The causes of synonymous rate variation in the rodent genome: Can substitution rates be used to estimate the sex bias in mutation rate?

Genetics

Volumn 152, Issue 2, 1999, Pages 661-673

  Smith, Nick G C ^a,b   Hurst, Laurence D ^a  

^a University of Bath   (United Kingdom)

^b UNIVERSITY OF BATH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFACT; AUTOSOME; EVOLUTION; GENE REPLICATION; GENETIC VARIABILITY; GENOME; GERM LINE; MUTATION RATE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; RODENT; SEX DIFFERENCE; SILENT GENE; STATISTICAL ANALYSIS; X CHROMOSOME LINKAGE; Y CHROMOSOME LINKAGE;

RODENTIA;

EID: 0033054281     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (62)

1. AKASIII, H., 1994 S)iion)mous codon usage in Drosophila melanogaster-natural selection and translational accuracy. Genetics 136: 927-935.
2. ALTSCIIUI., S. F., 1997 Sequence comparison and alignment, pp. 137-168 in DXA and Protein Sequence Analysis, edited by M. J. BISHOP and C. J. RAWLINGS. Oxford University Press, Oxford.
3. AITSCIIUL, S. F., T. L. MADDEN, A. A. SCHAFFERJ. H. ZIIANG, Z. ZIIANG etal, 1997 Gapped BI AST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3-402.
4. BAUER, V. L., and C. F. AQUADRO, 1997 Rates of DNA sequence evolution are not sex-biased in Drosophila melanogaster and D-simulans. Mol. Biol. Evol. 14: 1252-1257.
5. BUIMFR, M., 1986 Neighboring base effects on substitution rates in pseudogenes. Mol. Biol. Evol. 3: 322-329.
6. BUIMFK, M., 1990 The effects of context on synonymous codon usage in genes with low codon usage bias. Nucleic Acids Res. 18: 2869-2873.
7. CIIANC, B. HJ., and W-H. Li, 1995 Estimating the intensity of maledriven evolution in rodents by using X-linked and Y-linkcd Ube-1 genes and pseudogenes. J. Mol. Evol. 40: 70-77.
8. CIIANG, B. H. J., L. C. SIIIMMIK, S. K. SHYUE, D. HEWETT-EMMETT and W-H. Li, 1994 Weak male-driven molecular evolution in rodents. Proc. Natl. Acad. Sei. USA 91: 827-831.
9. CIIARIKSWORTII, B,J. A. COVNE and N. H. BARTON, 1987 The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130: 113-146.
10. COMFRONJ. M., and M. AGUADE, 1998 An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47: 268-274.
11. CONSTANCIA, M., B. PICKARU, G. KELSEY and W. REIK, 1998 Imprinting mechanisms. Genet. Res. 8: 881-900.
12. CUIIAT, C. T., L. J. STUBBS, R. P. WOVCIIIK, L. B. RUSSFII., D. K. JOHNSON el al, 1995 Deficiency of the beta-3 subimit of the type-a gamma-aminobutyric-acid receptor causes cleft-palate in mice. Nat. Genet. 11: 344-346.
13. DKIORKY, T. M., A. HANDFORTII, S. G. ANAGOSTARAS, G. E. ROMANICS, B. A. MINASSIAN et al., 1998 Mice lacking the bctaS subunit of the GABAA receptor have the epilepsy phenotype and many of the behavioural characteristics of Angelman syndrome. J. Neurosci. 18: 8505-8514.
14. DURFT, I., D. MoucniROun and M. Gouv, 1994 Hovergen-a database of homologous vertebrate genes. Nucleic Acids Res. 22: 23GO-23C5.
15. EFSTRATIADIS, A., 1994 Parental imprinting of autosomal mammalian genes. Curr. Opin. Genet. Dcv. 4: 265-280.
16. EYRE-WAIKKR, A., 1991 An analysis of codon usage in mammals: selection or mutation biasPJ. Mol. Evol. 33: 442-449.
17. GENETICS COMPUTER GROUP, 1994 Program Manual for the Wisconsin Package, Version 8, September 1994, Genetics Computer Group, 575 Science Drive, Madison, Wisconsin 53711.
