Codon Signature Extremes In Eukaryote genomes

References

• Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
   Google Scholar
• Aravind, L., Koonin, J.E. 2000. The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates. Genome Biol. 1: Res 0007.
   Google Scholar
• Beutler, E., Gelbart, T., Han, J., Koziol, J.A., Beutler, B. 1989. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc. Natl. Acad. Sci. USA 86: 192-196.
   Google Scholar
• Blaisdell, B.E., Campbell, A.M., Karlin, S. 1996. Genomic comparisons among phages. Proc. Natl. Acad. Sci. USA 93: 5854-5859.
   Google Scholar
• Blumenthal, A.B., Kriegstein, H.J., Hogness, D.S. 1974. The units of DNA replication in Drosophila melanogaster chromosomes. Cold Spring Harb. Symp. Quant. Biol. 38: 205-223.
   Google Scholar
• Bohr, V.A., Phillips, D.H., Hanawalt, P.C. 1987. Heterogeneous DNA damage and repair in the mammalian genome. Cancer Res. 47: 6426-6436.
   Google Scholar
• Brandin, C., Tooze, C. 1991. Introduction to protein structure. Garland, New York.
   Google Scholar
• Breslauer, K.J., Frank, R., Blocker, H., Marky, L.A. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83: 3746-3750.
   Google Scholar
• Cardon, L.R., Burge, C., Clayton, D.A., Karlin, S. 1994. Pervasive CpG suppression in animal mitochondrial genomes. Proc. Natl. Acad. Sci. USA 91: 3799-3803.
   Google Scholar
• De Cock, J.G., Klink, E.C., Ferro, W., Lohman, P.H., Eeken, J.C. 1992. Neither enhanced removal of cyclobutane pyrimidine dimers nor strand-specific repair is found after transcription induction of the beta 3-tubulin gene in a Drosophila embryonic cell line Kc. Mutat. Res. 293: 11-20.
   Google Scholar
• Delcourt, S.G., Blake, R.D. 1991. Stacking energies in DNA. J. Biol. Chem. 266: 15160-15169.
   Google Scholar
• Dujon, B., Sherman, D., Fischer, G., et al. 2004. Genome evolution in yeasts (Candida glabrata). Nature 430: 35-44.
   Google Scholar
• Duret, L. 2002. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12: 640-649.
   Google Scholar
• El-Sayed, N.M., Myler, P.J., Bartholomeu, D.C., et al., 2005. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309: 409-415.
   Google Scholar
• Finnegan, E.J., Bretell, R.I., Dennis, E.S. 1993. The role of DNA methylation in the regulation of plant gene expression. In: Jost, J.B., Saluz, H.P., eds. DNA methylation: molecular biology and biological significance. Birkhauser Verlag, Berlin, pp. 218-261.
   Google Scholar
• Friedberg, E.C., Walker, G.C., Siede, W. 1995. DNA repair and mutagenesis. ASM Press, Washington, D.C.
   Google Scholar
• Galagan, J.E., Calvo, S.E., Borkovich, K.A., Selker, E.U., et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
   Google Scholar
• Gardner, M.J., Hall, N., Fung, E., et al. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
   Google Scholar
• Gentles, A.J., Karlin, S. 2001. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11: 540-546.
   Google Scholar
• Goffeau, A., Barrell, B.G., Bussey, H., et al. 1996. Life with 6000 genes. Science 546: 563-567.
   Google Scholar
• Holt, R.A., Subramanian, G.M., Halpern, A., et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
   Google Scholar
• Ikemura, T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2: 12-34.
   Google Scholar
• International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
   Google Scholar
• Irwin, B., Heck, J.D., Hatfield, G.W. 1995. Codon pair utilization biases influence translational elongation step times. J. Biol. Chem. 270: 22801-22806.
   Google Scholar
• Ivens, A.C., Peacock, C.S., Worthey, E.A., et al. 2005. The genome of the kinetoplastid parasite, Leishmania major. Science 309: 436-442.
