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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 常玉強(Yuh-Chyang Charng) | |
dc.contributor.advisor | 常玉強(Yuh-Chyang Charng | bocharng@ntu.edu.tw | ), | |
dc.contributor.author | Yun-Chen Chang | en |
dc.contributor.author | 張云甄 | zh_TW |
dc.date.accessioned | 2023-03-19T21:06:46Z | - |
dc.date.copyright | 2022-10-14 | |
dc.date.issued | 2022 | |
dc.date.submitted | 2022-09-19 | |
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SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. BMC Genet 8: 78. Mola, G., Vela, E., Fern?ndez-Figueras, M.T., Isamat, M. and Mu?oz-M?rmol, A.M. 2007. Exonization of Alu-generated Splice Variants in the Survivin Gene of Human and Non-human Primates. J Mol Biol 366: 1055-1063. Ram, O., Schwartz, S. and Ast, G. 2008. Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons. Mol Cell Biol 28: 3513-3525. Schmitz, J.R. and Brosius, J.R. 2011. Exonization of transposed elements: A challenge and opportunity for evolution. Biochimie 93: 1928-1934. Schuler, M.A., Reddy, A.S.N. and Golovkin, M. 2008. Splice Site Requirements and Switches in Plants Nuclear pre-mRNA Processing in Plants. Springer Berlin Heidelberg, pp. 39-59. Sela, N., Kim, E. and Ast, G. 2010. The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol 11: R59. 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Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103: 7175-7180. Wessler, S.R. 1991. The maize transposable Ds1 element is alternatively spliced from exon sequences. Mol Cell Biol 11: 6192-6196. Wu, M., Li, L. and Sun, Z. 2007. Transposable element fragments in protein-coding regions and their contributions to human functional proteins. Gene 401: 165-171. Yi, P., Zhang, W., Zhai, Z., Miao, L., Wang, Y. and Wu, M. 2003. Bcl-rambo beta, a special splicing variant with an insertion of an Alu-like cassette, promotes etoposide- and Taxol-induced cell death. FEBS Lett 534: 61-68. Zabala, G., Vodkin, L. 2007. Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biol. 7(1):38. 賴薇云。2017。玉米Ds轉位子家族參與非生物逆境下的選擇性剪接。臺灣大學農藝學研究所學位論文。1-74。 許龍欣。2015。轉位子Ds1顯子化序列提供之功能性訊息對提高蛋白體豐富度之探討。臺灣大學農藝學研究所學位論文。1-83。 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/83404 | - |
dc.description.abstract | 轉位子顯子化(exonization)指當轉位子插入基因隱子時,插入的轉位子序列能夠在轉錄時為插入基因提供取代其原顯子剪接位之新剪接位點,使後續轉錄產物除保有原顯子序列外,亦帶有部分轉位子及部分隱子之遺傳訊息。過去的研究顯示轉位子雖能提供新剪接位並發生顯子化,然而由於其序列本身所能夠提供的遺傳訊息很少,故此過程對基因多樣性之貢獻主要在於被導入的基因隱子序列。本次試驗模擬了轉位子Ds與Ds1在玉米基因體中的顯子化過程,分析轉位子於單一插入位點提供不同剪接組合對玉米基因組豐富度的影響。在所有Ds及Ds1顯子化轉錄產物分析中,有超過90%的產物其後續將衍生出功能受損之縮短蛋白。被預期能夠產生完整功能蛋白異構物的第4、5類非NMD顯子化產物在所有Ds1顯子化轉錄產物中的比例約為3.3%,而在Ds的結果中則顯示為1.8%。在顯子化蛋白質異構物方面,與參考蛋白相似度高於50%的C端異構物比例約為70%,此類蛋白產物有高機率能夠在盡可能不破壞原有蛋白功能的前提下,為植物體提供更多的篩選優勢。而內部異構物則大多為新增蛋白片段長度小於30的產物,這些新增的小片段蛋白可能會精細修飾參考基因,然而實際的蛋白功能仍需未來進一步分析。 | zh_TW |
