Chromosomal location effects on gene sequence evolution in mammals

Current Biology

Volumn 9, Issue 15, 1999, Pages 786-791

  Matassi, Giorgio ^a,c   Sharp, Paul M ^a   Gautier, Christian ^b  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b UNIVERSITÉ LYON 1   (France)

^c INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOSOME; CHROMOSOMAL LOCALIZATION; EVOLUTION; GENE LOCATION; MAMMALIAN GENETICS; NUCLEOTIDE SEQUENCE;

MAMMALIA; MURIDAE;

EID: 0033615073     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-9822(99)80361-3     Document Type: Article

References (62)

1. Kimura M: Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 1977, 267:275-276.
2. Sueoka N: Directional mutation pressure, selective constraints and genetic equilibria. Proc Natl Acad Sci USA 1991, 85:2653-2657.
3. Filipski J: Why the rate of silent codon substitutions is variable within a vertebrate's genome. J Theor Biol 1988, 134:159-164.
4. Wolfe KH, Sharp PM, Li WH: Mutation rates differ among regions of the mammalian genome. Nature 1989, 337:283-285.
5. Eyre-Walker A: An analysis of codon usage in mammals: Selection or mutation bias? J Mol Evol 1991, 33:504-510.
6. Ikemura T, Wada K: Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res 1991, 19:4333-4339.
7. Wolfe KH, Sharp PM: Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat. J Mol Evol 1993, 37:441-456.
8. Bernardi G: The human genome: Organization and evolutionary history. Annu Rev Genet 1995, 29:445-476.
9. Aota S, Ikemura T: Diversity in G+C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res 1986, 14:6345-6355.
10. Mouchiroud D, D'Onofrio G, Aissani B, Macaya G, Gautier C, Bernardi G: The distribution of genes in the human genome. Gene 1991, 100:181-187.
11. D'Onofrio G, Mouchiroud D, Aissani B, Gautier C, Bernardi G: Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 1991, 32:504-510.
12. Ikemura T, Wada K, Aota S: Giant G+C% mosaic structures of the human genome found by arrangement of GenBank human DNA sequences according to genetic positions. Genomics 1990, 8:207-216.
13. Fukagawa T, Sugaya K, Matsumoto K, Okumura K, Ando A, Inoko H, et al.: A boundary of long-range G+C% mosaic domains in the human MHC locus: Pseudoautosomal boundary-like sequence exists near the boundary. Genomics 1995, 25:184-191.
14. Bulmer M, Wolfe KH, Sharp PM: Synonymous nucleotide substitution rates in mammalian genes: Implications for the molecular clock and the relationship of mammalian orders. Proc Natl Acad Sci USA 1991, 88:5974-5978.
15. Mouchiroud D, Gautier C, Bernardi G: Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J Mol Evol 1995, 40:107-113.
16. Mouchiroud D, Robinson M, Gautier C: Impact of changes in GC content on the silent molecular clock in murids. Gene 1997, 205:317-322.
17. Ticher A, Graur D: Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J Mol Evol 1989, 28:286-298.
18. Bernardi G, Mouchiroud D, Gautier C: Silent substitutions in mammalian genomes and their evolutionary implications. J Mol Evol 1993, 37:583-589.
19. The Jackson Laboratory: Chromosome Committee Reports. 1997.
20. Zoubak S, Clay O, Bernardi G: The gene distribution of the human genome. Gene 1996, 174:95-102.
21. Nei M: Molecular Evolutionary Genetics. New York: Columbia University Press; 1987.
22. Makalowski W, Boguski MS: Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA 1998, 95:9407-9412.
23. Macaya G, Thiery JP, Bernardi G: An approach to the organization of eukaryotic genomes and their evolutionary implications. J Mol Biol 1976, 108:237-254.
24. Bettecken T, Aissani B, Muller CR, Bernardi G: Compositional mapping of the human dystrophin-encoding gene. Gene 1992, 122:329-335.
25. Silver LM: Mouse Genetics. Concepts and Applications. Oxford: Oxford University Press; 1995.
26. Sharp PM, Matassi G: Codon usage and genome evolution. Curr Opin Genet Dev 1994, 4:851-860.
27. Koop BF: Human and rodent DNA sequence comparison: A mosaic model of genomic evolution. Trends Genet 1995, 11:367-371.
28. Casane D, Boissinot S, Chang BH, Shimmin LC, Li WH: Mutation pattern variation among regions of the primate genome. J Mol Evol 1997, 45:216-226.
29. Koop BF, Hood L: Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat Genet 1994, 7:48-53.
30. Epp TA, Wang R, Sole MJ, Liew CC: Concerted evolution of mammalian cardiac myosin heavy chain genes. J Mol Evol 1995, 41:284-292.
