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研究生: 康星源
Sin-Guan Kong
論文名稱: 基因體中的倒位對稱及全基因體的倒位複製
Inverse symmetry in genomes and whole-genome inverse duplication
指導教授: 李弘謙
Hoong-Chien Lee
口試委員:
學位類別: 博士
Doctor
系所名稱: 理學院 - 物理學系
Department of Physics
畢業學年度: 96
語文別: 中文
論文頁數: 71
中文關鍵詞: 基因體複製倒位對稱
外文關鍵詞: duplication, inverse symmetry
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  • 片段複製長久以來被當作基因體成長及演化的重要機制[40,57],最近確實了全基因體複製的確發生在酵母菌[50]及一些硬骨魚種類當中[53-54]。在這裡,我們提供了證據證明全基因體的倒位複製非常可能發生在至少一半的真細菌當中,更甚至絕大部份的染色體裡。我們研究了現有資料庫提供的染色體的倒位對稱並從中得到了證據。發現了絕大部份的染色體都擁有全域的倒位對稱,但在局部上的倒位對稱卻有幾種不同的樣式。這些樣式為倒位對稱的片段複製發生在基因體中的統一論述提供了線索。


    Segmental duplication has long been known to be an important mechanism for genome growth and evolution [40,57], and recently it has been firmly established that whole-genome duplications have at least occurred in yeast [50] and in some species of fishes ray-finned fishes [53-54]. Here we present evidence showing that whole-genome inverse duplication very likely occurred in one half of eubacterial genomes, and possibly in most chromosomes, prokaryotic as well as eukaryotic. We derive our evidence through a comprehensive study of the inverse symmetry in all publicly available complete genomes. We find that a vast majority of chromosomes have close to maximum global inverse symmetry, but the chromosomes exhibit starkly distinct patterns of local inverse symmetry. These patterns provide clues for a consistent narrative of the many ways inverse segmental duplications may have occurred in genomes.

    英文摘要---------------------------------------------------------------------------------------------------i 中文摘要--------------------------------------------------------------------------------------------------ii 誌謝--------------------------------------------------------------------------------------------------------iii 目錄--------------------------------------------------------------------------------------------------------iv 圖目錄-----------------------------------------------------------------------------------------------------vi 表目錄----------------------------------------------------------------------------------------------------vii 第一章 簡介-------------------------------------------------------------------------------------------1 1.1 從Chargaff的宇稱規則談起-------------------------------------------------------1 1.2 鹼基對偶對稱指數(Base-complement symmetry index)介紹-------------2 1.3 全域及局部對稱指數(Symmetric indices)簡介-------------------------------2 1.4 鹼基扭曲方法簡介-------------------------------------------------------------------4 1.5 單鹼基扭曲的延伸-多鹼基扭曲簡介-----------------------------------------6 第二章 實驗方法及材料---------------------------------------------------------------------------8 2.1 字串出現頻率及配分---------------------------------------------------------------8 2.2 鹼基對偶對稱指數的定義-------------------------------------------------------10 2.3 對稱指數的定義--------------------------------------------------------------------11 2.4 局部的倒位對稱分析-------------------------------------------------------------12   2.4.1 不同尺度下的平均倒位對稱指數------------------------------------12   2.4.2倒位對稱矩陣---------------------------------------------------------------13   2.4.3 的滑動掃瞄--------------------------------------------------------------14   2.4.4 以ori及ter為中心的 掃瞄------------------------------------------14 2.5 單鹼基及多鹼基的扭曲----------------------------------------------------------14 2.6 實驗材料------------------------------------------------------------------------------15 2.7 程式碼---------------------------------------------------------------------------------16 第三章 結果------------------------------------------------------------------------------------------17 3.1 鹼基對偶對稱指數----------------------------------------------------------------17 3.2 對稱指數------------------------------------------------------------------------------19 3.3 