Strand compositional asymmetries of nuclear DNA in eukaryotes

Journal of Molecular Evolution

Volumn 57, Issue 3, 2003, Pages 325-334

  Niu, Deng K ^a   Lin, Kui ^a   Zhang, Da Yong ^a  

^a BEIJING NORMAL UNIVERSITY   (China)

Author keywords

DNA replication; Eukaryote; Mutational bias; Single strand; Strand asymmetry; Transcription

Indexed keywords

CELL NUCLEUS DNA;

AMINO ACID SUBSTITUTION; ANOPHELES GAMBIAE; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CODON; CODON USAGE; DNA REPLICATION; DNA STRAND; DNA TRANSCRIPTION; DROSOPHILA MELANOGASTER; ENCEPHALITOZOON CUNICULI; EUKARYOTE; PLASMODIUM FALCIPARUM; REPLICON; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

ANIMALS; BASE COMPOSITION; CODON; DNA; DNA REPLICATION; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENOME; HUMANS; MODELS, GENETIC; MUTATION;

ANOPHELES GAMBIAE; ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; ENCEPHALITOZOON CUNICULI; EUKARYOTA; HOMO; HOMO SAPIENS; MELANOGASTER; MUS; MUS MUSCULUS; MUSCULUS; PLASMODIUM FALCIPARUM; PROKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 0042834265     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2483-9     Document Type: Article

References (50)

1. Adams MD, Celniker SE, Holt RA, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287:2185-2195
2. Beletskii A, Bhagwat AS (2001) Transcription-induced cytosine-to-thymine mutations are not dependent on sequence context of the target cytosine. J Bacteriol 183:6491-6493
3. Blattner FR, Plunkett G III, Bloch CA, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462
4. Brewer BJ, Fangman WL (1993) Initiation at closely spaced replication origins in a yeast chromosome. Science 262:1728-1731
5. Bulmer M (1991) Strand symmetry of mutation-rates in the beta-globin region. J Mol Evol 33:305-310
6. Buss LW (1987) The evolution of individuality. Princeton University Press, Princeton, NJ
7. Fijalkowska IJ, Jonczyk P, Tkaczyk MM, Bialoskorska M, Schaaper RM (1998) Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc Natl Acad Sci USA 95:10020-10025
8. Francino MP, Ochman H (2000) Strand symmetry around the β-globin origin of replication in primates. Mol Biol Evol 17:416-422
9. Francino MP, Ochman H (2001) Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol Biol Evol 18:1147-1150
10. Frank AC, Lobry JR (1999) Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms. Gene 238:65-77
11. Fraser CM, Casjens S, Huang WM, et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-586
12. Frederico LA, Kunkel TA, Shaw BR (1990) A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy. Biochemistry 29:2532-2537
13. Gardner MJ, Hall N, Fung E, et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498-511
14. Gawel D, Jonczyk P, Bialoskorska M, Schaaper RM, Fijalkowska IJ (2002) Asymmetry of frameshift mutagenesis during leading and lagging-strand replication in Escherichia coli. Mutat Res 501:129-136
15. Gierlik A, Kowalczuk M, Mackiewicz P, Dudek MR, Cebrat S (2000) Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J Theor Biol 202:305-314
16. Goffeau A, Barrell BG, Bussey H, et al. (1996) Life with 6000 genes. Science 274:546-567
17. Graur D, Li W-H (2000) Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA
18. Green P, Ewing B, Miller W, et al. (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nature Genet 33:514-517
19. Grigoriev A (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 26:2286-2290
20. Grigoriev A (1999) Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Res 60:1-19
21. Holt RA, Subramanian GM, Halpern A, et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149
22. Hyrien O, Marheineke K, Goldar A (2003) Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays 25:116-125
23. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
24. Izuta S, Roberts JD, Kunkel TA (1995) Replication error rates for G·GTP, T·GTP, and A·GTP mispairs and evidence for differential proofreading by leading and lagging strand DNA replication complexes in human cells. J Biol Chem 270:2595-2600
25. Katinka MD, Duprat S, Cornillot E, et al. (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450-453
26. Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S (2001) DNA asymmetry and the replicational mutational pressure. J Appl Genet 42:553-577
27. Kunkel TA (1992) Biological asymmetries and the fidelity of eukaryotic DNA replication. Bioessays 14:303-308
28. Kunst F, Ogasawara N, Moszer I, et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256
29. Lewin B (1997) Genes VI. Oxford University Press, Oxford
30. Lobry JR (1995) Properties of a general-model of DNA evolution under no-strand-bias conditions. J Mol Evol 40:326-330
31. Lobry JR (1996a) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13:660-665
32. Lobry JR (1996b) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78:323-326
33. Lobry JR, Lobry C (1999) Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant. Mol Biol Evol 16:719-723
34. McLean MJ, Wolfe KH, Devine KM (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47:691-696
35. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
36. Mrazek J, Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 95:3720-3725
37. Picardeau M, Lobry JR, Hinnebusch BJ (2000) Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Res 10:1594-1604
38. Raghuraman MK, Winzeler EA, Collingwood D, et al. (2001) Replication dynamics of the yeast genome. Science 294:115-121
39. Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 15:957-966
40. Rocha EPC, Danchin A (2001) Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 18:1789-1799
41. Rocha EPC, Danchin A, Viari A (1999) Universal replication biases in bacteria. Mol Microbiol 32:11-16
42. Shioiri C, Takahata N (2001) Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry. J Mol Evol 53:364-376
43. Sueoka N (1995) Intrastrand parity rules of DNA-base composition and usage biases of synonymous codons. J Mol Evol 40:318-325
44. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
45. The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018
46. Tillier ERM, Collins RA (2000) The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 50:249-257
47. Wood V, Gwilliam R, Rajandream MA, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880
48. Wu CI, Maeda N (1987) Inequality in mutation-rates of the 2 strands of DNA. Nature 327:169-170
49. Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP, Aparicio OM (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: High-resolution mapping of replication origins. Science 294:2357-2360
50. Zawilak A, Cebrat S, Mackiewicz P, Krol-Hulewicz A, Jakimowicz D, Messer W, Gosciniak G, Zakrzewska-Czerwinska J (2001) Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA. Nucleic Acids Res 29:2251-2259