Deviations from Chargaff's second parity rule correlate with direction of transcription

Journal of Theoretical Biology

Volumn 197, Issue 1, 1999, Pages 63-76

  Bell, S J ^a   Forsdyke, D R ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA; MESSENGER RNA;

ARTICLE; DNA BASE COMPOSITION; DNA SUPERCOILING; DNA TRANSCRIPTION; ESCHERICHIA COLI; GENE LOCATION; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; VACCINIA VIRUS;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE; VACCINIA; VACCINIA VIRUS;

EID: 0033531431     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1998.0858     Document Type: Article

References (47)

1. Bell, S. J. & Forsdyke, D. R. (1998). Accounting units in DNA. J. Theor. Biol. 197, 51-61.
2. Bell, S. J., Chow, Y. C., Ho, J. Y. K. & Forsdyke, D. R. (1998). Correlation of Chi orientation with transcription indicates a fundamental relationship between recombination and transcription. Gene 216, 285-292.
3. Bernardi, G. (1993). The vertebrate genome: Isochores and evolution. Mol. Biol. Evol. 10, 186-204.
4. Bernardi, G., Mouchiroud, D. & Gautier, C. (1993). Silent substitutions in mammalian genomes and their evolutionary implications. J. Mol. Evol. 37, 583-589.
5. Bernstein, C. & Bernstein, H. (1991). Aging, Sex and DNA Repair. San Diego, CA: Academic Press.
6. Bowring, F. J. & Catcheside, D. E. A. (1996). Gene conversion alone accounts for more than 90% of recombination events at the am locus of Neurospora crassa. Genetics 143, 129-136.
7. Bussey, H., Kaback, D. B., Zhong, W. W., Vo, D. T., Clark, M. W., Fortin, N., Hall, J., Ouellette, B. F. F., Keng, T., Barton, A. B., Su, Y., Davies, C. J. & Storms, R. K. (1995). The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. Proc. Nat. Acad. Sci. U.S.A. 92, 3809-3813.
8. Cantor, C. R. & Schimmel, P. R. (1980). Biophysical Chemistry, pp. 1183-1264. San Francisco, CA: W. H. Freeman & Co.
9. Cook, P. R. (1997). The transcriptional basis of chromosome pairing. J. Cell Sci. 110, 1033-1040.
10. Cristillo, A. D., Lillicrap, T. P. & Forsdyke, D. R. (1998). Purine-loading of EBNA-1 mRNA avoids sense-antisense "collisions". FASEB J. 12, A1453.
11. Dang, K. D., Dutt, P. B. & Forsdyke, D. R. (1998). Chargaff differences correlate with transcription direction in the bithorax complex of Drosophila. Biochem. Cell Biol. 76, 129-137.
12. Dawkins, R. (1989). The Selfish Gene. New York, NY: Oxford University Press.
13. Eguchi, Y., Itoh, T. & Tomizawa, J. (1991). Antisense RNA. Annu. Rev. Biochem. 60, 631-652.
14. Forsdyke, D. R. (1981). Are introns in-series error-detecting codes? J. Theor. Biol. 93, 861-866.
15. Forsdyke, D. R. (1995). Entropy-driven protein self-aggregation as the basis for self/not-self discrimination in the crowded cytosol. J. Biol. Sys. 3, 273-287.
16. Forsdyke, D. R. (1996). Different biological species "broadcast" their dnas at different (C + G)% "wavelengths". J. Theor. Biol. 178, 405-417.
17. Forsdyke, D. R. (1999). The origin of species, revisited. Queen's Q. 106, 112-134.
18. Forsdyke, D. R. & Bell, S. J. (1997). Deviations from Chargaff's second rule correlate with direction of transcription and genome structure. Proc. Can. Fed. Biol. Socs. 40, 87.
19. Fraser, C. M. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
20. Goebel, S. J., Johnson, G. P., Perkus, M. E., Davis, S. W., Winslow, J. P. & Paoletti, J. (1990). The complete DNA sequence of vaccinia virus. Virology 179, 247-266.
21. Hanawalt, P. C. (1991). Heterogeneity of DNA repair at the gene level. Mut. Res. 247, 203-211.
22. Izant, J. G. & Weintraub, H. (1984). Inhibition of thymidine kinase gene expression by anti-sense RNA: A molecular approach to genetic analysis. Cell 36, 1007-1015.