局部的對稱指數--------------------------------------------------------------------24   3.3.1 在不同尺度下的局部對稱指數---------------------------------------24   3.3.2 倒位對稱矩陣圖-----------------------------------------------------------31   3.3.3 倒位對稱指數掃瞄-------------------------------------------------------34   3.3.4 以ori及ter為中心的掃瞄---------------------------------------------36 3.4 累積的單鹼基及多鹼基扭曲---------------------------------------------------39 3.4.1 CIR是累積的單及多鹼基扭曲的轉折點---------------------------39   3.4.2對偶及反向扭曲的大小是普適的並與分類無關-----------------41 3.4.3倒位對稱扭曲與局部倒位對稱呈負相干關係 -------------------41 第四章 討論------------------------------------------------------------------------------------------42 4.1 鹼基對偶對稱指數----------------------------------------------------------------42 4.2 對稱指數------------------------------------------------------------------------------44   4.2.1 對稱指數方法上的比較-------------------------------------------------44   4.2.2 倒位對稱在基因體中的證實------------------------------------------45   4.2.3 倒位對稱矩陣的啟發----------------------------------------------------47      4.2.3.1 倒位對稱因倒位對稱複製造成----------------------------47      4.2.3.2 A類型暗示著如染色體般全長的複製---------------------47      4.2.3.3 D類型暗示著發生過許多prox-ISD事件------------------49      4.2.3.4對於所有類型的統一詮釋------------------------------------49 4.3 鹼基扭曲與倒位對稱的關聯---------------------------------------------------50 4.4倒位對稱複製及染色體複製-----------------------------------------------------53 第五章 結論、推測結論及未來展望---------------------------------------------------------54 5.1 鹼基對偶對稱指數----------------------------------------------------------------54 5.2全基因體的對稱指數--------------------------------------------------------------55 5.3局部的倒位對稱指數--------------------------------------------------------------55 5.4單或多鹼基扭曲-------------------------------------------------------------------57 5.5未來展望------------------------------------------------------------------------------58 參考文獻------------------------------------------------------------------------------------------------59

    [1] Donald R. Forsdyke, James R. Mortimer. Chargaff’s legacy. Gene 261, 127-137
    (2000).
    [2] E. Chargaff, Chemical specificity of nucleic acids and mechanism of their enzymic
    degradation. Experientia 6, 201-209 (1950).
    [3] E. Chargaff, Structure and function of nucleic acids as cell constituents. Fed. Proc.
    10, 654-659 (1951).
    [4] J. D. Watson, F. H. C. Crick, Genetical implications of the structure of
    deoxyribonucleic acid. Nature 171, 964-967 (1953).
    [5] R. Rudner, J. D. Karkas, E. Chargaff, Separation of B. subtilis DNA into
    complementary strands. III. Proc. Natl. Acad. Sci. USA 60, 921-922 (1968).
    [6] S. J. Bell, D. R. Forsdyke, Accounting units in DNA. J. Theor. Biol. 197, 51-61 (1999).
    [7] N. T. Perna, T. D. Kocher, Patterns of nucleotide composition at fourfold
    degenerate sites of animal mitochondrial genomes, J. Mol. Evol. 41 (3), 353-358
    (1995).
    [8] J. R. Lobry, Asymmetric substitution patterns in the two DNA strands of bacteria,
    Mol. Biol. Evol. 13 (5), 660-665 (1995).
    [9] A. Grigoriev, Analyzing genomes with cumulative skew diagrams, Nucl. Acids Res.
    26 (10), 2286-2290 (1998).
    [10] J. Sanchez, M. V. Jose, Analysis of bilateral inverse symmetry in whole bacterial
    chromosomes, Biochem. Biophy. Res. Comm. 299, 126-134 (2002).
    [11] P. Worning, L. J. Jensen, P. F. Hallin, H. Staerfeld, D. W. Ussery, Origin of
    replication in circular prokaryotic chromosomes, Env. Micro. 8 (2), 353-361
    (2006).
    [12] Jiuzhou Song, A. Ware, SL Liu, Wavelet to predict bacterial ori ad ter: a tendency
    towards a physical balance, BMC Genomics 4:17 (2003).
    [13] N. P. Robinson, I. Dionne, M. Lundgren, V. L. Marsh, R. Bernander, S. D. Bell,
    Identification of two origins of replication in the single chromosome of the
    archaeon Sulfolobus solfataricus, Cell 116, 25-38 (2004).
