Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes

Genome Research

Volumn 13, Issue 5, 2003, Pages 838-844

  Subramanian, Sankar ^a   Kumar, Sudhir ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GENOMIC DNA; SPACER DNA;

ARTICLE; BABOON; CONTROLLED STUDY; CPG ISLAND; EVOLUTION; EXON; GENE MUTATION; GENE SEQUENCE; GENETIC CODE; HUMAN; INTERMETHOD COMPARISON; INTRON; MACACA; NONHUMAN; NONLINEAR SYSTEM; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; ORANG UTAN; POINT MUTATION; PREDICTION; PRIMATE; PRIORITY JOURNAL; PSEUDOGENE; REGULATORY MECHANISM; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

ANIMALS; BASE COMPOSITION; CPG ISLANDS; DATABASES, GENETIC; DNA, INTERGENIC; EXONS; GENOME; GENOME, HUMAN; HUMANS; MACACA; MODELS, GENETIC; MUTAGENESIS; PAPIO; POINT MUTATION; PONGO PYGMAEUS; PSEUDOGENES;

MACACA; MAMMALIA; PAN TROGLODYTES; PAPIO HAMADRYAS; PONGO PYGMAEUS; PRIMATES;

EID: 0038781903     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1152803     Document Type: Article

References (55)

1. Batzer, M.A., Kilroy, G.E., Richard, P.E., Shaikh, T.H., Desselle, T.D., Hoppens, C.L., and Deininger, P.L. 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18: 6793-6798.
2. Bergstrom, T.F., Erlandsson, R., Engkvist, H., Josefsson, A., Erlich, H.A., and Gyllensten, U. 1999. Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences. Immunol. Rev. 167: 351-365.
3. Bielawski, J.P., Dunn, K.A., and Yang, Z. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions. Genetics 156: 1299-1308.
4. Bird, A. 1999. DNA methylation de novo. Science 286: 2287-2288.
5. Bird, A.P. 1980. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8: 1499-1504.
6. Bohossian, H.B., Skaletsky, H., and Page, D.C. 2000. Unexpectedly similar rates of nucleotide substitution found in male and female hominids, Nature 406: 622-625.
7. Britten, R.J., Baron, W.F., Stout, D.B., and Davidson, E.H. 1988. Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. 85: 4770-4774.
8. Caccio, S., Jabbari, K., Matassi, G., Guermonprez, F., Desgres, J., and Bernardi, G. 1997. Methylation patterns in the isochores of vertebrate genomes. Gene 205: 119-124.
9. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N., et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
10. Chen, F.C., Vallender, E.J., Wang, H., Tzeng, C.S., and Li, W.H. 2001. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J. Hered. 92: 481-489.
11. Cooper, D.N. and Krawczak, M. 1989. Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet. 83: 181-188.
12. Coulondre, C., Miller, J.H., Farabaugh, P.J., and Gilbert, W. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775-780.
13. Denver, D.R., Morris, K., Lynch, M., Vassilieva, L.L., and Thomas, W.K. 2000. High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289: 2342-2344.
14. Drake, J.W., Charlesworth, B., Charlesworth, D., and Crow, J.F. 1998. Rates of spontaneous mutation. Genetics 148: 1667-1686.
15. Duret, L., Mouchiroud, D., and Gouy, M. 1994. HOVERGEN: A database of homologous vertebrate genes. Nucleic Acids Res. 22: 2360-2365.
16. Duret, L., Semon, M., Piganeau, G., Mouchiroud, D., and Galtier, N. 2002. Vanishing GC-rich isochores in mammalian genomes. Genetics 162: 1837-1847.
17. Easteal, S. 1991. The relative rate of cDNA evolution in primates. Mol. Biol. Evol. 8: 115-127.
18. Ebersberger, I., Metzler, D., Schwarz, C., and Paabo, S. 2002. Genome-wide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70: 1490-1497.
19. Giannelli, F., Anagnostopoulos, T., and Green, P.M. 1999. Mutation rates in humans. II. Sporadic mutation-specific rates and rate of detrimental human mutations inferred from hemophilia B. Am. J. Hum. Genet. 65: 1580-1587.
20. Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R., and Chakravarti, A. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22: 239-247.
21. Hardison, R.C., Roskin, K.M., Yang, S., Diekhans, M., Kent, W.J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, D., et al. 2003. Covariation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Res. 13: 13-26.
