Genome Informatics: The Role of DNA in Cellular Computations

Biological Theory

Volumn 1, Issue 3, 2006, Pages 288-301

  Shapiro, James A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

computation; evolution; formatting; genome system architecture; natural genetic engineering; repetitive DNA

Indexed keywords

EID: 49949108738     PISSN: 15555542     EISSN: 15555550     Source Type: Journal    
DOI: 10.1162/biot.2006.1.3.288     Document Type: Article

References (123)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular Biology of the Cell. 4th ed. New York: Garland.
2. Almeida R, Allshire RC (2005) RNA silencing and genome regulation. Trends in Cell Biology 15: 251–258.
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
4. Armitage JP, Holland IB, Jenal U, Kenny B (2005) “Neural networks” in bacteria: Making connections. Journal of Bacteriology 187: 26–36.
5. Arnone MI, Davidson EH (1997) The hardwiring of development: Organization and function of genomic regulatory systems. Development 124: 1851–1864.
6. Atlan H, Koppel M (1990) The cellular computer DNA: Program or data. Bulletin of Mathematical Biology 52: 335–348.
7. Avery OT, MacLeod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus Type III. Journal of Experimental Medicine 79: 137–158.
8. Bailey JA, Liu G, Eichler EE (2003) An Alu transposition model for the origin and expansion of human segmental duplications. American Journal of Human Genetics 73: 823–834.
9. Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends in Microbiology 12: 406–411.
10. Benzer S (1962) The fine structure of the gene. Scientific American 206: 70–84.
11. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes and Development 19: 1635–1655.
12. Bibikova M, et al. (2006) Human embryonic stem cells have a unique epigenetic signature. Genome Research 16: 1075–83.
13. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes and Development 16: 6–21.
14. Bonifacino JS, Glick BS (2004) The mechanisms of vesicle budding and fusion. Cell 116: 153–166.
15. Bray D (1990) Intracellular signalling as a parallel distributed process. Journal of Theoretical Biology 143: 215–231.
16. Bray D (1995) Protein molecules as computational elements in living cells. Nature 376: 307–312.
17. Bray D, Duke T (2004) Conformational spread: The propagation of allosteric states in large multiprotein complexes. Annual Review of Biophysics and Biomolecular Structure 33: 53–73.
18. Bregliano, JC, Kidwell MG (1983) Hybrid dysgenesis determinants: In: Mobile Genetic Elements (Shapiro JA, ed), 363–410. New York: Academic Press.
19. Britten RJ (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proceedings of the National Academy of Sciences USA 93: 9374–9377.
20. Brosius J (1999) RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115–134.
21. Brosius J (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118: 99–116.
22. Butturini A, Sthivelman E, Canaani E, Gale RP (1988) Oncogenes in human leukemias. Cancer Investigation 6: 305–316.
23. Carroll SB (1995) Homeotic genes and the evolution of arthropods and chordates. Nature 376: 479–485.
24. Cases I, de Lorenzo V (1998) Expression systems and physiological control of promoter activity in bacteria. Current Opinion in Microbiology 1: 303–310.
25. Craig NL, Craigie R, Gellert M, Lambowitz AM (2002) Mobile DNA II. Washington DC: ASM Press.
26. Crick F (1970) Central dogma of molecular biology. Nature 227: 561–563.
27. Davidson EH (2001) Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.
28. Davidson EH, Britten RJ (1979) Regulation of gene expression: Possible role of repetitive sequences. Science 204: 1052–1059.
29. Driesch H (1908) The Science and Philosophy of the Organism. London: A&C Black.
30. Duboule D, Wilkins AS (1998) The evolution of “bricolage.” Trends in Genetics 14: 54–59.
31. Eichler EE (2001) Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends in Genetics 17: 661–669.