18. HAI,DANK, J. B. S., 1947 The mutation rate of the gene for hemophilia and its segregation ratios in males and females. Ann. Fugen. 13: 262-271.
19. HUGHES, A. L., and MYEAGER, 1997 Comparative evolutionary-rates of introns and cxons in murine rodentsJ. Mol. Evol. 45:125-130.
20. HURST, L. D., and H. EIIKGRKN, 1998 Sex biases in the mutation rate. Trends Genet. 14: 446-452.
21. KENDREW, J. (Editor), 1994 The Encyclopedia of Molecular Biology. Blackwcll, Oxford.
22. KKTTKRIING, R. P., E. VIELIIABER, C. D. K. BOTTEMA, D. J. SCIIAIII, M. P. COIIFN et al., 1993 Germ-line origins of mutation in families with hemophilia-B: the sex-ratio varies with the type of mutation. Am. J. Hum. Genet. 52: 152-166.
23. KIMURA, M., 1980 A simple method for estimating evolutionary-rates of base substitutions through comparative studies of nucleotidc sequences. J. Mol. Evol. 16: 111-120.
24. KIMURA, M., 1983 The Neutral Theory of Evolution. Cambridge University Press, Cambridge, United Kingdom.
25. Li, W. H., 1993 Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
26. Li, W. II., 1997 Molecular Evolution. Sinauer Associates, Sunderland, MA.
27. Li,W. H,C. I. Wu and C. C. luo, 1985 A new method for estimating synonymous and nonsynonymous rates of nucleotidc substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
28. MAKAIOWSKIW., andM. S. BOGUSKI, 1998 Evolutionary-parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sei. USA 95: 9407-9412.
29. McVKAN, G. T., and L. D. HURST, 1997 Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature 386: 388-392.
30. McVEANGT., L. D. HURST and T. MOORE, 199G Genomic evolution in mice and men-imprinted genes have little intronic content. Bioessays 18: 773-775.
31. MEGURO, M., K. MITSUVA, H. Sui, K. SHIGEXAMI, H. KUGOII et al, 1997 Evidence for uniparental, paternal expression of the human GABA(A) receptor subunit genes, using microcell-mediated chromosome transfer. Hum. Mol. Genet. 6: 2127-2133.
32. MILLER, N., A. H. MCCANN, D. O'CoN'NELL, I. S. PEDERSEN, V. SPIERS et al, 1997 The MAS proto-oncogene is imprinted in human breast tissue. Genomics 46: 509-512.
33. MIYATAT., H. HAVASHIDA, K. KUMA, K. MiTSuvAsuandT. YASUNAGA, 1987 Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symp. Quant. Biol. 52: 863-867.
34. MONK, M., M. BOUBEIIK and S. LEHNERT, 1987 Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineage during mouse embryo development. Development 99: 371-386.
35. MORIYAMA, E. N., andj. R. POWKIJ, 1997 Synonymous substitution rates in Drosophila: Mitochondria! versus nuclear genes. J. Mol. Evol. 45: 378-391.
36. MORIYAMA, E. N., andj. R. POWKIJ, 1998 Gene length and codon usage bias in Drosophila mclanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26: 3188-3193.
37. MORTON, B. R., and M. T. CLEGG, 1995 Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome. J. Mol. Evol. 41: 597-603.
38. MORTOV, B. R., V. M. QUERHoLZER and M. T. CI-KCG, 1997 The influence of specific neighboring bases on substitution bias in noncocling regions of the plant chloroplnst genome. J. Mol. Evol. 45: 227-231.
39. MOUCIIIROUD, D., C. GAUTIER and G. BERNARDI, 1995 Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40: 107-113.
40. NEUMANN, B., P. KuniCKA and D. P. BARLOW, 1995 Characteristics of imprinted genes. Nat. Genet. 9: 12-13.