31. Oeltjen JC, Malley TM, Muzny DM, Miller W, Gibbs RA, Belmont JW: Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res 1997, 7:315-329.
32. den Dunnen JT, van Neck JW, Cremers FP, Lubsen NH, Schoenmakers JG: Nucleotide sequence of the rat gamma-crystallin gene region and comparison with an orthologous human region. Gene 1989, 78:201-213.
33. Shehee WR, Loeb DD, Adey NB, Burton FH, Casavant NC, Cole P, et al.: Nucleotide sequence of the BALB/c mouse beta-globin complex. J Mol Biol 1989, 205:41-62.
34. Hardison R, Krane D, Vandenbergh D, Cheng JF, Mansberger J, Taddie J, et al.: Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G+C-rich region of mammalian genomes. J Mol Biol 1991, 222:233-249.
35. Lamerdin JE, Montgomery MA, Stilwagen SA, Scheidecker LK, Tebbs RS, Brookman KW, et al.: Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions. Genomics 1995, 25:547-554.
36. Lamerdin JE, Stilwagen SA, Ramirez MH, Stubbs L, Carrano AV: Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes. Genomics 1996, 34:399-409.
37. Koop BF, Richards JE, Durfee TD, Bansberg J, Wells J, Gilliam AC, et al.: Analysis and comparison of the mouse and human immunoglobulin heavy chain JH-Cmu-Cdelta locus. Mol Phylogenet Evol 1996, 5:33-49.
38. Ansari-Lari MA, Oeltjen JC, SChwartz S, Zhang Z, Muzny DM, Lu J, et al.: Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res 1998, 8:29-40.
39. Lichtenauer-Kaligis EG, Van Der Velde-Van Dijke I, Den Dulk H, Van De Putte P, Giphart-Gassler M, Tasseron-De Jong JG: Genomic position influences spontaneous mutagenesis of an integrated retroviral vector containing the hprt cDNA as target for mutagenesis. Hum Mol Genet 1993, 2:173-182.
40. Maynard-Smith J, Haigh J: The hitch-hiking effect of a favourable gene. Genet Res 1974, 23:23-25.
41. Charlesworth D, Charlesworth B: Sequence variation: Looking for effects of genetic linkage. Curr Biol 1998, 8:R658-R661.
42. Birky CW, Walsh JB: Effects of linkage on rates of molecular evolution. Proc Natl Acad Sci USA 1988, 85:6414-6418.
43. Holmquist GP, Filipksi J: Organization of mutations along the genome: A prime determinant of genome evolution. Trends Ecol Evol 1994, 9:65-69.
44. Boulikas T: The evolutionary consequences of nonrandom damage and repair of chromatin domains. J Mol Evol 1992, 35:156-180.
45. Holmquist GP: Endogenous lesions, S-phase-independent spontaneous mutations, and evolutionary strategies for base excision repair. Mutation Res 1998, 400:59-68.
46. Eyre-WAlker A: DNA mismatch repair and synonymous codon evolution in mammals. Mol Biol Evol 1994, 11:88-98.
47. Bohr VA, Smith CA, Okumoto DS, Hanawalt PC: DNA repair in an active gene: Removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell 1985, 40:359-369.
48. Bohr VA, Phillips DH, Hanawalt PC: Heterogeneous DNA damage and repair. Cancer Res 1987, 47:6426-6436.
49. Hanawalt PC: Preferential repair of damage in actively transcribed DNA sequences in vivo. Genome 1989, 31:605-611.
50. Svetlova MP, Solovjeva LV, Pleskach NA, Tomilin NV: Focal sites of DNA repair synthesis in human chromosomes. Biochem Biophys Res Commun 1999, 257:378-383.
51. Kantor GJ, Barsalou LS, Hanawalt PC: Selective repair of specific chromatin domains in UV-irradiated cells from xeroderma pigmentosum complementation group C. Mutation Res 1990, 235:171-180.
52. Tolbert DM, Kantor GJ: Definition of a DNA repair domain in the genomic region containing the human p53 gene. Cancer Res 1996, 56:3324-3330.
53. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
54. Duret L, Mouchiroud D, Gouy M: HOVERGEN: A database of homologous vertebrate genes. Nucleic Acids Res 1994, 22:2360-2365.
55. The Jackson Laboratory: Encyclopedia of the Mouse Genome. URL: http://www.informatics.jax.org/
56. Gouy M, Gautier C, Attimonelli M, Lanave C, Di Paola G: ACNUC - A portable retrieval system for nucleic acid sequence databases: Logical and physical designs and usage. Comput Appl Biosci 1985, 1:167-172.
57. Higgins DG, Bleasby AJ, Fuchs R: CLUSTAL V: Improved software for multiple sequence alignment Comput Appl Biosci 1992, 8:189-191.
58. Li WH: Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 1993, 36:96-99.
59. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120.
60. Moran PAP: Notes on continuous stochastic phenomena. Biometrika 1950, 37:17-23.
61. Cliff AD, Ord JK: Spatial Autocorrelation. London: Pion; 1981.
62. Press WH, Teukolsky SA, Vetterling WT: Numerical Recipes in C. Cambridge: Cambridge University Press; 1992.