    [14] L. M. Kelman, Zvi Kelman, Multiple origins of replication in archaea, TRENDS
    Microbiol. 12 (9), 400-401 (2004).
    [15] Ren Zhang, C. T. Zhang, Multiple replication origins of the archaeon
    Halobacterium species NRC-1, Biochem. Biophy. Res. Comm. 302, 728-734
    (2003).
    [16] M. J. McLean, K. H. Wolfe, K. M. Devine, Base composition skews, replication
    orientation, and gene orientation in 12 prokaryote genomes, J. Mol. Evol. 47,
    691-696 (1998).
    [17] M. Lundgren, A. Andersson, L. Chen, P. Nilsson, R. Bernander, Three replication
    origins in Sulfolobus species: synchronous initiation of chromosome replication
    and asynchronous termination, Proc. Natl. Acad. Sci. USA 101 (18), 7046-7051
    (2004).
    [18] D. P. Clark, L. D. Russell, Molecular biology, Cache River Press (2000).
    [19] J. M. Freeman, T. N. Plasterer, T. F. Smith, and S. C. Mohr, Patterns of genome
    organization in bacteria, Science 279, 1827a- (1998).
    [20] J. R. Lobry, Origin of replication of Mycoplasma genitalium, Science 272, 745-746
    (1996).
    [21] A. Grigoriev, Strand-specific compositional asymmetries in double-stranded DNA
    virus, Virus Res. 60, 1-19 (1999).
    [22] S. Fujimori, T. Washio, M. Tomita, GC-compositional strand bias around
    transcription start sites in plants and fungi, BMC Genomics 6, 26-37 (2005).
    [23] D. K. Niu, Kui Lin, Da-Yong Zhang, Strand compositional asymmetries of nuclear
    DNA in eukaryotes, J. Mol. Evol. 57, 325-334 (2003).
    [24] R. Zhang, Chun-Ting Zhang, Identification of replication origins in archaeal
    genomes based on the Z-curve method, Archaea 1, 335-346 (2005).
    [25] S. P. Li, K. L. Ng, M. C. Chung, Quantitative linguistic study of DNA sequences,
    Physica A 321, 189-192 (2003).
    [26] R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons,
    H. E. Stanley, Linguistic features of noncoding DNA sequence, Phys. Rev. Lett. 73,
    3169-3172 (1994).
    [27] J. J. Shen, Shuyu Zhang, H. C. Lee, Bailin Hao, SeeDNA: A visualization for K-string
    content of long DNA sequences and their randomized counterparts, Geno. Prot.
    Bioinfo. 2(3), 192-196 (2004).
    [28] Bailin Hao, H. C. Lee, Shuyu Zhang, Fractals related to long DNA sequences and
    complete genomes, Chaos, Solitons and Fractals 11, 825-836 (2000).
    [29] C. H. Chang, L. C. Hsieh, T. Y. Chen, H. D. Chen, L. F. Luo, H. C. Lee, Shannon
    information in complete genome, Computational Systems Bioinformatics
    Conference, 2004. CSB 2004. Proceedings. 2004 IEEE.
    [30] H. D. Chen, C. H. Chang, L. H. Hsieh, H. C. Lee, Divergence and Shannon
    information in genomes, Phys. Rev. Lett. 94, 178103 (2005).
    [31] Rice Annotation Project Database; http://rapdb.lab.nig.ac.jp/
    [32] National Center for Biotechnology Information genome database;
    http://www.ncbi.nlm.nih.gov/
    [33] Motoo Kimura, Evolutionary rate at the molecular level, Nature 217, 624-626
    (1968).
    [34] GenomeMine Database,
    http://www.genomics.ceh.ac.uk/cgi-bin/genomemine/gminemenu.cgi
    [35] P. F. Baisnee, Steve Hampson, Pierre Baldi, Why are complementary DNA strands
    symmetric? Bioinformatics 18 (8), 1021-1033 (2002).
    [36] D. Qi and A. J. Cuticchia, Compositional symmetries in complete chromosomes.
    Bioinformatics 17, 557-559 (2001).
    [37] D. R. Forsdyke, Symmetry observations in long nucleotide sequences: a
    commentary on the Discovery Note of Qi and Cuticchia. Bioinformatics 18,
    215-217 (2002).