32. Eichler EE, Sankoff D (2003) Structural dynamics of eukaryotic chromosome evolution. Science 301: 793–797.
33. Errede B, Cardillo TS, Wever G, Sherman F, Stiles JI, Friedman LR, Sherman F (1981) Studies on transposable elements in yeast. I. ROAM mutations causing increased expression of yeast genes: Their activation by signals directed toward conjugation functions and their formation by insertion of Ty1 repetitive elements. II. deletions, duplications, and transpositions of the COR segment that encompasses the structural gene of yeast iso-1-cytochrome c. Cold Spring Harbor Symposium Quantitative Biology 45 (Pt 2): 593–607.
34. Galli C, Lagutina I, Lazzari G (2003) Introduction to cloning by nuclear transplantation. Cloning Stem Cells 5: 223–232.
35. Gao S, Latham KE (2004) Maternal and environmental factors in early cloned embryo development. Cytogenetic and Genome Research 105: 279–284.
36. Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annual Review of Biochemistry 71: 101–132.
37. Gerhart J, Kirschner M (1997) Cells, Embryos, and Evolution. Malden, MA: Blackwell Science.
38. Goday C, Esteban MR (2001) Chromosome elimination in sciarid flies. Bioessays 23: 242–250.
39. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, and 45 others (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.
40. Gurdon JB, Byrne JA, Simonsson S (2003) Nuclear reprogramming and stem cell creation. Proceedings of the National Academy of Sciences USA 100 (Suppl 1): 11819–11822.
41. Haber JE (1998) Mating-type gene switching in Saccharomyces cerevisiae. Annual Review of Genetics 32: 561–599.
42. Hall IM, Noma K, Grewal SI (2003) RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proceedings of the National Academy of Sciences USA 100: 193–198.
43. Harden N, Ashburner M (1990) Characterization of the FB-NOF transposable element of Drosophila melanogaster. Genetics 126: 387–400.
44. Hartmann N, Scherthan H (2004) Characterization of ancestral chromosome fusion points in the Indian muntjac deer. Chromosoma 112: 213–220.
45. Hartwell L (1992) Defects in a cell cycle checkpoint may be responsible for the genomic instability of cancer cells. Cell 71: 543–546.
46. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402 (Suppl 6761): C47–C52.
47. Hazelrigg T, Levis R, Rubin GM (1984) Transformation of white locus DNA in drosophila: Dosage compensation, zeste interaction, and position effects. Cell 36: 469–481.
48. Henikoff S, Ahmad K (2005) Assembly of variant histones into chromatin. Annual Review of Cell and Developmental Biology 21: 133–153.
49. Hey J (2003) Speciation and inversions: Chimps and humans. Bioessays 25: 825–828.
50. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
51. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318–356.
52. Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nature Genetics 33 (Suppl): 245–254.
53. Jenuwein T (2002) An RNA-guided pathway for the epigenome. Science 297: 2215–2218.
54. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569–573.
55. Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV (2001) Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Research 11: 55–65.
56. Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics 19: 68–72.
57. Judson HF (1979) The Eighth Day of Creation: Makers of the Revolution in Biology. New York: Simon and Schuster.
58. Kinoshita K, Honjo T (2001) Linking class-switch recombination with somatic hypermutation. Nature Reviews Molecular Cell Biology 2: 493–503.
59. Kosak ST, Groudine M (2004) Gene order and dynamic domains. Science 306: 644–647.
60. Kuhn TS (1962) The Structure of Scientific Revolutions. Chicago: University of Chicago Press.
61. Kunkel TA, Erie DA (2005) DNA mismatch repair. Annual Review of Biochemistry 74: 681–710.
62. Landy A (1989) Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annual Review of Biochemistry 58: 913–949.
