Isochores and tissue-specificity

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5212-5220

  Vinogradov, Alexander E ^a  

^a INSTITUTE OF CYTOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

ARTICLE; CELL DIFFERENTIATION; CENTRAL NERVOUS SYSTEM; CONTROLLED STUDY; GC RICH SEQUENCE; GENE CONVERSION; GENE EXPRESSION; GENE LOCATION; GENETIC TRANSCRIPTION; GENOME; GERM LINE; HOUSEKEEPING GENE; HUMAN; ISOCHORE; MAMMAL; MOUSE; NONHUMAN; OVARY; PRIORITY JOURNAL; PROBABILITY; SPECIES COMPARISON; TESTIS; TISSUE DIFFERENTIATION; TISSUE SPECIFICITY;

ANIMALS; BASE COMPOSITION; CODON; DATABASES, NUCLEIC ACID; FEMALE; GC RICH SEQUENCE; GENE EXPRESSION PROFILING; GENOME; HUMANS; ISOCHORES; MALE; MICE;

MAMMALIA;

EID: 0345411919     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg699     Document Type: Article

References (69)

1. Bernardi, G. (2000) Isochores and the evolutionary genomics of vertebrates. Gene, 241, 3-17.
2. Bernardi, G. (2000) The compositional evolution of vertebrate genomes. Gene, 259, 31-43.
3. Bernardi, G. (2001) Misunderstandings about isochores. Part 1. Gene, 276, 3-13.
4. Eyre-Walker, A. and Hurst, L.D. (2001) The evolution of isochores. Nat. Rev. Genet., 2, 549-555.
5. Suoeka, N. (1988) Directional mutation pressure and neutral molecular evolution. Proc. Natl Acad. Sci. USA, 85, 2653-2657.
6. Wolfe, K., Sharp, P.M. and Li, W.H. (1989) Mutation rates differ among regions of the mammalian genome. Nature, 337, 441-456.
7. Francino, M.P. and Ochman, H. (1999) Isochores result from mutation not selection. Nature, 400, 30-31.
8. Fryxell, K.J. and Zuckerkandl, E. (2000) Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol. Biol. Evol., 17, 1371-1383.
9. Sueoka, N. and Kawanishi, Y. (2000) DNA G+C content of the third codon position and codon usage biases of human genes. Gene, 261, 53-62.
10. Eyre-Walker, A. (1993) Recombination and mammalian genome evolution. Proc. R. Soc. Lond. B, 252, 237-243.
11. Galtier, N., Piganeau, G., Mouchiroud, D. and Duret, L. (2001) GC content evolution in mammalian genomes, the biased gene conversion hypothesis. Genetics, 159, 907-911.
12. Smith, N.G. and Eyre-Walker, A. (2001) Synonymous codon bias is not caused by mutation bias in human. Mol. Biol. Evol., 18, 982-986.
13. Duret, L., Semon, M., Piganeau, G., Mouchiroud, D. and Galtier, N. (2002) Vanishing GC-rich isochores in mammalian genomes. Genetics, 162, 1837-1847.
14. Lercher, M.J., Smith, N.G., Eyre-Walker, A. and Hurst, L.D. (2002) The evolution of isochores. Evidence from sup frequency distributions. Genetics, 162, 1805-1810.
15. Galtier, N. (2003) Gene conversion drives GC content evolution in mammalian histories. Trends Genet., 19, 65-68.
16. Bernardi, G. and Bernardi, G. (1986) Compositional constraints and genome evolution. J. Mol. Evol., 24, 1-11.
17. Vinogradov, A.E. (2001) Bendable genes of warm-blooded vertebrates. Mol. Biol. Evol., 18, 2195-2200.
18. Vinogradov, A.E. (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Res., 31, 1838-1844.
19. Eyre-Walker, A. (1999) Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics, 152, 675-683.
20. Smith, N.G., and Eyre-Walker, A. (2001) Synonymous codon bias is not caused by mutation bias in human. Mol. Biol. Evol., 18, 982-986.
21. Lercher, M.J., Smith, N.G., Eyre-Walker, A. and Hurst, L.D. (2002) The evolution of isochores. Evidence from sup frequency distributions. Genetics, 162, 1805-1810.
