Chromosome evolution with naked eye: Palindromic context of the life origin

Chaos

Volumn 18, Issue 1, 2008, Pages

  Larionov, Sergei ^a   Loskutov, Alexander ^a   Ryadchenko, Eugeny ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 41549106212     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2826631     Document Type: Article

References (59)

1. V. V. Lobzin, and V. R. Chechetkin, " Order and correlations in genomic DNA sequences. The spectral approach.," Usp. Fiz. Nauk 0042-1294 170, 57-83 (2000); Lobzin, V. V., and Chechetkin, V. R. [Phys. Usp. 43, 55-81 (2000)].
2. S. W. Golomb, " The genetic code.," in Mathematical Problems in the Biological Sciences, edited by, R. Bellman, (Amer. Math. Soc., Providence, RI, 1962).
3. M. A. Gates, " Simpler DNA sequence representations.," Nature 316, 219-219 (1985).
4. E. Mizraji and J. Ninio, " Graphical coding of nucleic acid sequences.," Biochimie 67, 445-448 (1985).
5. Ch. Berthelsen, J. A. Glazier, and M. H. Skolnik, " Global fractal dimension of human DNA sequences treated as pseudorandom walks.," Phys. Rev. A 45, 8902-8913 (1992).
6. A. Nandy, " New graphical representation and analysis of DNA sequence structure. I: Methodology and application to globin genes.," Curr. Sci. 66, 309-314 (1994).
7. G. Abramson, P. A. Alemany, and H. A. Cerdeira, " Noisy Levy walk analog of two-dimensional DNA walks for chromosomes of S. cerevisiae.," Phys. Rev. E 58, 914-918 (1998).
8. A. Rosas, E. Nogueira, and J. F. Fontanari, " Multifractal analysis of DNA walks and trails.," Phys. Rev. E 66, 061906 (2002).
9. P. Vincens, L. Buffat, C. Andre, J.-P. Chevrolat, J.-F. Boisvieux, and S. Hazout, " A strategy for finding regions of similarity in complete genome sequences.," Bioinformatics 14, 715-725 (1998).
10. S. A. Larionov, A. Loskutov, and E. V. Ryadchenko, " Genome as a two-dimensional walk.," Dokl. Phys. 50, 634-638 (2005).
11. Y.-H. Kim, D. Ishikawa, H. Ph. Ha, M. Sugiyama, Y. Kaneko, and S. Harashima, " Chromosome XII context is important for rDNA function in yeast.," Nucleic Acids Res. 34, 2914-2924 (2006).
12. http://www.ncbi.nlm.nih.gov
13. E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Graf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. Hubbard, " Ensembl 2006.," Nucleic Acids Res. 34, D556-D561 (2006).
14. S. A. Larionov, A. Loskutov, and E. V. Ryadchenko, " What can we learn from 2D DNA walk? " Proc. of Int. Conf.: ISMB-2005, SIG "Automatic function prediction," Detroit, June, 2005.
15. L. Lu, H. Jia P. Droge, and J. Li, " The human genome-wide distribution of DNA palindromes.," Funct. Integr. Genomics 7, 221-227 (2007).
16. S. A. Larionov, A. Loskutov, A. D. Rybalko, and E. V. Ryadchenko, " Genome as a fractal set generated by inversion-diffusion dynamics.," in Nonlinear Waves-2006, edited by, A. V. Gaponov-Grekhov, and, V. I. Nekorkin, (Institute of Applied Physics, Nizhnii Novgorod, 2007), pp. 491-508 (Russian).
17. S. A. Larionov, A. Loskutov, E. V. Ryadchenko, and S. Rybalko (unpublished).
18. H. Skaletsky, T. Kuroda-Kawaguchi, P. J. Minx, H. S. Cordum, L. Hillier, L. G. Brown, S. Repping, T. Pyntikova, J. Ali, T. Bieri, A. Chinwalla, A. Delehaunty, K. Delehaunty, H. Du, G. Fewell, L. Fulton, R. Fulton, T. Graves, S. F. Hou, P. Latrielle, S. Leonard, E. Mardis, R. Maupin, J. McPherson, T. Miner, W. Nash, C. Nguyen, P. Ozersky, K. Pepin, S. Rock, T. Rohlfing, K. Scott, B. Schultz, C. Strong, A. Tin-Wollam, S. P. Yang, R. H. Waterston, R. K. Wilson, S. Rozen, and D. C. Page, " The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.," Nature 423, 825-837 (2003).
19. B. K. Bhowmick, Y. Satta, and N. Takahata, " The origin and evolution of human ampliconic gene families and ampliconic structure.," Genome Res. 17, 441-450 (2007).
