Transcription-associated mutational asymmetry in mammalian evolution

Nature Genetics

Volumn 33, Issue 4, 2003, Pages 514-517

  Green, Phil ^a   Ewing, Brent ^a   Miller, Webb ^b   Thomas, Pamela J ^c   Thomas, J ^c   Touchman, J ^c   Blakesley, R ^c   Bouffard, G ^c   Beckstrom Sternberg, S ^c   McDowell, J ^c   Maskeri, B ^c   Smit, A ^c   Haussler, D ^c   Green, Eric D ^c  

^a UNIVERSITY OF WASHINGTON   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYTOSINE;

AMINO ACID SUBSTITUTION; ARTICLE; DEAMINATION; DNA REPLICATION; ENTEROBACTERIACEAE; EVOLUTION; GENETIC TRANSCRIPTION; MUTATION; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; CELL LINEAGE; CHROMOSOMES, HUMAN, PAIR 22; CPG ISLANDS; DATABASES; DNA MUTATIONAL ANALYSIS; EVOLUTION; HUMANS; MODELS, GENETIC; PAPIO; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

ENTEROBACTERIACEAE; MAMMALIA;

EID: 0037380022     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1103     Document Type: Article

References (30)

1. Gojobori, T., Li, W.H. & Graur, D. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18, 360-369 (1982).
2. Li, W.H., Wu, C.I. & Luo, C.C. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21, 58-71 (1984).
3. Hess, S.T., Blake, J.D. & Blake, R.D. Wide variations in neighbor-dependent substitution rates. J. Mol. Biol. 236, 1022-1033 (1994).
4. Li, W.H. Estimating the number of nucleotide substitutions between sequences. in Molecular Evolution (Sinauer Associates, Sunderland, Massachusetts, 1997).
5. Francino, M.P. & Ochman, H. Strand asymmetries in DNA evolution. Trends Genet. 13, 240-245 (1997).
6. Frank, A.C. & Lobry, J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238, 65-77 (1999).
7. Lobry, J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13, 660-665 (1996).
8. Tanaka, M. & Ozawa, T. Strand asymmetry in human mitochondrial DNA mutations. Genomics 22, 327-335 (1994).
9. Francino, M.P., Chao, L., Riley, M.A. & Ochman, H. Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science 272, 107-109 (1996).
10. Beletskii, A. & Bhagwat, A.S. Correlation between transcription and C to T mutations in the non-transcribed DNA strand. Biol. Chem. 379, 549-551 (1998).
11. Francino, M.P. & Ochman, H. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 18, 1147-1150 (2001).
12. Hanawalt, P.C. Transcription-coupled repair and human disease. Science 266, 1957-1958 (1994).
13. Karlin, S. & Altschul, S.F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87, 2264-2268 (1990).
14. Francino, M.P. & Ochman, H. Strand symmetry around the β-globin origin of replication in primates. Mol. Biol. Evol. 17, 416-422 (2000).
15. Wu, C.I. & Maeda, N. Inequality in mutation rates of the two strands of DNA. Nature 327, 169-170 (1987).
16. Bulmer, M. Strand symmetry of mutation rates in the β-globin region. J. Mol. Evol. 33, 305-310 (1991).
17. Sueoka, N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol. 40, 318-325 (1995).
18. Dunham, I. et al. The DNA sequence of human chromosome 22. Nature 402, 489-495 (1999).
19. Tillier, E.R. & Collins, R.A. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J. Mol. Evol. 50, 249-257 (2000).
20. Krawczak, M., Ball, E.V. & Cooper, D.N. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am. J. Hum. Genet. 63, 474-488 (1998).
21. Svejstrup, J.Q. Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell Biol. 3, 21-29 (2002).
22. Leadon, S.A. & Avrutskaya, A.V. Differential involvement of the human mismatch repair proteins, hMLH1 and hMSH2, in transcription-coupled repair. Cancer Res. 57, 3784-3791 (1997).
23. Mellon, I., Rajpal, D.K., Koi, M., Boland, C.R. & Champe, G.N. Transcription-coupled repair deficiency and mutations in human mismatch repair genes. Science 272, 557-560 (1996).
24. Bebenek, K., Joyce, C.M., Fitzgerald, M.P. & Kunkel, T.A. The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I. J. Biol. Chem. 265, 13878-13887 (1990).
25. Mendelman, L.V., Boosalis, M.S., Petruska, J. & Goodman, M.F. Nearest neighbor influences on DNA polymerase insertion fidelity. J. Biol. Chem. 264, 14415-11423 (1989).
26. Jiricny, J. Replication errors: cha(IIe)nging the genome. EMBO J. 17, 6427-6436 (1998).
27. Thomas, J.W. et al. Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12, 1277-1285 (2002).
28. Schwartz, S. et al. Human-mouse alignments with BLA5TZ. Genome Res. 13, 103-107 (2003).
29. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
30. Collins, J.E. et al. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res. 13, 27-36 (2003).