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研究生:許龍欣
研究生(外文):Lung-Hsin Hsu
論文名稱: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
論文名稱(外文):Important message offered by Ds1 transposon for yielding unique profiles of protein isoforms to enrich proteome complexity via exonization
指導教授:常玉強
口試委員:劉力瑜杜鎮
口試日期:2015-07-22
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:農藝學研究所
學門:農業科學學門
學類:一般農業學類
論文種類:學術論文
論文出版年:2015
畢業學年度:103
語文別:中文
論文頁數:83
中文關鍵詞:Ds1轉位子選擇性剪接顯子化無義介導之mRNA降解途徑蛋白質活性位點
外文關鍵詞:Ds1 transposonalternative splicingexonizationnonsense-mediated decay pathwayprotein function profile
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轉位子插入基因隱子中,可造成該基因轉錄產物產生選擇性剪接 (alternative splicing) 或顯子化 (exonization) 現象。針對單一插入事件,Ds轉位子可提供4組剪接供位 (splice donor),至多產生4種異構物;而Ds1轉位子可提供3組剪接供位以及2組剪接受位 (splice acceptor),至多產生11種異構物。先前模擬Ds及Ds1插入植物基因隱子之研究顯示,顯子化事件利用Ds/Ds1提供之剪接位點,將插入位點上下游隱子序列導入轉錄產物中,可提高轉錄體豐富度及其蛋白質異構物多樣性。為進一步探討蛋白質異構物序列多樣性對其預測功能的影響,本試驗將先前模擬Ds1插入水稻全基因組隱子之顯子化異構物序列比對PROSITE資料庫之蛋白質活性位點。將顯子化蛋白異構物與參考蛋白相比,每個Ds1插入之隱子平均可產生228個新增活性位點,相較於Ds之152個新增活性位點高出許多;比較同源異構物間,顯子化序列對新增活性位點的貢獻度,如插入同一位點採用D1或D3兩組相同讀序之donor間之比較,共有135種活性位點差異,而之D1A2、D2A1或D3A2三組相同讀序donor/acceptor組合之比較,其顯子化序列雖僅差異2至7個胺基酸,仍具有42種之活性位點多樣性。根據以上結果,分析49個插入玉米基因區之Ds-like轉位子,顯示多數Ds-like轉位子插入隱子區並構成隱子一部分;亦有Ds-like轉位子插入顯子區後成為新的隱子;在cDNA中包含Ds-like訊息者多位於UTR,僅2例顯示Ds-like插入隱子區後造成顯子化現象,而Ds1轉位子插入玉米GRMZM2G085600基因第5隱子之衍生之蛋白質異構產物,分析其序列包含2個新增活性位點。本研究首先以程式模擬Ds1轉位子於水稻中創造顯子化產物之潛力,並分析異構物之序列及功能多樣性,與僅提供donor之Ds相比, Ds1顯子化產物具較高的活性位點豐富度;最後於玉米基因中找到Ds顯子化且產生新增活性位點之實例,呈現轉位子顯子化對蛋白體功能性豐富度之貢獻。


An intronic transposable elements (TE) which provides splice site may lead to alternative splicing or exonization. For a sigle insertion event, Ds1 transposon could offer 3 splice donors and 2 splice acceptors (yield 11 transcripts and protein isoforms) while Ds element could offer the maximum of 4 splice donors (yield 4 transcripts and protein isoforms). Previous studies show that both of Ds and Ds1 exonization could increase transcripts’ and proteins’ sequence diversity by incorporating the intron sequences with different reading frame.
This study aims to analyze how the exonized sequence diversity contributes to protein functional complexity. First, the functional profiles of all simulated exonized isoforms and the references were scanned according to PROSITE database. Compared with the reference proteins, a Ds1-inserted intron may yield 228 new profiles on average, while a Ds-inserted intron may yield only 152 new profiles on average. To prevent overestimating the diversity of added profiles, we analyzed the new functional profiles among the orthologous exonized protein isoforms which spliced using the third donor site (D3) versus the first one (D1) with the same reading frame. The analysis of protein orthologs yielded by using donor/acceptor sites of D1A2, D2A1 and D3A2 is conducted likewise. Though differ in the presence or absence merely 2 to 7 additional amino aciDs, the new profiles of protein orthologs remain diversified. In brief, the simulation results imply that Ds1 transposon offers message important for yielding unique profiles of protein isoforms in rice genome. To access the simulated results, 49 maize genes which contain Ds-like sequence are investigated to test previous result in rice. The annotation and transcripts of these genes indicate that 44 Ds-like element insert to intron and most of them make a part of intron. Besides, 3 Ds-like elements insert to exon regions and 2 Ds-like elements insert to untranslated regions. One Ds-like elements which insert to the 5th intron of GRMZM2G085600 resulted in exonized transcripts and yielding 2 new functional profiles.
We analyze the exonized messages offered from Ds1 for yielding unique profiles according the simulation in rice, compare with the results of Ds and find an actual example in maize. Based on our research, exonization could be considered one of the reasons in the evolution of plant proteome complexity.


誌謝 ii
摘要 iii
Abstract iv
圖列 viii
表列 ix
縮寫及名詞中英對照 x
第一章、前言 1
第二章、前人研究 3
2.1 轉位子簡介 3
2.2 轉位子的演化意義 4
2.3選擇性剪接與顯子化 4
2.4哺乳動物之MIR及Alu轉位子顯子化象 5
2.5 植物體Ds與Ds1剪接位特性 6
2.5 蛋白質活性位點資料庫-PROSITE 7
2.6 Ds顯子化可提高植物轉錄體及蛋白體多樣性 7
2.7 玉米B73基因組之Ac/Ds轉位子家族 8
第三章、材料與方法 9
3.1 轉位子剪接位及基因體序列來源 9
3.2 顯子化轉錄產物構築 9
3.3 判斷顯子化轉錄產物終止碼位置、預測其蛋白質異構物 10
3.4 分析顯子化轉錄產物及其預測蛋白質之新增活性位點 10
3.5 尋找玉米基因組Ds-like轉位子之顯子化事件 11
第四章、結果 12
4.1 新增活性位點來自Ds1本身或該插入隱子及上下游顯子共同貢獻 12
4.2 構成活性位點之顯子化訊息分析 13
4.3 Ds1與Ds對活性位點貢獻度比較 15
4.4 玉米B73基因組之Ds-like顯子化事件 16
第五章、討論 18
5.1 Ds1提供之剪接位組合對異構物活性位點影響 18
5.2 Ds1顯子化訊息區間對異構物活性位點多樣性之貢獻 19
5.3 Ds與Ds1貢獻活性位點比較 19
5.4比較玉米Ds-like顯子化比例與模擬水稻顯子化比例之落差原因 20
第六章、結論 22
參考文獻 23
附錄1. Ds1於水稻基因顯子化之序列 61
附錄2.程式碼00getProtein.r 61
附錄3.程式碼riceDs1_1.cmd 64
附錄4.程式碼01ClassifyProfile.r 64
附錄5.程式碼00Summary 68
附錄6.玉米基因體註解資訊 83


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