23. Jaeger, J. A., Turner, D. H. & Zuker, M. (1990). Predicting optimal and suboptimal secondary structure for RNA. Meth. Enzymol. 183, 281-306.
24. Karkas, J. D., Rudner, R. & Chargaff, E. (1968). Separation of B. Subtilis DNA into complementary strands - II. Template functions and composition as determined by transcription with RNA polymerase. Proc. Nat. Acad. Sci. U.S.A. 60, 915-920.
25. Karlin, S. & Mrazek, J. (1996). What drives codon choice in human genes? J. Mol. Biol. 262, 459-471.
26. Kleckner, N. (1997). Interactions between and along chromosomes during meiosis. Harvey Lectures 91, 21-45.
27. Kleckner, N. & Weiner, B. M. (1993). Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic and premeiotic cells. Cold Spring Harbor Symp. Quant. Biol. 58, 553-565.
28. Krol, A. R., van der Mol, J. N. M. & Stuitje, A. R. (1988). Modulation of eukaryotic gene expression by complementary RNA or DNA sequences. Biotechniques 6, 958-976.
29. Lauffer, M. A. (1975). Entropy-driven Processes in Biology. New York, NY: Springer-Verlag.
30. Lobry, J. R. (1995). Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40, 326-330.
31. Lobry, J. R. (1996a). Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13, 660-665.
32. Lobry, J. R. (1996b). Origin of replication of Mycoplasma genitalium. Science 272, 745-746.
33. Marino, J. P., Gregorian, R. S., Csankovszki, G. & Crothers, D. M. (1996). Bent helix formation between RNA hairpins with complementary loops. Science 268, 1448-1454.
34. Melton, D. A. (1985). Injected anti-sense RNAs specifically block messenger RNA translation in vivo. Proc. Nat. Acad. Sci. U.S.A. 82, 144-148.
35. Mrazek, J. & Kypr, J. (1994). Biased distribution of adenine and thymine in gene nucleotide sequences. J. Mol. Evol. 39, 439-447.
36. Murchie, A. I. H., Bowater, R., Aboul-Ela, F. & Lilley, D. M. J. (1992). Helix opening transitions in supercoiled DNA. Biochem. Biophys. Acta 1131, 1-15.
37. Nicolas, A. (1998). Relationship between transcription and initiation of meiotic recombination: Towards chromatin accessibility. Proc. Nat. Acad. Sci. U.S.A. 95, 87-89.
38. Ohta, T. (1996). The current significance and standing of the neutral and near-neutral theories. BioEssays 18, 673-684.
39. Oliver, S. G. et al. (1992). The complete DNA sequence of yeast chromosome III. Nature 357, 38-46.
40. Rudner, R., Karkas, J. D. & Chargaff, E. (1968). Separation of B. Subtilis DNA into complementary strands - III. Direct analysis. Proc. Nat. Acad. Sci. U.S.A. 60, 921-922.
41. Rudner, R., Karkas, J. D. & Chargaff, E. (1969). Separation of microbial deoxyribonucleic acids into complementary strands. Proc. Nat. Acad. Sci. U.S.A. 63, 152-159.
42. Santalucia, J., Allawa, H. T. & Seneviratne, P. A. (1996). Improved nearest neighbour parameters for predicting DNA duplex stability. Biochemistry 35, 3555-3562.
43. Smithies, O., Engels, W. R., Devereux, J. R., Slightom, J. L. & Shen, S. (1981). Base substitutions, length differences and DNA strand asymmetries in the human Gλ and Aλ fetal globin gene region. Cell 26, 345-353.
44. Szybalski, W., Kubinski, H. & Sheldrick, P. (1966). Pyrimidine clusters on the transcribing strands of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harbor Symp. Quant. Biol. 31, 123-127.
45. Tracy, R. B., Chedin, F. & Kowalczykowski, S. C. (1997). The recombinational hot-spot Chi is embedded within islands of preferred DNA pairing sequences in the E. Coli genome. Cell 90, 205-206.
46. Yura, T., Mori, H., Nagai, H., Nagata, T., Ishihama, A., Fijita, N., Isono, K., Mizobuchi, K. & Nakata, A. (1992). Systematic sequencing of the Escherichia coli genome: Analysis of the 0-2.4 min region. Nucl. Acids Res. 20, 3305-3308.
47. Zimmerman, S. B. & Murphy, L. D. (1996). Macromolecular crowding and the mandatory condensation of DNA in bacteria. FEBS Lett 390, 245-248.