Modeling the impact of DNA methylation on a the evolution of BRCA1 in mammals

Molecular Biology and Evolution

Volumn 21, Issue 9, 2004, Pages 1760-1768

  Huttley, Gavin A ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

BRCA1; Codon substitution model; CpG; DNA methylation; Maximum likelihood; Molecular evolution

Indexed keywords

5 METHYLCYTOSINE; BRCA1 PROTEIN; DINUCLEOTIDE; DNA; NUCLEOTIDE;

ARTICLE; CODON; CODON SUBSTITUTION; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; EXON; GENE MUTATION; MAMMAL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; PROBABILITY; SPONTANEOUS MUTATION; STATISTICAL ANALYSIS;

ANIMALS; BIOMETRY; CHIROPTERA; CPG ISLANDS; DNA METHYLATION; EVOLUTION, MOLECULAR; GENES, BRCA1; HUMANS; MAMMALS; MODELS, GENETIC; PRIMATES;

MAMMALIA; PRIMATES;

EID: 4143132023     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh187     Document Type: Article

References (32)

1. Butterfield, A., V. Vedagiri, E. Lang, C. Lawrence, M. J. Wakefield, A. Isaev, and G. A. Huttley. 2004. PyEvolve: a toolkit for statistical modelling of molecular evolution. BMC Bioinformat. 5:1.
2. Cooper, D. N., and H. Youssoufian. 1988. The CpG dinucleotide and human genetic disease. Hum. Genet. 78:151-155.
3. Coulondre, C., J. H. Miller, P. J. Farabaugh, and W. Gilbert. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775-780.
4. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
5. Girard, M., P. Couvert, A. Carrie, M. Tardieu, J. Chelly, C. Beldjord, and T. Bienvenu. 2001. Parental origin of de novo MECP2 mutations in Rett syndrome. Eur. J. Hum. Genet. 9:231-236.
6. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
7. Haines, T. R., D. I. Rodenhiser, and P. J. Ainsworth. 2001. Allele-specific non-CpG methylation of the Nfl gene during early mouse development. Dev. Biol. 240:585-598.
8. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
9. Huttley, G. A., S. Easteal, M. C. Southey, G. G. Giles, M. R. E. McCredie, J. L. Hopper, and D. J. Venter. 2000a. Adaptive evolution of the tumor suppressor BRCA1 in humans and chimpanzees. Nat. Genet. 24:410-413.
10. Huttley, G. A., I. B. Jakobsen, S. R. Wilson, and S. Easteal. 2000b. How important is DNA replication for mutagenesis? Mol. Biol. Evol. 17:929-937.
11. Killian, J. K., T. R. Buckley, N. Stewart, B. L. Munday, and R. L. Jirtle. 2001. Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution. Mammal. Genome 12:513-517.
12. Monk, M., M. Boubelik, and S. Lehnert. 1987. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99:371-382.
13. Murphy, W. J., E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
14. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
15. Ota, R., P. J. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol. Biol. Evol. 17:798-803.
16. Pedersen, A. K., C. Wiuf, and F. B. Christiansen. 1998. A codon-based model designed to describe lentiviral evolution. Mol. Biol. Evol. 15:1069-1081.
17. Pedersen, A. M., and J. L. Jensen. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol. 18:763-776.
18. Ramsahoye, B. H., D. Biniszkiewicz, F. Lyko, V. Clark, A. P. Bird, and R. Jaenisch. 2000. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA 97:5237-5242.
19. Reik, W., and J. Walter. 2001a. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2:21-32.
20. -. 2001b. Evolution of imprinting mechanisms: the battle of the sexes begins in the zygote. Nat. Genet. 27:255-256.
21. Rideout, W. M., 3rd, G. A. Coetzee, A. F. Olumi, and P. A. Jones. 1990. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 249:1288-1290.
22. Rousseau, F., J. Bonaventure, L. Legeai-Mallet, A. Pelet, J. M. Rozet, P. Maroteaux, M. Le Merrer, and A. Munnich. 1994. Mutations in the gene encoding fibroblast growth factor receptor-3 in achondroplasia. Nature 371:252-254.
23. Schmitz, J., M. Ohme, B. Suryobroto, and H. Zischler. 2002. The colugo (Cynocephalus variegatus, Dermoptera): the primates' gliding sister? Mol. Biol. Evol. 19:2308-2312.
24. Siepel, A., and D. Haussler. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21:468-488.
25. Sommer, S. S., W. A. Scaringe, and K. A. Hill. 2001. Human germline mutation in the factor IX gene. Mut. Res. 487:1-17.
26. Templeton, A. R., A. G. Clark, K. M. Weiss, D. A. Nickerson, E. Boerwinkle, and C. F. Sing. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66:69-83.
27. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
28. Tomatsu, S., K. O. Orii, M. R. Islam, G. N. Shah, J. H. Grubb, K. Sukegawa, Y. Suzuki, T. Orii, N. Kondo, and W. S. Sly. 2002. Methylation patterns of the human beta-glucuronidase gene locus: boundaries of methylation and general implications for frequent point mutations at CpG dinucleotides. Genomics 79:363-375.
29. Trappe, R., F. Laccone, J. Cobilanschi, M. Meins, P. Huppke, F. Hanefeld, and W. Engel. 2001. MECP2 mutations in sporadic cases of Rett syndrome are almost exclusively of paternal origin. Am. J. Hum. Genet. 68:1093-1101.
30. Tsunoyama, K., M. I. Bellgard, and T. Gojobori. 2001. Intragenic variation of synonymous substitution rates is caused by nonrandom mutations at methylated CpG. J. Mol. Evol. 53:456-464.
31. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform Ser Workshop Genome Inform 12:141-154.
32. Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.