20. E. L. L. Sonnhammer, and R. Durbin, " A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.," Gene 167, GC1-GC10 (1995).
21. P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand, and G. Benson, " Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes.," Genome Res., 14, 1861-1869 (2004).
22. S. A. Larionov, A. Loskutov, and E. V. Ryadchenko, " Lessons of large scale comparisons from 2D DNA walk.," Proc. of ESF Research Conf.: Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, Spain, 12-17 November 2005.
23. H. Tanaka, D. A. Bergstrom, M. C. Yao, and S. J. Tapscott, " Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification.," Nat. Genet. 37, 320-327 (2005).
24. S. A. Larionov, A. Loskutov, E. V. Ryadchenko, and S. Rybalko, " Gigantic palindrome diffusion and certain features of genomes evolution.," Proc. of the Int. Symposium on Evolution of Biomolecular Structure, University of Vienna, Austria, 25-27 May 2006.
25. A. H. Sturtevant, A History of Genetics (Harper and Row, New York, 1965).
26. B. McClintock, " The stability of broken ends of chromosomes in Zea mays.," Genetics 41, 234-282 (1941).
27. M. Ford, and M. Fried, " Large inverted duplications are associated with gene amplification.," Cell 45, 425-430 (1986).
28. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, " Basic local alignment search tool.," J. Mol. Biol. 215, 403-410 (1990).
29. A. L. Delcher, S. Kasif, R. D. Fleischmann, J. Peterson, O. White, and S. L. Salzberg, " Alignment of whole genomes.," Nucleic Acids Res. 27, 2369-2376 (1999).
30. M. Brudno, C. B. Do, G. M. Cooper, M. F. Kim, E. Davydov, NISC Comparative Sequencing Program, E. D. Green, A. Sidow, and S. Batzoglou, " LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.," Genome Res. 13, 721-731 (2003).
31. A. Y. Ogurtsov, M. A. Roytberg, S. A. Shabalina, and A. S. Kondrashov, " OWEN: aligning long collinear regions of genomes.," Bioinformatics 18, 1703-1704 (2002).
32. M. Eigen, Self-organization of Matter and the Evolution of Biological Macromolecules (Springer-Verlag, Berlin, 1971).
33. S. M. Lewis, E. Akgun, and M. Jasin, " Palindromic DNA and genomic stability: further studies.," Ann. N.Y. Acad. Sci. 870, 45-57 (1999).
34. The International HapMap Consortium, " A second generation human haplotype map of over 3.1 million SNPs.," Nature 449, 851-861 (2007).
35. J. A. Bailey, Zh. Gu, and R. A. Clark, " Recent segmental duplications in the human genome.," Science 297, 1003-1007 (2002).
36. A. J. Sharp, D. P. Locke, S. D. McGrath, Z. Cheng, J. A. Bailey, R. U. Vallente, L. M. Pertz, R. A. Clark, S. Schwartz, R. Segraves, V. V. Oseroff, D. G. Albertson, D. Pinkel, and E. E. Eichler, " Segmental duplications and copy-number variation in the human genome.," Am. J. Hum. Genet. 77, 78-88 (2005).
37. A. J. Iafrate, L. Feuk, M. N. Rivera, M. L. Listewnik, P. K. Donahoe, Y. Qi, S. W. Scherer, and Ch. Lee, " Detection of large-scale variation in the human genome.," Nat. Genet. 36, 949-951 (2004).
38. V. Bansal, A. Bashir, and V. Bafna, " Evidence for large inversion polymorphisms in the human genome from HapMap data.," Genome Res. 17, 219-230 (2007).
39. L. Feuk, J. R. MacDonald, T. Tang, A. R. Carson, M. Li, G. Rao, R. Khaja, and S. W. Scherer, Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.," PLoS Genet. 1, e56 (2005).
40. G. Bourque, and P. A. Pevzner, " Genome-scale evolution: Reconstructing gene orders in the ancestral species.," Genome Res. 12, 26-36 (2002).
41. J. A. Bailey, R. Baertsch, W. J. Kent, D. Haussler, and E. E. Eichler, " Hotspots of mammalian chromosomal evolution.," Genome Biol. 5, R23.1-R23.7 (2004).
