A prominent role for segmental duplications in modeling Eukaryotic genomes

Comptes Rendus - Biologies

Volumn 332, Issue 2-3, 2009, Pages 254-266

  Koszul, Romain ^a,d   Fischer, Gilles ^b,c,d  

^a HARVARD UNIVERSITY   (United States)

^b INSTITUT PASTEUR   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d CNRS   (France)

Author keywords

Chromosome rearrangements; CNV; Genome evolution; Genomic disease; Replication; Replication factory; Segmental duplication

Indexed keywords

DOUBLE STRANDED DNA;

CHROMOSOME; EUKARYOTE; EVOLUTION; GENE FLOW; GENOME; POLYMORPHISM; POPULATION GENETICS;

CAENORHABDITIS ELEGANS; CAT; CHROMOSOMAL INSTABILITY; CROSSING OVER; DNA STRAND BREAKAGE; DOG; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE DUPLICATION; GENE REPLICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; HUMAN; MOLECULAR MECHANICS; NONHUMAN; PRIMATE; SHORT SURVEY;

ANIMALS; EUKARYOTIC CELLS; EVOLUTION; GENE DOSAGE; GENE DUPLICATION; GENOME; HUMANS; MODELS, GENETIC; PRIMATES;

EUKARYOTA; HOMINIDAE;

EID: 61549130938     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crvi.2008.07.005     Document Type: Short Survey

References (103)