63. Levis R, Hazelrigg T, Rubin GM (1985) Effects of genomic position on the expression of transduced copies of the white gene of Drosophila. Science 229: 558–561.
64. Li E (2002) Chromatin modification and epigenetic reprogramming in mammalian development. Nature Reviews Genetics 3: 662–673.
65. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471–476.
66. London M, Hausser M (2005) Dendritic computation. Annual Review of Neuroscience 28: 503–532.
67. Lucas I, Hyrien O (2000) Hemicatenanes form upon inhibition of DNA replication. Nucleic Acids Research 28: 2187–2193.
68. Mann JR (2001) Imprinting in the germ line. Stem Cells 19: 287–294.
69. Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK (2005) Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenetic and Genome Research 110: 333–341.
70. McClintock B (1984) Significance of responses of the genome to challenge. Science 226: 792–801.
71. Moran JV, DeBerardinis RJ, Kazazian HH Jr (1999) Exon shuffling by L1 retrotransposition. Science 283: 1530–1534.
72. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562.
73. Murai KK, Pasquale EB (2004) Eph receptors, ephrins, and synaptic function. Neuroscientist 10: 304–314.
74. Muller C, Leutz A (2001) Chromatin remodeling in development and differentiation. Current Opinion in Genetics and Development 11: 167–174.
75. Muller F, Bernard V, Tobler H (1996) Chromatin diminution in nematodes. Bioessays 18: 133–138.
76. Muotri AR, Chu VT, Marchetto MCN, Deng W, Moran JV, Gage FH (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435: 903–910.
77. Murray AW (2004) Recycling the cell cycle: Cyclins revisited. Cell 116: 221–234.
78. Navarro A, Barton NH (2003) Chromosomal speciation and molecular divergence: accelerated evolution in rearranged chromosomes. Science 300: 321–324.
79. Neel NF, Schutyser E, Sai J, Fan GH, Richmond A (2005) Chemokine receptor internalization and intracellular trafficking. Cytokine and Growth Factor Reviews 16: 637–658.
80. Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annual Review of Genetics 22: 121–152.
81. Nusslein-Volhard C (1991) Determination of the embryonic axes of Drosophila. Development, (Suppl 1): 1–10.
82. Patel NH, Prince VE (2000) Beyond the Hox complex. Genome Biology 1: reviews 1027.1–1027.4.
83. Peaston AE, et al. (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell 7: 597–606.
84. Pelkmans L (2005) Viruses as probes for systems analysis of cellular signalling, cytoskeleton reorganization and endocytosis. Current Opinion in Microbiology 8: 331–337.
85. Pollard TD, Borisy GG (2003) Cellular motility driven by assembly and disassembly of actin filaments. Cell 112: 453–465.
86. Pool MR (2005) Signal recognition particles in chloroplasts, bacteria, yeast and mammals (review). Molecular Membrane Biology 22: 3–15.
87. Prescott DM (2000) Genome gymnastics: Unique modes of DNA evolution and processing in ciliates. Nature Reviews Genetics 1: 191–198.
88. Ptashne M (1986) A Genetic Switch: Phage lambda and Higher Organisms. 2nd ed. Cambridge, MA: Cell Press and Blackwell Scientific.
89. Razin SV, Petrov A, Hair A, Vassetzky YS (2004) Chromatin domains and territories: Flexibly rigid. Critical Reviews in Eukaryotic Gene Expression 214: 79–88.
90. Rothenburg S, Koch-Nolte F, Haag F (2001) DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles. Immunological Reviews 184: 286–298.
91. Schotta G, Ebert A, Dorn R, Reuter G (2003) Position effect variegation and the genetic dissection of chromatin regulation in Drosophila. Seminars in Cell and Developmental Biology 14: 67–75.
92. Shapiro JA (1997) Genome organization, natural genetic engineering, and adaptive mutation. Trends in Genetics 13: 98–104.
93. Shapiro JA (1999) Genome system architecture and natural genetic engineering in evolution. In: Molecular Strategies for Biological Evolution (Caporale L, ed), Annals of the New York Academy of Sciences 870: 23–35.