   Google Scholar
• Kamath, R.S., Fraser, A.G., Dong, Y., et al. 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
   Google Scholar
• Kamper, J., Kahmann, R., Bolker, M., et al. 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101.
   Google Scholar
• Karlin, S. 1998. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1: 598-610.
   Google Scholar
• Karlin, S., Burge, C. 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11: 283-290.
   Google Scholar
• Karlin, S., Cardon, L.R. 1994. Computational DNA sequence analysis. Annu. Rev. Microbiol. 48: 619-654.
   Google Scholar
• Karlin, S., Mrazek, J. 1996. What drives codon choices in human genes? J. Mol. Biol. 262: 459-472.
   Google Scholar
• Karlin, S., Mrazek, J. 1997. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. USA 94: 10227-10232.
   Google Scholar
• Katinka, M.D., Duprat, S., Cornillot, E., et al. 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414: 450-453.
   Google Scholar
• Lander, E.S., Linton, L.M., Birren, B., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
   Google Scholar
• Li, W.-H., Ellsworth, D.L., Krushkal, J., Chang, B.H.-J., Hewett-Emmett, D. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5: 182-187.
   Google Scholar
• Loftus, B.J., Fung, E., Roncaglia, P., et al. 2005a. The genome of the Basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324.
   Google Scholar
• Loftus, B.J., Anderson, R.I., Davies, U., Alsmark, C.M., et al. 2005b. The genome of the protist parasite Entamoeba histolytica. Nature 433: 865-868.
   Google Scholar
• Matsuzaki, M., Misumi, O., Shin-I, T., et al., 2004. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyion merolae 10D. Nature 428: 653-657.
   Google Scholar
• McArthur, A.G., Morrison, H.G., Nixon, J.E., et al. 2000. The Giardia genome project database. FEMS Microbiol. Lett. 189: 271.
   Google Scholar
• Morrison, J.M., Keir, H.M., Subak-Sharpe, H., Crawford, L.V. 1967. Nearest neighbor base sequence analysis of the deoxyribonucleic acids of a further three mammalian viruses: simian virus 40, human papilloma virus and adenovirus type 2. J. Gen. Virol. 1: 101-108.
   Google Scholar
• Nierman, W.C., Pain, A., Anderson, M.J., et al. 2005. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151-1156.
   Google Scholar
• Paz, A., Mester, D., Baca, I., Nevo, E., Korol, A. 2004. Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc Natl. Acad. Sci. USA 101: 2951-2956.
   Google Scholar
• Petrov, D.A., Hartl, D.L. 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol. Biol. Evol. 15: 293-302.
   Google Scholar
• Roos, A., Boron, W.F. 1981. Intracellular pH. Physiol. Rev. 61: 296-434.
   Google Scholar
• Russel, G.J., Subak-Sharpe, J.H. 1977. Similarity of the general designs of protochordates and invertebrates. Nature 266: 533-536.
   Google Scholar
• Russel, G.J., Walker, P.M.B., Elton, R.A., Subak-Sharpe, J.H. 1976. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J. Mol. Biol. 108: 1-28.
   Google Scholar
• Shadel, G.S., Clayton, D.A. 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409-434.
   Google Scholar
• Sharp, P.M., Bailes, E., Grocock, R.J., Peden, J.F., Sockett, R.E. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33: 1141-1153.
   Google Scholar
• The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
   Google Scholar
• Travers, A.A. 1993. DNA-Protein interactions. Chapman & Hall, New York.
   Google Scholar
• Waterston, R.H., Lindblad-Toh, K., Birney, E., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
   Google Scholar
• Wood, V., Gwilliam, R., Rajandream, M.A., et al. 2002. The genome sequence of Schizosaccharomyces pombe Nature 415: 871-880.
   Google Scholar
• Yakes, F.M., Van Houten, B. 1997. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc. Natl. Acad. Sci. USA 94: 514-519.
   Google Scholar