Hypervariable noncoding sequences in Saccharomyces cerevisiae

Genetics

Volumn 170, Issue 4, 2005, Pages 1575-1587

  Fay, Justin C ^a,b   Benavides, Joseph A ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Box 8510 ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA POLYMORPHISM; EVOLUTION; FUNGAL GENE; FUNGAL STRAIN; GENE CLUSTER; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; MLS1 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PDR10 GENE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; UNINDEXED SEQUENCE;

BASE PAIRING; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, FUNGAL; EVOLUTION, MOLECULAR; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS (GENETICS); RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SELECTION (GENETICS); SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; VARIATION (GENETICS);

SACCHAROMYCES CEREVISIAE;

EID: 25444530606     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.105.042283     Document Type: Article

References (68)

1. AEBI, M., G. KIRCHNER, J. Y. CHEN, U. VIJAYRAGHAVAN, A. JACOBSON et al., 1990 Isolation of a temperature-sensitive mutant with an altered tRNA nucleotidyltransferase and cloning of the gene encoding tRNA nucleotidyltransferase in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 265: 16216-16220.
2. AKASHI, H., 1996 Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144: 1297-1307.
3. BALZI, E., and A. GOFFEAU, 1995 Yeast multidrug resistance: the PDR network. J. Bioenerg. Biomembr. 27: 71-76.
4. BEGUN, D. J., 2001 The frequency distribution of nucleotide variation in Drosophila simulans. Mol. Biol. Evol. 18: 1343-1352.
5. BENNETZEN, J. L., and B. D. HALL, 1982 Codon selection in yeast. J. Biol. Chem. 257: 3026-3031.
6. BI, E., and J. R. PRINGLE, 1996 ZDS1 and ZDS2, genes whose products may regulate Cdc42p in Saccharomyces cerevisiae. Mol. Cell. Biol. 16: 5264-5275.
7. BIERNE, N., and A. EYRE-WALKER, 2003 The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics 165: 1587-1597.
8. BULMER, M., 1987 Coevolution of codon usage and transfer RNA abundance. Nature 325: 728-730.
9. CARGILL, M., D. ALTSHULER, J. IRELAND, P. SKLAR, K. ARDLIE et al., 1999 Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
10. CASPARY, F., A. HARTIG and H. J. SCHULLER, 1997 Constitutive and carbon source-responsive promoter elements are involved in the regulated expression of the Saccharomyces cerevisiae malate synthase gene MLS1. Mol. Gen. Genet. 255: 619-627.
11. CHERRY, J. M., C. BALL, S. WENG, G. JUVIK, R. SCHMIDT et al., 1997 Genetic and physical maps of Saccharomyces cerevisiae. Nature 387: 67-73.
12. CHIN, C. S., J. H. CHUANG and H. LI, 2005 Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Res. 15: 205-213.
13. CLIFTEN, P., P. SUDARSANAM, A. DESIKAN, L. FULTON, B. FULTON et al., 2003 Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
14. DERMITZAKIS, E. T., C. M. BERGMAN and A. G. CLARK, 2003 Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol. Biol. Evol. 20: 703-714.
15. DONIGER, S., J. HUH and J. C. FAY, 2005 Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Res. 15: 701-709.
16. DRAKE, J. W., 1991 A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.
17. DUNN, K. A., J. P. BIELAWSKI and Z. YANG, 2001 Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157: 295-305.
18. EWING, B., and P. GREEN, 1998 Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
19. FAY, J. C., and J. A. BENAVIDES, 2005 Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1: e5.
20. FAY, J. C., and C.-I WU, 2001 The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11: 642-646.
21. FAY, J. C., and C.-I WU, 2003 Sequence divergence, functional constraint, and selection in protein evolution. Annu. Rev. Genomics Hum. Genet. 4: 213-235.
22. FAY, J. C, G. J. WYCKOFF and C.-I WU, 2001 Positive and negative selection on the human genome. Genetics 158: 1227-1234.
23. FAY, J. C., G. J. WYCKOFF and C.-I WU, 2002 Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026.
24. HAGERMAN, R. A., P. J. TROTTER and R. A. WILLIS, 2002 The regulation of COQ5 gene expression by energy source. Free Radic. Res. 36: 485-490.
25. HALUSHKA, M. K., J. B. FAN, K. BENTLEY, L. HSIE, N. SHEN et al., 1999 Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22: 239-247.
26. HARTIG, A., M. M. SIMON, T. SCHUSTER, J. R. DAUGHERTY, H. S. YOO et al., 1992 Differentially regulated malate synthase genes participate in carbon and nitrogen metabolism of S. cerevisiae. Nucleic Acids Res. 20: 5677-5686.
27. HELLMANN, I., S. ZOLLNER, W. ENARD, I. EBERSBERGER, B. NICKEL et al., 2003 Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13: 831-837.
28. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
29. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
30. HUDSON, R. R., D. D. BOOS and N. L. KAPLAN, 1992 A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.