22. Mouchiroud, D., Fichant, G. and Bernardi, G. (1987) Compositional compartmentalization and gene composition in the genome of vertebrates. J. Mol. Evol., 26, 198-204.
23. Bernardi,G. (1993) The isochore organization of the human genome and its evolutionary history - a review. Gene, 135, 57-66.
24. Bernardi, G. (1995) The human genome: organization and evolutionary history. Annu. Rev. Genet., 29, 445-476.
25. Pesole, G., Bernardi, G. and Saccone, C. (1999) Isochore specificity of AUG initiator context of human genes. FEBS Lett., 464, 60-62.
26. Goncalves, I., Duret, L. and Mouchiroud, D. (2000) Nature and structure of human genes that generate retropseudogenes. Genome Res., 10, 672-678.
27. Ponger, L., Duret, L. and Mouchiroud, D. (2001) Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res., 11, 1854-1860.
28. D'Onofrio, G. (2002) Expression patterns and gene distribution in the human genome. Gene, 300, 155-160.
29. Voelkel-Meiman, K. and Roeder, G.S. (1990) Gene conversion tracts stimulated by HOT1-promoted transcription are long and continuous. Genetics, 126, 851-867.
30. Shenkar, R., Shen, M.H. and Arnheim, N. (1991) DNase I-hypersensitive sites and transcription factor-binding motifs within the mouse E beta meiotic recombination hot spot. Mol. Cell Biol. 11, 1813-1819.
31. Nickoloff, J.A. (1992) Transcription enhances intrachromosomal homologous recombination in mammalian cells. Mol. Cell Biol., 12, 5311-5318.
32. Droge, P. (1993) Transcription-driven site-specific DNA recombination in vitro. Proc. Natl Acad. Sci. USA, 90, 2759-2763.
33. Cook, P.R. (1997) The transcriptional basis of chromosome pairing. J. Cell Sci., 110, 1033-1040.
34. Bell, S.J, Chow, Y.C., Ho, J.Y. and Forsdyke, D.R. (1998) Correlation of chi orientation with transcription indicates a fundamental relationship between recombination and transcription. Gene, 216, 285-292.
35. Nicolas, A. (1998) Relationship between transcription and initiation of meiotic recombination: towards chromatin accessibility. Proc. Natl Acad. Sci. USA, 95, 87-89.
36. Koren, A., Ben-Aroya, S. and Kupiec, M. (2002) Control of meiotic recombination initiation: a role for the environment? Curr. Genet., 42, 129-139.
37. Brazma, A. and Vilo, J. (2000) Gene expression data analysis. FEBS Lett., 480, 17-24.
38. Schulze, A. and Downward, J. (2001) Navigating gene expression using microarrays-a technology review. Nature Cell Biol., 3, E190-E195.
39. Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A. et al. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc. Natl Acad Sci. USA, 99, 4465-4470.
40. Duboule, D. and Wilkins, A.S. (1998) The evolution of 'bricolage'. Trends Genet., 14, 54-59.
41. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard,J., Hallbeck, B., Masson, G. et al. (2002) A high-resolution recombination map of the human genome. Nature Genet., 31, 241-247.
42. Konu, O.O. and Li, M.D. (2002) Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. J. Mol. Evol., 54, 35-41.
43. D'Onofrio, G., Jabbari, K., Musto, H., Alvarez-Valin, F., Cruveiller, S. and Bernardi, G. (1999) Evolutionary genomics of vertebrates and its implications. Ann. N. Y. Acad. Sci., 870, 81-94.
44. Galtier, N. and Lobry, J.R. (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol., 44, 632-636.