    [38] V. V. Prabhu, Symmetry observations in long nucleotide sequences, Nucl. Acids
    Res. 21 (12) 2797-2800 (1993).
    [39] Aaron C.E. Darling, Bob Mau, F. R. Blattner and Nicole T. Perna, Mauve: Multiple
    Alignment of Conserved Genomic Sequence With Rearrangements. Genome
    Res. 14, 1394-1403 (2004).
    [40] M. Lynch, Gene duplication and evolution, Science 297, 945-947 (2002).
    [41] M. V. Jose, T. Govezensky, and J. R. Bobadilla, Statistical properties of DNA
    sequences revisited: the role of inverse bilateral symmetry in bacterial
    chromosomes, Physica A: Statistical Mechanics and its Applications 351,
    477-498 (2005).
    [42] F. R. Blattner, G. Plunkett, C. A. Bloch et al., The complete genome sequence of
    Escherichia coli K-12, Science 277, 1453-1474 (1997).
    [43] J. Mrazek and S. Karlin, Strand compositional asymmetry in bacterial and large
    viral genome, Proc. Natl. Acad. Sci. USA 95, 3720-3725 (1998).
    [44] M. Picardeau, J. R. Lobry, and B. J. Hinnebusch, Analyzing DNA strand
    compositional asymmetry to identify candidate replication origins of Borrelia
    burgdoferi linear and circular plasmids, Genome Res. 10, 159401604 (2000).
    [45] R. Nussinov, Some indications for inverse DNA duplication, J. Theor. Biol. 95,
    783-791 (1982).
    [46] C. K. Biebricher and R. Luce, In vitro recombination and terminal elongation of
    RNA by Q beta replicase. Embo. J. 11, 5129-5135 (1992).
    [47] A. Volz, H. Wende, K. Laun, and A. Ziegler, Genesis of the ILT/LIR/MIR clusters
    within the human leukocyte receptor complex. Immunol. Rev. 181, 39-51 (2001).
    [48] P. W. Messer, P. F. Amdt, and M. Lassig, Solvable sequence evolution models and
    genomic correlations. Phys. Rev. Lett. 94, 138103 (2005).
    [49] S. Ohno, Evolution by gene duplication. George Allen and Unwin, London (1970).
    [50] K. H. Wolfe and D. C. Shields, Molecular structure of nucleic acids; a structure for
    deoxyribose nucleic acid. Nature 387, 708-713 (1997).
    [51] M. Kellis, B. W. Birren, and E. S. Lander, Proof and evolutionary analysis of
    ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature 428,
    617-624 (2004).
    [52] I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, Natural history and
    evolutionary principles of gene duplication in fungi. Nature 449, 54-61 (2007).
    [53] A. Christoffels, E. G. Koh, J. M. Chia, S. Brenner, S. Aparicio, and B. Venkatesh,
    Fugu genome analysis provides evidence for a whole-genome duplication early
    during the evolution of ray-finned fishes. Mol. Biol. Evol. 21, 1146-1151 (2004).
    [54] O. Jaillon, J. M. Aury, F. Brunet et al., Genome duplication in the teleost fish
    Tetradon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431,
    946-957 (2004).
    [55] Inverse Symmetry Database,
    http://pooh.phy.ncu.edu.tw/~kensinro/InvSym/Index.htm
    [56] S. L. Salzberg, A. J. Salzberg, A. R. Kerlavage, and J. F. Tomb, Skewed oligomers
    and origins of replication, Gene 217, 57-67 (1998).
    [57] J. A. Bailey, Z. Gu, R. A. Clark et al., Recent segmental duplications in the human
    genome. Science 297, 1003-1007 (2002).
    [58] Hsieh L. C., L. Luo, F. Ji, and H. C. Lee, Minimal model for genome evolution and
    growth. Phys. Rev. Lett. 90, 018101 (2003).
    [59] Zhang L., H. H. Lu, W. Y. Chung, J. Yang and W. H. Li, Patterns of segmental
    duplication in the human genome. Mol. Biol. Evol. 22, 135-141 (2005).
    [60] D. M. Gilbert, Making sense of eukaryotic DNA replication origins. Science 294,
    96-100 (2001).

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