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研究生:王柏龍
研究生(外文):Po-Long Wang
論文名稱:利用基於RNA二級結構之生物性準則預測microRNA
論文名稱(外文):Biological criteria based on RNA secondary structure for the prediction of the microRNA
指導教授:曾怜玉曾怜玉引用關係
學位類別:碩士
校院名稱:國立中興大學
系所名稱:資訊網路多媒體研究所
學門:電算機學門
學類:網路學類
論文種類:學術論文
論文出版年:2010
畢業學年度:98
語文別:中文
論文頁數:93
中文關鍵詞:pri-miRNApre-miRNAmiRNA預測系統
外文關鍵詞:pri-miRNApre-miRNAmiRNAprediction system
相關次數:
  • 被引用被引用:0
  • 點閱點閱:115
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微核糖核酸(micro RNA,miRNA)屬於未編碼核糖核酸(non-coding RNA),在生物體中扮演重要角色。miRNA主要參與調控基因表現像是細胞發展時機、細胞增殖、分化、凋零甚至胚胎發育、組織器官形成以及癌症發生與調控,透過研究miRNA機制將其運用在病理方面,可以有效達到預防疾病發生或是治療的成果。除了透過生物實驗尋找miRNA外,計算導向方式預測將不受miRNA組織特異性和階段特異性所影響,並減少大量生物實驗成本。本論文提供一個預測系統,利用miRNA結構特徵與互動蛋白特徵,找尋序列中是否有pri-miRNA、pre-miRNA及miRNA存在並標記其在序列中的位置。

致謝辭 ii
摘要. iii
Abstract iv
目次. v
表目錄 vii
圖目錄 ix
1. 緒論 1
1.1 研究背景 1
1.1.1 siRNA簡介 2
1.1.2 siRNA生源論 3
1.1.3 miRNA簡介 4
1.1.4 miRNA生源論及生物作用 5
1.2 研究動機 7
1.3 研究目的 8
1.3.1 探討轉錄(transcription)過程 9
1.3.2 探討Drosha和Pasha/DGCR8 10
1.3.3 Exportin 5功能 11
1.3.4 Dicer作用機制 12
2. 文獻探討 14
2.1 實驗導向預測 14
2.1.1 複製方式尋找miRNA基因 14
2.1.2 檢測miRNA表現方法 15
2.2 計算導向預測 16
2.2.1 計算方式預測miRNA基因 16
2.2.2 程式計算模擬RNA二級結構 19
2.3 小結 20
3. 研究與預測方法 21
3.1 生物特徵整理 21
3.1.1 互動蛋白方面 21
3.1.2 成熟miRNA方面 22
3.2 統計數據 23
3.2.1 結構能量統計 23
3.2.2 pri-miRNA莖環結構統計 24
3.2.3 pre-miRNA莖環結構統計 24
3.2.4 Drosha剪切點相鄰兩端距離15 nt內凸起大小 25
3.2.5 Drosha剪切點相鄰兩端距離10 nt內凸起大小 28
3.2.6 Drosha剪切點相鄰兩端距離5 nt內凸起大小 29
3.2.7 Dicer剪切點鄰近距離15 nt內凸起大小 31
3.2.8 Dicer剪切點鄰近距離10 nt內凸起大小 32
3.2.9 Dicer剪切點鄰近距離5 nt內凸起大小 33
3.2.10 莖環與5’端和3’端的Drosha剪切點距離 34
3.2.11 莖環與5’端和3’端的Dicer剪切點距離 36
3.2.12 Drosha剪切點與loop間的鍵結量 39
3.2.13 Dicer剪切點與loop間的鍵結量 41
3.2.14 成熟miRNA長度統計 45
3.2.15 成熟miRNA鍵結率統計 45
3.2.16 統計數據整理 47
3.3 預測方法 48
3.4 加強預測方法 49
3.4.1 二級結構限制條件 49
3.4.2 結構挑選機制 52
3.5 限制結構數據統計 53
3.5.1 剪切位點統計 53
3.5.2 Drosha位點鍵結率統計 54
3.5.3 Dicer 位點鍵結率統計 57
3.5.4 限制結構挑選後能量統計 62
3.6 調整限制條件式 64
3.7 偵測限制條件式結果統計 67
4. 實驗結果 72
4.1 原方法與其他預測比較 72
4.2 叢集miRNA預測 73
4.3 不同物種比較 78
4.4 開發預測系統畫面 82
5. 結果討論與未來方向 86
參考文獻 88


