage per gene visualization and comparisons 137 4.15 Data and Code Availability 137 REFERENCE 139 | |
dc.language.iso | zh-TW | |
dc.title | 響應環境變化而發生的截然不同的剪接調控 | zh_TW |
dc.title | Distinct splicing regulation in response to environmental changes | en |
dc.type | Thesis | |
dc.date.schoolyear | 108-1 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 黃明經 | |
dc.contributor.oralexamcommittee | 李文雄,呂俊毅,林倩伶 | |
dc.subject.keyword | 內含子積累,低效率剪接,剪接調控,調控網絡, | zh_TW |
dc.subject.keyword | Intron accumulation,Inefficient splicing,Splicing regulation,Regulatory networks, | en |
dc.relation.page | 145 | |
dc.identifier.doi | 10.6342/NTU202000399 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2020-02-10 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 基因體與系統生物學學位學程 | zh_TW |
顯示於系所單位: | 基因體與系統生物學學位學程 |
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