Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

PLoS Genetics

Volumn 5, Issue 6, 2009, Pages

  Faddah, Dina A ^a,c   Ganko, Eric W ^a   McCoach, Caroline ^b,d   Pickrell, Joseph K ^a,e   Hanlon, Sean E ^a   Mann, Frederick G ^a,b   Mieczkowska, Joanna O ^a   Jones, Corbin D ^a   Lieb, Jason D ^a   Vision, Todd J ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b STANFORD UNIVERSITY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF COLORADO   (United States)

^e UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA TRANSPOSITION; FUNGAL STRAIN; FUNGUS ISOLATION; GENE; GENE IDENTIFICATION; GENE LOCUS; GENE NUMBER; GENE REARRANGEMENT; GENETIC POLYMORPHISM; HIGH THROUGHPUT SCREENING; NONHUMAN; NUCLEOTIDE REPEAT; PHENOTYPE; PREDICTOR VARIABLE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; TELOMERE; X CHROMOSOME; BIOLOGICAL MODEL; FUNGAL GENOME; GENE DOSAGE; GENETICS; TRANSPOSON;

SACCHAROMYCES CEREVISIAE;

FUNGAL DNA;

COMPARATIVE GENOMIC HYBRIDIZATION; DNA TRANSPOSABLE ELEMENTS; DNA, FUNGAL; GENE DOSAGE; GENOME, FUNGAL; MODELS, GENETIC; POLYMORPHISM, GENETIC; SACCHAROMYCES CEREVISIAE;

EID: 67651053274     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000502     Document Type: Article

References (67)

1. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951. (Pubitemid 39167488)
2. Eichler EE, Sankoff D (2003) Structural dynamics of eukaryotic chromosome evolution. Science 301: 793-797.
3. Hurles ME, Dermitzakis ET, Tyler-Smith C (2008) The functional impact of structural variation in humans. Trends Genet 24: 238-245.
4. Nguyen DQ, Webber C, Ponting CP (2006) Bias of selection on human copynumber variants. PLoS Genet 2: e20.
5. Reymond A, Henrichsen CN, Harewood L, Merla G (2007) Side effects of genome structural changes. Curr Opin Genet Dev 17: 381-386. (Pubitemid 350019564)
6. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23: 41-46. (Pubitemid 29418785)
7. Carson AR, Feuk L, Mohammed M, Scherer SW (2006) Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics 2: 403-414. (Pubitemid 44110986)
8. Sebat J (2007) Major changes in our DNA lead to major changes in our thinking. Nat Genet 39: S3-5.
9. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, et al. (2000) Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25: 333-337. (Pubitemid 30437324)
10. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, et al. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 99: 16144-16149. (Pubitemid 35462763)
11. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528. (Pubitemid 38971344)
12. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64. (Pubitemid 351630326)
13. Gray YH (2000) It takes two transposons to tango: transposable- elementmediated chromosomal rearrangements. Trends Genet 16: 461-468.
14. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, et al. (2006) Global mapping of transposon location. PLoS Genet 2: e212.
15. Rachidi N, Barre P, Blondin B (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850. (Pubitemid 29286764)
16. Henikoff S (1990) Position-effect variegation after 60 years. Trends Genet 6: 422-426.
17. Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310. (Pubitemid 38435625)
18. Lupski JR (2006) Genome structural variation and sporadic disease traits. Nat Genet 38: 974-976. (Pubitemid 44325918)
19. Lynch M, Conery JS (2003) The evolutionary demography of duplicate genes. J Struct Funct Genomics 3: 35-44.
20. Masly JP, Jones CD, Noor MA, Locke J, Orr HA (2006) Gene transposition as a cause of hybrid sterility in Drosophila. Science 313: 1448-1450. (Pubitemid 44360275)
21. Bikard D, Patel D, Le Mette C, Giorgi V, Camilleri C, et al. (2009) Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science 323: 623-626.
22. Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48: 821-827.
23. Kehrer-Sawatzki H, Cooper DN (2007) Structural divergence between the human and chimpanzee genomes. Hum Genet 120: 759-778. (Pubitemid 46128832)
24. Wolfe KH (2006) Comparative genomics and genome evolution in yeasts. Philos Trans R Soc Lond B Biol Sci 361: 403-412. (Pubitemid 44870097)
25. Wong S, Wolfe KH (2005) Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet 37: 777-782. (Pubitemid 41754898)
26. Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17: 343-360. (Pubitemid 41672960)
27. Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, et al. (2007) Completing the map of human genetic variation. Nature 447: 161-165. (Pubitemid 46763071)
28. Conrad DF, Hurles ME (2007) The population genetics of structural variation. Nat Genet 39: S30-36.
29. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, et al. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A 94: 13057-13062. (Pubitemid 27518475)
30. Winzeler EA, Castillo-Davis CI, Oshiro G, Liang D, Richards DR, et al. (2003) Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163: 79-89. (Pubitemid 36222655)
31. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334. (Pubitemid 32702421)
32. Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A 104: 12825-12830. (Pubitemid 47255239)
33. Daran-Lapujade P, Daran JM, Kotter P, Petit T, Piper MD, et al. (2003) Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 259-269. (Pubitemid 37494724)
34. McAllister L, Penland L, Brown PO (1998) Enrichment for loci identical-bydescent between pairs of mouse or human genomes by genomic mismatch scanning. Genomics 47: 7-11. (Pubitemid 28080076)
35. Nelson SF, McCusker JH, Sander MA, Kee Y, Modrich P, et al. (1993) Genomic mismatch scanning: a new approach to genetic linkage mapping. Nat Genet 4: 11-18. (Pubitemid 23165906)
36. Gunnarsson GH, Thormar HG, Gudmundsson B, Akesson L, Jonsson JJ (2004) Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples. Nucleic Acids Res 32: e23.
37. Saccharomyces cerevisiae RM11-1a Sequencing Project. Broad Institute of Harvard and MIT.
38. Saccharomyces Genome Resequencing Project. Sanger Institute and Institute of Genetics, University of Nottingham.
39. Liti G, Carter DM, Moses AM, Warringer J, Parts L, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.
40. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254. (Pubitemid 40852689)
41. Casaregola S, Nguyen HV, Lepingle A, Brignon P, FG, et al. (1998) A family of laboratory strains of Saccharomyces cerevisiae carry rearrangements involving chromosomes I and III. Yeast 14: 551-564. (Pubitemid 28189547)
42. Udall JA, Quijada PA, Osborn TC (2005) Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L. Genetics 169: 967-979.
43. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Pairedend mapping reveals extensive structural variation in the human genome. Science 318: 420-426. (Pubitemid 47614521)
44. Horowitz H, Thorburn P, Haber JE (1984) Rearrangements of highly polymorphic regions near telomeres of Saccharomyces cerevisiae. Mol Cell Biol 4: 2509-2517. (Pubitemid 15212266)
45. Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, et al. (2005) Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437: 94-100. (Pubitemid 41613430)
46. Venter U, Horz W (1989) The acid phosphatase genes PHO10 and PHO11 in S. cerevisiae are located at the telomeres of chromosomes VIII and I. Nucleic Acids Res 17: 1353-1369.
47. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, et al. (2000) Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 97: 11383-11390. (Pubitemid 30780904)
48. Louis EJ (1995) The chromosome ends of Saccharomyces cerevisiae. Yeast 11: 1553-1573.
49. Blasco MA (2007) The epigenetic regulation of mammalian telomeres. Nat Rev Genet 8: 299-309.
50. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391. (Pubitemid 34826834)
51. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546, 563-1547
52. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ (2000) Chromosomal evolution in Saccharomyces. Nature 405: 451-454.
53. Ryu SL, Murooka Y, Kaneko Y (1998) Reciprocal translocation at duplicated RPL2 loci might cause speciation of Saccharomyces bayanus and Saccharomyces cerevisiae. Curr Genet 33: 345-351. (Pubitemid 28297111)
54. Lupski JR, Stankiewicz P (2005) Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1: e49.
55. Lee JA, Carvalho CM, Lupski JR (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235-1247.
56. Batada NN, Hurst LD (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39: 945-949.
57. Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18: 74-82. (Pubitemid 34127806)
58. Lewontin RC, Moore JA, Provine WB, Wallace B, editors (1981) Dobzhansky's Genetics of Natural Populations I-XLIII: Columbia University Press.
59. Feuk L, MacDonald JR, Tang T, Carson AR, Li M, et al. (2005) Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genet 1: e56.
60. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
61. Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57: 267-272.
62. Hogan GJ, Lee CK, Lieb JD (2006) Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2: e158.
63. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538. (Pubitemid 32144361)
64. Buck MJ, Nobel AB, Lieb JD (2005) ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol 6: R97.
65. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
66. Lobachev KS, Gordenin DA, Resnick MA (2002) The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108: 183-193.
67. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, et al. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res 26: 73-79.