dc.description.abstract | Exonization means that when a transposed element (TE) is inserted into intronic sequences, the TE sequence can provide new splice sites for the inserted gene to replace its original exon splice site during transcription, so that subsequent transcripts will contain both the original exon sequence and genetic informations from TEs and introns. Previous studies showed that although TEs can provide new splice sites and undergo exonization, since TE sequences can provide little genetic information, the contribution of exonization to gene diversity is mainly due to the exonized gene introns. We simulated the exonization of Ds and Ds1 in maize genome, and analyzed the effect of different splice sites provided by TEs at a single insertion site on the maize genome richness. Of all Ds and Ds1 exonization transcripts, more than 90% of the transcripts would subsequently produce functionally impaired shortened proteins. Type 4 and 5 non-NMD exonization transcripts, which is expected to produce fully functional protein isoforms, accounted for approximately 3.3% of all Ds1 exonization transcripts, compared with 1.8% in the Ds results. In terms of protein isomers, the proportion of C-terminal isomers that are more than 50% similar to the reference protein is about 70%. These protein products may be able to provide more screening advantages for plants without destroying the original protein function. Most of the interior isoforms are the products which number of additional amino acids less than 30. These newly additional small protein fragments may finely modify the reference gene, but the actual protein function still needs further analysis in the future. | en |
dc.description.provenance | Made available in DSpace on 2023-03-19T21:06:46Z (GMT). No. of bitstreams: 1 U0001-0809202218052100.pdf: 7224211 bytes, checksum: 1db8407589319c3eda60bfc7d618ec87 (MD5) Previous issue date: 2022 | en |
dc.description.tableofcontents | 口試委員審定書………………………………………………………………………i 誌謝……………………………………………………………………………………ii 摘要……………………………………………………………………………………..iii Abstract…………………………………………………………………………………iv 圖目錄…………………………………………………………………………………..vi 表目錄..………………………………………………………………………………vii 第一章、前言…………………………………………………………………………….1 第二章、材料與方法…………………………………………………………………….3 2.1 基因體序列來源…………………………………………………………………3 2.2 構築顯子化轉錄產物……………………………………………………………3 2.3 顯子化轉錄產物分析及異構物預測……………………………………………4 第三章、結果…………………………………………………………………………….5 3.1 超過半數之Ds/Ds1顯子化轉錄產物受NMD機制降解或產生不含有轉位子遺傳訊息之蛋白異構物……………………………………………………………...5 3.2 轉位子Ds/Ds1及插入位點下游隱子表現顯子化轉錄產物終止碼…………5 3.3 第4類顯子化事件使下游顯子中隱藏的終止碼表現在讀序中……………….6 3.4 不表現終止碼之產物可能提高蛋白質異構物豐富度但發生頻率低…………7 3.5 顯子化蛋白質異構物之特徵……………………………………………………7 第四章、討論…………………………………………………………………………….9 第五章、結論…………………………………………………………………………...11 參考文獻……………………………………………………………………………….12 附錄1、從NCBI下載之玉米染色體數據提取顯子及隱子序列…………………..27 附錄2、產生Ds1顯子化產物並根據終止碼位置將產物分為5類………………..30 附錄3、產生Ds顯子化產物並根據終止碼位置將產物分為5類…………………37 附錄4、圖表(圖4 -圖7)繪製程式碼……………………………………………….42 | |
dc.language.iso | zh-TW | |
dc.title | 轉位子Ds及Ds1經由顯子化提高玉米轉錄體及蛋白質組豐富度 | zh_TW |
dc.title | The Extent of Ds and Ds1 Exonization to Enrich Transcriptomes and Proteome in Maize | en |
dc.type | Thesis | |
dc.date.schoolyear | 110-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 劉力瑜(Li-Yu Daisy Liu),杜鎮(Jenn Tu) | |
dc.subject.keyword | Ds轉位子,Ds1轉位子,顯子化,無意義密碼子媒介式mRNA分解,選擇性剪接, | zh_TW |
dc.subject.keyword | Ds transposon,Ds1 transposon,exonization,Nonsense-mediated mRNA decay,alernative spilcing, | en |
dc.relation.page | 50 | |
dc.identifier.doi | 10.6342/NTU202203253 | |
dc.rights.note | 未授權 | |
dc.date.accepted | 2022-09-20 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 農藝學研究所 | zh_TW |
顯示於系所單位: | 農藝學系 |
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