1. Bridges C.B. Non-disjunction as proof of the chromosome theory of heredity. Genetics 1 (1916) 1-52
2. Bridges C.B. Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. Journal of Heredity 26 (1935) 60-64
3. Lewis E.B. A gene complex controlling segmentation in Drosophila. Nature 276 (1978) 565-570
4. McGinnis W., Garber R.L., Wirz J., Kuroiwa A., and Gehring W.J. A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37 (1984) 403-408
5. Muller H.J. The origination of chromatin deficiencies as minute deletions subject to insertion elsewhere. Genetica 17 (1935) 237-252
6. Bainbridge B.W., and Roper J.A. Observations on the effects of a chromosome duplication in Aspergillus nidulans. J. Gen. Microbiol. 42 (1966) 417-424
7. Daud F., Ortori G.S., and Roper J.A. Spontaneous IR duplications generated at mitosis in Aspergillus nidulans: further evidence of a preferential site of transposed attachment. Genetics 110 (1985) 229-245
8. Sexton C.E., and Roper J.A. Spontaneous duplications and transpositions of a large chromosome segment in Aspergillus nidulans. J. Gen. Microbiol. 130 Pt 3 (1984) 583-595
9. Kuwada Y. Meiosis in the pollen of mother cells in Zea Mays. L. Bot. Mag. 25 (1911) 163
10. Blanc G., and Wolfe K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16 (2004) 1667-1678
11. Jaillon O., Aury J.-M., and Wincker P. "Changing by Doubling", the impact of Whole Genome Duplication in the evolution of eukaryotes. C. R. Biologies 332 (2009) 241-253
12. Bailey J.A., Gu Z., Clark R.A., et al. Recent segmental duplications in the human genome. Science 297 (2002) 1003-1007
13. Eichler E.E. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17 (2001) 661-669
14. Cheung J., Estivill X., Khaja R., MacDonald J.R., Lau K., Tsui L.C., and Scherer S.W. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4 (2003) R25
15. Zhang L., Lu H.H., Chung W.Y., Yang J., and Li W.H. Patterns of segmental duplication in the human genome. Mol. Biol. Evol. 22 (2005) 135-141
16. Conrad D.F., Andrews T.D., Carter N.P., Hurles M.E., and Pritchard J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38 (2006) 75-81
17. Hinds D.A., Kloek A.P., Jen M., Chen X., and Frazer K.A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet. 38 (2006) 82-85
18. McCarroll S.A., Hadnott T.N., Perry G.H., et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38 (2006) 86-92
19. Iafrate A.J., Feuk L., Rivera M.N., Listewnik M.L., Donahoe P.K., Qi Y., Scherer S.W., and Lee C. Detection of large-scale variation in the human genome. Nat. Genet. 36 (2004) 949-951
20. Redon R., Ishikawa S., Fitch K.R., et al. Global variation in copy number in the human genome. Nature 444 (2006) 444-454
21. Sebat J., Lakshmi B., Troge J., et al. Large-scale copy number polymorphism in the human genome. Science 305 (2004) 525-528
22. Sharp A.J., Locke D.P., McGrath S.D., et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77 (2005) 78-88
23. Slater H.R., Bailey D.K., Ren H., Cao M., Bell K., Nasioulas S., Henke R., Choo K.H., and Kennedy G.C. High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. Am. J. Hum. Genet. 77 (2005) 709-726
24. Wong K.K., deLeeuw R.J., Dosanjh N.S., et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80 (2007) 91-104
25. Cooper G.M., Nickerson D.A., and Eichler E.E. Mutational and selective effects on copy-number variants in the human genome. Nat. Genet. 39 (2007) S22-S29
26. Korbel J.O., Urban A.E., Affourtit J.P., et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318 (2007) 420-426
27. Sharp A.J., Hansen S., Selzer R.R., et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet. 38 (2006) 1038-1042
28. Stankiewicz P., and Lupski J.R. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18 (2002) 74-82
29. Lahortiga I., De Keersmaecker K., Van Vlierberghe P., et al. Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nat. Genet. 39 (2007) 593-595
30. Pollack J.R., Sorlie T., Perou C.M., et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl. Acad. Sci. USA (2002)
31. Weaver B.A., Silk A.D., Montagna C., Verdier-Pinard P., and Cleveland D.W. Aneuploidy acts both oncogenically and as a tumor suppressor. Cancer Cell 11 (2007) 25-36
32. Weir B.A., Woo M.S., Getz G., et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450 (2007) 893-898
33. Ullmann R., Turner G., Kirchhoff M., et al. Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation. Hum. Mutat. 28 (2007) 674-682
34. Bonaglia M.C., Giorda R., Tenconi R., Pessina M., Pramparo T., Borgatti R., and Zuffardi O. A 2.3 Mb duplication of chromosome 8q24.3 associated with severe mental retardation and epilepsy detected by standard karyotype. Eur. J. Hum. Genet. 13 (2005) 586-591