31. JENKINS, D. L., C. A. ORTORI and J. F. BROOKFIELD, 1995 A test for adaptive change in DNA sequences controlling transcription. Proc. R. Soc. Lond. Ser. B Biol. Sci. 261: 203-207.
32. JENSEN, M. A., H. L. TRUE, Y. O. CHERNOFF and S. LINDQUIST, 2001 Molecular population genetics and evolution of a prion-like protein in Saccharomyces cerevisiae. Genetics 159: 527-535.
33. JOHNSTON, J. R., C. BACCARI and R. K. MORTIMER, 2000 Genotypic characterization of strains of commercial wine yeasts by tetrad analysis. Res. Microbiol. 151: 583-590.
34. JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism III, edited by H. N. MUNRO. Academic Press, New York.
35. KANG, X. L., F. YADAO, R. D. GIETZ and B. A. KUNZ, 1992 Elimination of the yeast RAD6 ubiquitin conjugase enhances base pair transitions and G.C-T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutation. Genetics 130: 285-294.
36. KELLIS, M., N. PATTERSON, M. ENDRIZZI, B. BIRREN and E. S. LANDER, 2003 Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
37. KERN, A. D., and D. J. BEGUN, 2005 Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes. Mol. Biol. Evol. 22: 51-62.
38. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
39. KOHN, M. H., S. FANG and C. I. WU, 2004 Inference of positive and negative selection on the 5′ regulatory regions of Drosophila genes. Mol. Biol. Evol. 21: 374-383.
40. LAZZARO, B. P., and A. G. CLARK, 2001 Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster. Genetics 159: 659-671.
41. LUDWIG, M. Z., and M. KREITMAN, 1995 Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. Mol. Biol. Evol. 12: 1002-1011.
42. LUDWIG, M. Z., N. H. PATEL and M. KREITMAN, 1998 Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125: 949-958.
43. LUDWIG, M. Z., C. BERGMAN, N. H. PATEL and M. KREITMAN, 2000 Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
44. MCDONALD, J. H., 1996 Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 13: 253-260.
45. MCDONALD, J. H., 1998 Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 15: 377-384.
46. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
47. MORTIMER, R. K., P. ROMANO, G. SUZZI and M. POLSINELLI, 1994 Genome renewal: a new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast 10: 1543-1552.
48. MOSES, A. M., D. Y. CHIANG, M. KELLIS, E. S. LANDER and M. B. EISEN, 2003 Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 3: 19.
49. MOSES, A. M., D. Y. CHIANG and M. B. EISEN, 2004a Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pac. Symp. Biocomput., 324-335.
50. MOSES, A. M., D. Y. CHIANG, D. A. POLLARD, V. N. IYER and M. B. EISEN, 2004b MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol. 5: R98.
51. OECHSNER, U., H. HERMANN, A. ZOLLNER, A. HAID and W. BANDLOW, 1992 Expression of yeast cytochrome c1 is controlled at the transcriptional level by glucose, oxygen and haem. Mol. Gen. Genet. 232: 447-459.
52. PHINCHONGSAKULDIT, J., S. MACARTHUR and J. F. BROOKFIELD, 2004 Evolution of developmental genes: molecular microevolution of enhancer sequences at the Ubx locus in Drosophila and its impact on developmental phenotypes. Mol. Biol. Evol. 21: 348-363.
53. PTAK, S. E., D. A. HINDS, K. KOEHLER, B. NICKEL, N. PATIL et al., 2005 Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37: 429-434.
54. RICHARDS, S., Y. LIU, B. R. BETTENCOURT, P. HRADECKY, S. LETOVSKY et al., 2005 Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18.
55. ROY, N., and K. W. RUNGE, 1999 The ZDS1 and ZDS2 proteins require the Sir3p component of yeast silent chromatin to enhance the stability of short linear centromeric plasmids. Chromosoma 108: 146-161.
56. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
57. SADLER, I., K. SUDA, G. SCHATZ, F. KAUDEWITZ and A. HAID, 1984 Sequencing of the nuclear gene for the yeast cytochrome c1 precursor reveals an unusually complex amino-terminal presequence. EMBO J. 3: 2137-2143.
58. SLATKIN, M., and T. WIEHE, 1998 Genetic hitch-hiking in a subdivided population. Genet. Res. 71: 155-160.
59. SOKAL, R. R., and F. J. ROHLF, 1995 Biometry: The Principles and Practice of Statistics in Biological Research. W. H. Freeman, New York.
60. STEPHENS, M., N. J. SMITH and P. DONNELLY, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
61. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
62. TAUTZ, D., and L. NIGRO, 1998 Microevolutionary divergence pattern of the segmentation gene hunchback in Drosophila. Mol. Biol. Evol. 15: 1403-1411.
63. TEMPLETON, A. R., 1996 Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263-1270.
64. THOMAS, J. W., J. W. TOUCHMAN, R. W. BLAKESLEY, G. G. BOUFFARD, S. M. BECKSTROM-STERNBERG et al., 2003 Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
65. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
66. WINCKLER, W., S. R. MYERS, D. J. RICHTER, R. C. ONOFRIO, G. J. MCDONALD et al., 2005 Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308: 107-111.
67. WRIGHT, F., 1990 The 'effective number of codons' used in a gene. Gene 87: 23-29.
68. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.