41. OIIANO, I., T. ANKZAKI, H. OIIKUBO, Y. YONKKURA, Y. ONISIII el al, 1996 Decrease in bcnzodiazepinc receptor-binding in a patient with Angelman Syndrome detected by 1-123 iomazenil and singlephoton emission tomography. Eur. J. Nucl. Med. 23: 598-604.
42. PIASS, C., H. SIIIBATA, I. KAICIIEVA, L. MUIIINS, N. KOTEIKiTSKVA et al., 1996 Identification of Grfl on mouse chromosome 9 as an imprinted gene by RLGS-M. Nat. Genet. 14: 106-109.
43. RICK, P., 1997 Program Manual for the EGCG Package. The Snngcr Centre, Hinxton Hall, Cambridge, CB10 IRQ, England.
44. RIESEWIJK, A. M., M. T. SciiKi'KNS, E. M. MAKIMAN, H. H. ROPERS and V. M. KAISCIIEUER, 1996 The MAS protooncogene is not imprinted in humans. Gcnomics 35: 380-382.
45. SAITOII, S., N. HARAIIA, YJiNNO, K. HASIIIMOTO, K. IMAIZUMI et al, 1994 Molecular and clinical-study of 61 angelman-syndrome patients. Am. J. Med. Genet. 52: 158-163.
46. SCIIWKIKEK, N., P. J. M. VAIK, R. DEIAVEL, R. Cox, F. FRANCIS el al, 1997 Characterization of the C3 YAC contig from proximal mouse chromosome 17 and analysis of allelic expression of genes flanking the imprinted Igf2r gene. Gcnomics 43: 285-297.
47. SHARP, P. M., and W. H. Li, 19S9 On the rale of DNA sequence evolution in Dtvsophila. J. Mol. Evol. 28: 398-402.
48. SHIELDS, D. C., P. M. SHARP, D. G. HIGCINS and F. WRIGHT, 1988 Silent sites in Drosophila genes arc not neutral-evidence of selection among synonymous codons. Mol. Biol. Evol. 5:704-716.
49. SIIIMMIN, L. C., B. H. J. CHAXG, D. HEWETT-EMMETT and W. H. Ii, 1993 Potential problems in estimating the niale-to-fcmalc mutation rate ratio from DNA sequence data. J. Mol. Evol. 37: 160-166.
50. SHIMMiN, L. C., B. H. J. CIIANG and W. H. Ll, 1994 Contrasting rates of nucleotide substitution in the X-linkcd and Y-Iinkcd zincfinger genes. J. Mol. Evol. 39: 569-578.
51. SMITH, N. G. C., and L. D. HURST, 1998a Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor. Genetics 150: 823-833.
52. SMITH, N. G. C., and L. D. HURST, 1998b Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager. J. Mol. Evol. 47: 493-500.
53. SOKAI, R. R., and F. J. ROIIIK, 1995 Biometry. W. H. Freeman and Company, New York.
54. TAMURA, K., 1992 Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases. Mol. Biol. Evol. 10: 512-52G.
55. TERAIIA, N., K. KUMA and T. MIYATA, 1997 Verification of maledriven molecular evolution. Genes Genet. Syst. 72: 428.
56. THOMPSON,!. D., D. G. HIGGINS and TJ. GIBSON, 1994 ClustalWimproving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
57. VIIIWR, A. J., and R. A. PEDERSEN, 1994 1994 parental imprinting of the Mas protooncogene in mouse. Nat. Genet. 8: 373-379.
58. WENTWORTII, B. M., I. M. SCIIAEFEK, L. VIUA-KOMAROKK and J. M. CIIIRGWIN, 1986 Characterization of the two nonallclic genes encoding mouse prcproînsulin. J. Mol. Evol. 23: 305-312.
59. WOLKE, K. H., and P. M. SHARP, 1993 Mammalian gene evolutionnucleotide-scquencc divergence between mouse and rat. J. Mol. Evol. 37: 441-456.
60. WRIGHT, F., 1990 The effective number of codons used in a gene. Gene 87: 23-29.
61. YANG, Z., 1997 PAML: a program package for phylogcnetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
62. YANG, W., K. CIIKN, N. C. IAN, T. K. GAIIJMIER and J. C. Sum, 1992 Gene structure and expression of the mouse 5-HT2 receptor. J. Neurosci. Res. 33: 196-204.