35. Rovelet-Lecrux A., Hannequin D., Raux G., et al. APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat. Genet. 38 (2006) 24-26
36. Aitman T.J., Dong R., Vyse T.J., et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439 (2006) 851-855
37. Pisitkun P., Deane J.A., Difilippantonio M.J., Tarasenko T., Satterthwaite A.B., and Bolland S. Autoreactive B cell responses to RNA-related antigens due to TLR7 gene duplication. Science 312 (2006) 1669-1672
38. Gonzalez E., Kulkarni H., Bolivar H., et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307 (2005) 1434-1440
39. Jiang Z., Tang H., Ventura M., Cardone M.F., Marques-Bonet T., She X., Pevzner P.A., and Eichler E.E. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet. 39 (2007) 1361-1368
40. She X., Liu G., Ventura M., et al. A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16 (2006) 576-583
41. Gibbs R.A., Rogers J., Katze M.G., et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316 (2007) 222-234
42. Goidts V., Armengol L., Schempp W., et al. Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum. Genet. 119 (2006) 185-198
43. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
44. Cheng Z., Ventura M., She X., et al. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437 (2005) 88-93
45. Wilson G.M., Flibotte S., Missirlis P.I., Marra M.A., Jones S., Thornton K., Clark A.G., and Holt R.A. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 16 (2006) 173-181
46. Newman T.L., Tuzun E., Morrison V.A., Hayden K.E., Ventura M., McGrath S.D., Rocchi M., and Eichler E.E. A genome-wide survey of structural variation between human and chimpanzee. Genome Res. 15 (2005) 1344-1356
47. Locke D.P., Segraves R., Carbone L., Archidiacono N., Albertson D.G., Pinkel D., and Eichler E.E. Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 13 (2003) 347-357
48. Bailey J.A., Baertsch R., Kent W.J., Haussler D., and Eichler E.E. Hotspots of mammalian chromosomal evolution. Genome Biol. 5 (2004) R23
49. Tuzun E., Bailey J.A., and Eichler E.E. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14 (2004) 493-506
50. Lindblad-Toh K., Wade C.M., Mikkelsen T.S., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 (2005) 803-819
51. Pontius J.U., Mullikin J.C., Smith D.R., et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 17 (2007) 1675-1689
52. Bailey J.A., and Eichler E.E. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat. Rev. Genet. 7 (2006) 552-564
53. Hillier L.W., et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 (2004) 695-716
54. Fiston-Lavier A.S., Anxolabehere D., and Quesneville H. A model of segmental duplication formation in Drosophila melanogaster. Genome Res. 17 (2007) 1458-1470
55. Coghlan A., and Wolfe K.H. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 12 (2002) 857-867
56. Dujon B., Sherman D., Fischer G., et al. Genome evolution in yeasts. Nature 430 (2004) 35-44
57. Wolfe K.H., and Shields D.C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387 (1997) 708-713
58. Lee J.A., Carvalho C.M., and Lupski J.R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131 (2007) 1235-1247
59. Pâques F., and Haber J.E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63 (1999) 349-404
60. Aylon Y., and Kupiec M. DSB repair: the yeast paradigm. DNA Repair (Amst) 3 (2004) 797-815
61. Krogh B.O., and Symington L.S. Recombination proteins in yeast. Annu. Rev. Genet. 38 (2004) 233-271
62. Chen L., Trujillo K., Ramos W., Sung P., and Tomkinson A.E. Promotion of Dnl4-catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes. Mol. Cell 8 (2001) 1105-1115
63. Riha K., Heacock M.L., and Shippen D.E. The role of the nonhomologous end-joining DNA double-strand break repair pathway in telomere biology. Annu. Rev. Genet. 40 (2006) 237-277
64. Linardopoulou E.V., Williams E.M., Fan Y., Friedman C., Young J.M., and Trask B.J. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437 (2005) 94-100
65. Koszul R., Dujon B., and Fischer G. Stability of large segmental duplications in the yeast genome. Genetics 172 (2006) 2211-2222
66. Cheng Q., Cloonan N., Fischer K., Thompson J., Waine G., Lanzer M., and Saul A. Stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens. Mol. Biochem. Parasitol. 97 (1998) 161-176
67. Corcoran L.M., Thompson J.K., Walliker D., and Kemp D.J. Homologous recombination within subtelomeric repeat sequences generates chromosome size polymorphisms in P. falciparum. Cell 53 (1988) 807-813
68. Ohta T. Simple model for treating evolution of multigene families. Nature 263 (1976) 74-76
69. Smith G.P. Evolution of repeated DNA sequences by unequal crossover. Science 191 (1976) 528-535