42. B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. de Montigny, Ch. Marck, C. Neuveglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisrame, J. Boyer, L. Cattolico, F. Confanioleri, A. de Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, Ch. Hennequin, N. Jauniaux, Ph. Joyet, R. Kachouri, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wesolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, Ch. Bouchier, B. Coudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker, and J.-L. Souciet, " Genome evolution in yeasts.," Nature 430, 35-44 (2004).
43. H. Ogata, S. Audic, P. Renesto-Audiffren, P. E. Fournier, V. Barbe, D. Samson, V. Roux, P. Cossart, J. Weissenbach, J. M. Claverie, and D. Raoult, " Mechanisms of evolution in Rickettsia conorii, and R. prowazekii.," Science 293, 2093-2098 (2001).
44. J. R. Lobry and N. Sueoka, " Asymmetric directional mutation pressures in bacteria.," Genome Biol. 3, R1-R14 (2002).
45. T. Dandekar, B. Snel, M. Huynen, and P. Bork, " Conservation of gene order: A fingerprint of proteins that physically interact.," Trends Biochem. Sci. 23, 324-328 (1998).
46. S. A. Larionov, A. Loskutov, E. V. Ryadchenko, and S. Rybalko, " Visual genomics methods: gigantic palindromes and protein clusters prediction.," Proc. of the Int Symp.: In-silico Analysis of Proteins: Celebrating the 20th Anniversary of Swiss-Prot, Fortaleza, Brazil, 30 July-4 August 2006.
47. R. Berezney, D. D. Dubey, and J. A. Huberman, " Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci.," Chromosoma 108, 471-484 (2000).
48. I. Lucas, A. Palakodeti, Y. Jiang, D. J. Young, N. Jiang, A. A. Fernald, and M. M. Le Beau, " High-throughput mapping of origins of replication in human cells.," EMBO Rep. 8, 770-777 (2007).
49. M. Huvet, S. Nicolay, M. Touchon, B. Audit, Y. d'Aubenton-Carafa, A. Arneodo, and C. Thermes, " Human gene organization driven by the coordination of replication and transcription.," Genome Res. 17, 1278-1285 (2007).
50. C. A. Nieduszynski, S. Hiraga, P. Ak, C. J. Benham, and A. D. Donaldson, " OriDB: a DNA replication origin database.," Nucleic Acids Res. 35, D40-D46 (2007).
51. C. K. Peng, S. V. Buldyrev, A. L. Goldberger, S. Havlin, F. Sciortino, M. Simons, and H. E. Stanley, " Long-range correlations in nucleotide sequences.," Nature 356, 168-170 (1992).
52. A. S. Mikhailov and A. Loskutov, From Chaos to Noise (Springer, Berlin, 1996).
53. P. W. Anderson, " Suggest model for prebiotic evolution. The use of chaos.," Proc. Natl. Acad. Sci. U.S.A. 80, 3386-3390 (1983).
54. F. Jacob, S. Brenner, and F. Cuzin, " On the regulation of DNA replication in bacteria.," Cold Spring Harb Symp. Quant Biol. 28, 329-438 (1963).
55. T. Miyata and H. Hayashida, " Extraordinarily high evolutionary rate of pseudogenes: Evidence for the presence of selective pressure against changes between synonymous codons.," Proc. Natl. Acad. Sci. U.S.A. 78, 5739-5743 (1981).
56. M. Touchon and E. P. C. Rocha, " Causes of insertion sequences abundance in prokaryotic genomes.," Mol. Biol. Evol. 24, 969-981 (2007).
57. Y. Ejima and L. Yang, " Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling.," Hum. Mol. Genet. 12, 1321-1328 (2003).
58. J. B. Pereira-Leal, E. D. Levy, and S. A. Teichmann, " The origins and evolution of functional modules: lessons from protein complexes.," Philos. Trans. R. Soc. London, Ser. B 361, 507-517 (2006).
59. See EPAPS Document No. E-CHAOEH-18-003801 for figures illustrating the human chromosome Y with different releases, the inversion polymorphism in the human and chimpanzee genomes, as well as two sites obtained from Ref.. This document can be reached through a direct link in the online article's HTML reference section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps. html).