94. Shapiro JA (2002a) Genome organization and reorganization in evolution: Formatting for computation and function. In: From Epigenesis to Epigenetics: The Genome in Context (Van Speybroeck L, Van de Vijver G, De Waele D, eds), Annals of the New York Academy of Sciences 981: 111–134.
95. Shapiro JA (2002b) A 21st century view of evolution. Journal of Biological Physics 28: 745–764.
96. Shapiro JA (2002c) Repetitive DNA, genome system architecture and genome reorganization. Research in Microbiology 153: 447–453.
97. Shapiro JA (2005) A 21st century view of evolution: Genome system architecture, repetitive DNA, and natural genetic engineering. Gene 345: 91–100.
98. Shapiro JA, Dworkin M, eds (1997) Bacteria as Multicellular Organisms. New York: Oxford University Press.
99. Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential for genome function. Biological Review 80: 227–250.
100. Sidiropoulou K, Pissadaki EK, Poirazi P (2006) Inside the brain of a neuron. EMBO Reports 7(9): 886–892.
101. Smith GR (1994) Hotspots of homologous recombination. Experientia 50: 234–241.
102. Spemann H (1938) Embryonic Development and Induction. New Haven, CT: Yale University Press.
103. Spemann H, Mangold H (1924) Über Induktion von Embryonanlagen durch Implantation artfremder Organisatoren. Roux’ Archiv für Entwicklungsmechanik 100: 599–638.
104. Spofford JB (1976) Position-effect variegation in Drosophila. In: The Genetics and Biology of Drosophila (Ashburner M, Novitski E, eds), 955–1018. New York: Academic Press.
105. Stros M, Muselikova-Polanska E, Pospisilova S, Strauss F (2004) High-affinity binding of tumor-suppressor protein p53 and HMGB1 to hemicatenated DNA loops. Biochemistry 43: 7215–7225.
106. Stuart LM, Ezekowitz RA (2005) Phagocytosis: Elegant complexity. Immunity 22: 539–550.
107. Szurmant H, Ordal GW (2004) Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiology and Molecular Biology Reviews 68: 301–319.
108. Tonzetich J, Lyttle TW, Carson HL (1988) Induced and natural break sites in the chromosomes of Hawaiian Drosophila. Proceedings of the National Academy of Sciences USA 85: 1717–1721.
109. Turing AM (1950) Computing machineryand intelligence. Mind 59: 433–460.
110. van der Woude MW, Baumler AJ. Phase and antigenic variation in bacteria. Clinical Microbiology Reviews 17: 581–611.
111. Van Driel R, Fransz PF, Verschure PJ (2003) The eukaryotic genome: A system regulated at different hierarchical levels. Journal of Cell Science 116: 4067–4075.
112. von Neumann J, Burks AW (1966) Theory of Self-Reproducing Automata. Urbana: University of Illinois Press.
113. von Sternberg R, Shapiro JA (2005) How repeated retroelements format genome function. Cytogenetic and Genome Research 110: 108–116.
114. Wang JY, Syvanen M (1992) DNA twist as a transcriptional sensor for environmental changes. Molecular Microbiology 6: 1861–1866.
115. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids. Nature 171: 737–738.
116. Wessler SR (1996) Plant retrotransposons: Turned on by stress. Current Biology 6: 959–961.
117. Williamson JR (1994) G-quartet structures in telomeric DNA. Annual Review of Biophysics and Biomolecular Structure 23: 703–730.
118. Wilmut I, Paterson L (2003) Somatic cell nuclear transfer. Oncology Research 13: 303–307.
119. Woese CR (2004) A new biology for a new century. Microbiology and Molecular Biology Reviews 68: 173–186.
120. Wulfing C, Tskvitaria-Fuller I, Burroughs N, Sjaastad MD, Klem J, Schatzle JD (2002) Interface accumulation of receptor/ligand couples in lymphocyte activation: Methods, mechanisms, and significance. Immunological Reviews 189: 64–83.
121. Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 279: 1896–1902.
122. Zaidi SK, Young DW, Choi JY, Pratap J, Javed A, Montecino M, Stein JL, van Wijnen AJ, Lian JB, Stein GS (2005) The dynamic organization of gene-regulatory machinery in nuclear microenvironments. EMBO Reports 6: 128–133.
123. Zhi D, Raphael B, Price A, Tang H, Pevzner P (2006) Identifying repeat domains in large genomes. Genome Biology 7: R7.