22. Hedges, S.B. and Kumar, S. 2003. Genomic clocks and evolutionary timescales. Trends Genet. (in press).
23. Hendrich, B., Hardeland, U., Ng, H.H., Jiricny, J., and Bird, A. 1999. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401: 301-304.
24. 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.
25. Karlin, S. and Mrazek, J. 1997. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. 94: 10227-10232.
26. Keightley, P.D. and Eyre-Walker, A. 2000. Deleterious mutations and the evolution of sex. Science 290: 331-333.
27. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.
28. Kondrashov, A.S. and Crow, J.F. 1993. A molecular approach to estimating the human deleterious mutation rate. Hum. Mutat. 2: 229-234.
29. Krawczak, M., Ball, E.V., and Cooper, D.N. 1998. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am. J. Hum. Genet. 63: 474-488.
30. Kumar, S. and Hedges, B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-919.
31. Kumar, S. and Subramanian, S. 2002. Mutation rates in mammalian genomes. Proc. Natl. Acad. Sci. 99: 803-808.
32. Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17: 1-2.
33. Li, W.-H. and Graur, D. 1991. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA.
34. Li, W.-H. and Tanimura, M. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93-96.
35. Lynch, M., Blanchard, J., Houle, D., Kibota, T., Schultz, S., Vassilieva, L., and Willis, J. 1999. Perspective: Spontaneous deleterious mutation. Evolution 53: 645-663.
36. Martinez-Arias, R., Calafell, F., Mateu, E., Comas, D., Andres, A., and Bertranpetit, J. 2001. Sequence variability of a human pseudogene. Genome Res. 11: 1071-1085.
37. Mathews, D.J., Kashuk, C., Brightwell, G., Eichler, E.E., and Chakravarti, A. 2001. Sequence variation within the fragile X locus. Genome Res. 11: 1382-1391.
38. Moriyama, E.N. and Powell, J.R. 1996. Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
39. Nachman, M.W. and Crowell, S.L. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
40. Nei, M. and Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford University Press, New York, NY.
41. Ponger, L., Duret, L., and Mouchiroud, D. 2001. Determinants of CpG islands: Expression in early embryo and isochore structure. Genome Res. 11: 1854-1860.
42. Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L., et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
43. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
44. Smith, N.G., Webster, M.T., and Ellegren, H. 2002. Deterministic mutation rate variation in the human genome. Genome Res. 12: 1350-1356.
45. Springer, M.S., Murphy, W.J., Eizirik, E., and O'Brien, S.J. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. 100: 1056-1061.
46. Sved, J. and Bird, A. 1990. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl. Acad. Sci. 87: 4692-4696.
47. Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
48. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
49. Wolfe, K.H., Sharp, P.M., and Li, W.-H. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
50. Yang, A.S., Gonzalgo, M.L., Zingg, J.M., Millar, R.P., Buckley, J.D., and Jones, P.A. 1996. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J. Mol. Biol. 258: 240-250.
51. Yi, S., Ellsworth, D.L., and Li, W.H. 2002. Slow molecular clocks in old world monkeys, apes, and humans. Mol. Biol. Evol. 19: 2191-2198.
52. Yu, N., Zhao, Z., Fu, Y.X., Sambuughin, N., Ramsay, M., Jenkins, T., Leskinen, E., Patthy, L., Jorde, L.B., Kuromori, T., et al. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18: 214-222.
53. Zhao, Z., Jin, L., Fu, Y.X., Ramsay, M., Jenkins, T., Leskinen, E., Pamilo, P., Trexler, M., Patthy, L., Jorde, L.B., et al. 2000. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. 97: 11354-11358.
54. Zmasek, C.M. and Eddy, S.R. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
55. Zwick, M.E., Cutler, D.J., and Chakravarti, A. 2000. Patterns of genetic variation in Mendelian and complex traits. Annu. Rev. Genomics Hum. Genet. 1: 387-407.