45. Hurst, L.D. and Merchant, A.R. (2001) High guanine-cytosine content is not an adaptation to high temperature, a comparative analysis amongst prokaryotes. Proc. R. Soc. Lond. B, 268, 493-497.
46. Belle, E.M., Smith, N. and Eyre-Walker, A. (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J. Mol. Evol., 55, 356-363.
47. Ream, R.A., Johns, G.C. and Somero, G.N. (2003) Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G + C content. Mol. Biol. Evol., 20, 105-110.
48. Anselmi, C., Bocchinfuso, G., De Santis, P., Savino, M. and Scipioni, A. (1999) Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol., 286, 1293-1301.
49. Anselmi, C., Bocchinfuso, G., De Santis, P., Savino, M. and Scipioni, A. (2000) A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys. J., 79, 601-613.
50. Herbert, A. and Rich, A. (1999) Left-handed Z-DNA, structure and function. Genetica, 106, 37-47.
51. Radic, M.Z., Lundgren, K. and Hamkalo, B.A. (1987) Curvature of mouse satellite DNA and condensation of heterochromatin. Cell, 50, 1101-1108.
52. Blomquist, P., Belikov, S. and Wrange, O. (1999) Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. Nucleic Acids Res., 27, 517-525.
53. Kiyama, R. and Trifonov, E.N. (2002) What positions nucleosomes? - A model. FEBS Lett., 523, 7-11.
54. Saccone, S., Federico, C. and Bernardi, G. (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene, 300, 169-178.
55. Vinogradov, A.E. (2003) Silent DNA: speaking RNA language? Bioinformatics, 19, 000-000.
56. Jaenisch, R. and Bird, A. (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genet., 33, 245-254.
57. Jabbari, K. and Bernardi, G. (1998) CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene, 224, 123-127.
58. Sabeur, G., Macaya, G., Kadi, F. and Bernardi, G. (1993) The isochore patterns of mammalian genomes and their phylogenetic implications. J. Mol. Evol., 37, 93-108.
59. Robinson, M., Gautier, C. and Mouchiroud, D. (1997) Evolution of isochores in rodents. Mol. Biol. Evol., 14, 823-828.
60. Galtier, N. and Mouchiroud, D. (1998) Isochore evolution in mammals, a human-like ancestral structure. Genetics, 150, 1577-1584.
61. Douady, C., Carels, N., Clay, O., Catzeflis, F. and Bernardi, G. (2000) Diversity and phylogenetic implications of CsCl profiles from rodent DNAs. Mol. Phylogenet. Evol., 17, 219-230.
62. Smith, N.G. and Eyre-Walker, A. (2002) The compositional evolution of the murid genome. J. Mol. Evol., 55, 197-201.
63. Furlong, R.F. and Holland, P.W. (2002) Were vertebrates octoploid? Philos. Trans. R. Soc. Lond. B, 357, 531-544.
64. Gu, X., Wang, Y. and Gu, J. (2002) Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genet., 31, 205-209.
65. McLysaght, A., Hokamp, K. and Wolfe, K.H. (2002) Extensive genomic duplication during early chordate evolution. Nature Genet., 31, 200-204.
66. VandePeer, Y., Taylor, J.S., Joseph, J. and Meyer, A. (2002) Wanda: a database of duplicated fish genes. Nucleic Acids Res., 30, 109-112.
67. Dean, W., Santos, F., Stojkovic, M., Zakhartchenko, V., Walter, J., Wolf, E. and Reik, W. (2001) Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc. Natl Acad. Sci. USA, 98, 13734-13738.
68. Adelman, R., Saul, R.L. and Ames, B.N. (1988) Oxidative damage to DNA: relation to species metabolic rate and life span. Proc. Natl Acad. Sci. USA, 85, 2706-2708.
69. Ames, B.N. (1989) Endogenous DNA damage as related to cancer and aging. Mutat. Res., 214, 41-46.