Allawi HT, Dahlberg JE, Olson S, Lund E, Olson M, Ma WP, Takova T, Neri BP, Lyamichev VI. 2004. Quantitation of microRNAs using a modified Invader assay. RNA 10: 1153-1161.
Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D. 2003. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13: 807-818.
Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
Bentwich I, et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766-770.
Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366.
Buckingham S. 2003. The major world of microRNAs. Horizon Symposia. Understanding the RNAissance. Nature Publishing Group.
Chang S, Johnston RJ, Jr., Frokjaer-Jensen C, Lockery S, Hobert O. 2004. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430: 785-789.
Chen CZ, Li L, Lodish HF, Bartel DP. 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
Chen X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. 2004. Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231-235.
Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G. 2003. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9: 180-186.
Esau C, et al. 2004. MicroRNA-143 regulates adipocyte differentiation. J Biol Chem 279: 52361-52365.
Esquela-Kerscher A, Slack FJ. 2006. Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6: 259-269.
Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R. 2004. The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA websuite. Nucleic Acids Res 36: W70-74.
Helvik SA, Snove O, Jr., Saetrom P. 2007. Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics 23: 142-149.
Hofacker IL, Stadler PF. 2006. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22: 1172-1176.
Hornstein E, Mansfield JH, Yekta S, Hu JK, Harfe BD, McManus MT, Baskerville S, Bartel DP, Tabin CJ. 2005. The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 438: 671-674.
Johnson SM, Lin SY, Slack FJ. 2003. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev Biol 259: 364-379.
Johnston RJ, Hobert O. 2003. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426: 845-849.
Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC. 2004. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428: 84-88.
Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G. 2004. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A 101: 360-365.
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
Lai EC, Tomancak P, Williams RW, Rubin GM. 2003. Computational identification of Drosophila microRNA genes. Genome Biology 4: R42.
Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
Lee Y, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Pages 415-419. Nature.
Leung AK, Sharp PA. 2007. microRNAs: a safeguard against turmoil? Cell 130: 581-585.
Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. 2003a. Vertebrate microRNA genes. Science 299: 1540.
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. 2003b. The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
Mansfield JH, et al. 2004. MicroRNA-responsive ''sensor'' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet 36: 1079-1083.
Meltzer PS. 2005. Cancer genomics: small RNAs with big impacts. Nature 435: 745-746.
Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB. 2004. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10: 1309-1322.
Pasquinelli AE, et al. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
Poy MN, et al. 2004. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432: 226-230.
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
Ritchie W, Theodule FX, Gautheret D. 2008. Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24: 1394-1396.
Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. 2004. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biology 5: -.
Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. 2005. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6: 267.
Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G. 2000. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell 5: 659-669.
Tomari Y, Zamore PD. 2005. MicroRNA biogenesis: drosha can''t cut it without a partner. Curr Biol 15: R61-64.
Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A. 2008. CID-miRNA: a web server for prediction of novel miRNA precursors in human genome. Biochem Biophys Res Commun 372: 831-834.
Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH. 2004. Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res 32: 1688-1695.
Wightman B, Ha I, Ruvkun G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
Yue J, Sheng Y, Orwig KE. 2008. Identification of novel homologous microRNA genes in the rhesus macaque genome. BMC Genomics 9: 8.
Zeng Y, Cullen BR. 2004. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 32: 4776-4785.
Zeng Y, Yi R, Cullen BR. 2005. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 24: 138-148.
Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W. 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21: 5875-5885.
Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y. 2007. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354: 585-590.
Zhao Y, Samal E, Srivastava D. 2005. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220.



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