70. Szostak J.W., and Wu R. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284 (1980) 426-430
71. Batzer M.A., and Deininger P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3 (2002) 370-379
72. Burwinkel B., and Kilimann M.W. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. J. Mol. Biol. 277 3 (1998) 513-517
73. Deininger P.L., and Batzer M.A. Alu repeats and human disease. Mol. Genet. Matabol. 67 3 (1999) 183-193
74. Bailey J.A., Liu G., and Eichler E.E. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73 (2003) 823-834
75. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
76. Koszul R., Caburet S., Dujon B., and Fischer G. Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23 (2004) 234-243
77. Payen C., Koszul R., Dujon B., and Fischer G. Segmental Duplications arise from Pol32-dependent Repair of Broken Forks through either Classical or Rad52-Independent Break-induced Replication. PLoS Genet. 4 9 (2008)
78. McClintock B. The stability of broken ends of chromosomes in Zea mays. Genetics 26 (1941) 234-282
79. Murnane J.P. Telomeres and chromosome instability, DNA Repair (Amst) 5 (2006) 1082-1092
80. Schacherer J., de Montigny J., Welcker A., Souciet J.L., and Potier S. Duplication processes in Saccharomyces cerevisiae haploid strains. Nucleic Acids Res. 33 (2005) 6319-6326
81. Fogel S., Welch J.W., Cathala G., and Karin M. Gene amplification in yeast: CUP1 copy number regulates copper resistance. Current Genetics 7 (1983) 347-355
82. Zhou Y., and Mishra B. Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. Proc. Natl. Acad. Sci. USA 102 (2005) 4051-4056
83. Admire A., Shanks L., Danzl N., Wang M., Weier U., Stevens W., Hunt E., and Weinert T. Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast. Genes Dev. 20 (2006) 159-173
84. Cha R.S., and Kleckner N. ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science 297 (2002) 602-606
85. Coquelle A., Pipiras E., Toledo F., Buttin G., and Debatisse M. Expression of fragile sites triggers intrachromosomal mammalian gene amplification and sets boundaries to early amplicons. Cell 89 (1997) 215-225
86. Lemoine F.J., Degtyareva N.P., Lobachev K., and Petes T.D. Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. Cell 120 (2005) 587-598
87. Raveendranathan M., Chattopadhyay S., Bolon Y.T., Haworth J., Clarke D.J., and Bielinsky A.K. Genome-wide replication profiles of S-phase checkpoint mutants reveal fragile sites in yeast. EMBO J. 25 (2006) 3627-3639
88. Gibson D.G., Aparicio J.G., Hu F., and Aparicio O.M. Diminished S-phase cyclin-dependent kinase function elicits vital Rad53-dependent checkpoint responses in Saccharomyces cerevisiae. Mol. Cell Biol. 24 (2004) 10208-10222
89. Malkova A., Ivanov E.L., and Haber J.E. Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication. Proc. Natl. Acad. Sci. USA 93 (1996) 7131-7136
90. Davis A.P., and Symington L.S. RAD51-dependent break-induced replication in yeast. Mol. Cell Biol. 24 (2004) 2344-2351
91. Lydeard J.R., Jain S., Yamaguchi M., and Haber J.E. Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature 448 (2007) 820-823
92. Richardson C., Moynahan M.E., and Jasin M. Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations. Genes Dev. 12 (1998) 3831-3842
93. Smith C.E., Llorente B., and Symington L.S. Template switching during break-induced replication. Nature 447 (2007) 102-105
94. Kitamura E., Blow J.J., and Tanaka T.U. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125 (2006) 1297-1308
95. Meister P., Taddei A., Ponti A., Baldacci G., and Gasser S.M. Replication foci dynamics: Replication patterns are modulated by S-phase checkpoint kinases in fission yeast. EMBO J. 26 5 (2007) 1315-1326
96. Nick McElhinny S.A., Gordenin D.A., Stith C.M., Burgers P.M.J., and Kunkel T.A. Division of labor at the Eukaryotic replication fork. Mol. Cell 30 (2008) 137-144
97. Nowak M.A., Boerlijst M.C., Cooke J., and Smith J.M. Evolution of genetic redundancy. Nature 388 (1997) 167-171
98. Hughes A.L. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256 (1994) 119-124
99. Ohno S. (1970), Springer-Verlag, New York
100. Wistow G., and Piatigorsky J. Recruitment of enzymes as lens structural proteins. Science 236 (1987) 1554-1556
101. Kitami T., and Nadeau J.H. Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication. Nat. Genet. 32 (2002) 191-194
102. Courseaux A., and Nahon J.L. Birth of two chimeric genes in the Hominidae lineage. Science 291 (2001) 1293-1297
103. Stankiewicz P., Shaw C.J., Withers M., Inoue K., and Lupski J.R. Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res. 14 (2004) 2209-2220