The Pattern of Gene Amplification Is Determined by the Chromosomal Location of Hairpin-Capped Breaks

Cell

Volumn 125, Issue 7, 2006, Pages 1283-1296

  Narayanan, Vidhya ^a   Mieczkowski, Piotr A ^b   Kim, Hyun Min ^a   Petes, Thomas D ^b   Lobachev, Kirill S ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PALINDROMIC DNA;

AMPLICON; ARTICLE; CHROMOSOMAL LOCALIZATION; CHROMOSOME; DNA STRAND BREAKAGE; GENE AMPLIFICATION; MAMMAL; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; YEAST;

MAMMALIA;

EID: 33745264366     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2006.04.042     Document Type: Article

References (49)

1. Albertson D.G., Collins C., McCormick F., and Gray J.W. Chromosome aberrations in solid tumors. Nat. Genet. 34 (2003) 369-376
2. Albrecht E.B., Hunyady A.B., Stark G.R., and Patterson T.E. Mechanisms of sod2 gene amplification in Schizosaccharomyces pombe. Mol. Biol. Cell 11 (2000) 873-886
3. Chan S.R., and Blackburn E.H. Telomeres and telomerase. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359 (2004) 109-121
4. Conti C., Caburet S., Schurra C., and Bensimon A. Molecular combing. Current Protocols in Cytometry (2001), John Wiley & Sons, Inc., New York 8.10.11-18.10.23
5. 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
6. Coquelle A., Rozier L., Dutrillaux B., and Debatisse M. Induction of multiple double-strand breaks within an hsr by meganucleaseI-SceI expression or fragile site activation leads to formation of double minutes and other chromosomal rearrangements. Oncogene 21 (2002) 7671-7679
7. Debatisse M., and Malfor B. Gene amplification mechanisms. In: Nigg E.A. (Ed). Genome Instability in Cancer Development (2005), Springer, Netherlands 343-361
8. Fletcher J.A. Cytogenetics of solid tumors. In: Gersen S.L., and Keagle M.B. (Eds). The Principles of Clinical Cytogenetics (2005), Humana Press, Totowa, New Jersey 365-420
9. Fried M., Feo S., and Heard E. The role of inverted duplication in the generation of gene amplification in mammalian cells. Biochim. Biophys. Acta 1090 (1991) 143-155
10. Haber J.E., Thorburn P.C., and Rogers D. Meiotic and mitotic behavior of dicentric chromosomes in Saccharomyces cerevisiae. Genetics 106 (1984) 185-205
11. Kaye J.A., Melo J.A., Cheung S.K., Vaze M.B., Haber J.E., and Toczyski D.P. DNA breaks promote genomic instability by impeding proper chromosome segregation. Curr. Biol. 14 (2004) 2096-2106
12. Kobayashi T., Horiuchi T., Tongaonkar P., Vu L., and Nomura M. SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell 117 (2004) 441-453
13. Kramer K.M., and Haber J.E. New telomeres in yeast are initiated with a highly selected subset of TG1-3 repeats. Genes Dev. 7 (1993) 2345-2356
14. Kramer K.M., Brock J.A., Bloom K., Moore J.K., and Haber J.E. Two different types of double-strand breaks in Saccharomyces cerevisiae are repaired by similar RAD52-independent, nonhomologous recombination events. Mol. Cell. Biol. 14 (1994) 1293-1301
15. Kraus E., Leung W.Y., and Haber J.E. Break-induced replication: a review and an example in budding yeast. Proc. Natl. Acad. Sci. USA 98 (2001) 8255-8262
16. Krogh B.O., and Symington L.S. Recombination proteins in yeast. Annu. Rev. Genet. 38 (2004) 233-271
17. Kuo M.T., Vyas R.C., Jiang L.X., and Hittelman W.N. Chromosome breakage at a major fragile site associated with P-glycoprotein gene amplification in multidrug-resistant CHO cells. Mol. Cell. Biol. 14 (1994) 5202-5211
18. 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
19. Lobachev K.S., Shor B.M., Tran H.T., Taylor W., Keen J.D., Resnick M.A., and Gordenin D.A. Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 148 (1998) 1507-1524
20. Lobachev K.S., Stenger J.E., Kozyreva O.G., Jurka J., Gordenin D.A., and Resnick M.A. Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J. 19 (2000) 3822-3830
21. Lobachev K.S., Gordenin D.A., and Resnick M.A. The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108 (2002) 183-193
22. Ma C., Martin S., Trask B., and Hamlin J.L. Sister chromatid fusion initiates amplification of the dihydrofolate reductase gene in Chinese hamster cells. Genes Dev. 7 (1993) 605-620
23. 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
24. Maringele L., and Lydall D. Telomerase- and recombination-independent immortalization of budding yeast. Genes Dev. 18 (2004) 2663-2675
25. McClintock B. The stability of broken ends of chromosomes in Zea mays. Genetics 26 (1941) 234-282
26. Mondello C., Rebuzzini P., Dolzan M., Edmonson S., Taccioli G.E., and Giulotto E. Increased gene amplification in immortal rodent cells deficient for the DNA-dependent protein kinase catalytic subunit. Cancer Res. 61 (2001) 4520-4525
27. Myung K., and Kolodner R.D. Induction of genome instability by DNA damage in Saccharomyces cerevisiae. DNA Repair (Amst.) 2 (2003) 243-258
28. Naeem R.C. Cytogenetics of hematologic neoplasms. In: Gersen S.L., and Keagle M.B. (Eds). The Principles of Clinical Cytogenetics (2005), Humana Press, Totowa, New Jersey 365-420
29. Paulson T.G., Almasan A., Brody L.L., and Wahl G.M. Gene amplification in a p53-deficient cell line requires cell cycle progression under conditions that generate DNA breakage. Mol. Cell. Biol. 18 (1998) 3089-3100
30. Pennaneach V., Putnam C.D., and Kolodner R.D. Chromosome healing by de novo telomere addition in Saccharomyces cerevisiae. Mol. Microbiol. 59 (2006) 1357-1368
31. Pipiras E., Coquelle A., Bieth A., and Debatisse M. Interstitial deletions and intrachromosomal amplification initiated from a double-strand break targeted to a mammalian chromosome. EMBO J. 17 (1998) 325-333
32. Poupon M.F., Smith K.A., Chernova O.B., Gilbert C., and Stark G.R. Inefficient growth arrest in response to dNTP starvation stimulates gene amplification through bridge-breakage-fusion cycles. Mol. Biol. Cell 7 (1996) 345-354
33. Putnam C.D., Pennaneach V., and Kolodner R.D. Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype. Mol. Cell. Biol. 25 (2005) 7226-7238
34. Rachidi N., Martinez M.J., Barre P., and Blondin B. Saccharomyces cerevisiae PAU genes are induced by anaerobiosis. Mol. Microbiol. 35 (2000) 1421-1430
35. Rattray A.J., Shafer B.K., Neelam B., and Strathern J.N. A mechanism of palindromic gene amplification in Saccharomyces cerevisiae. Genes Dev. 19 (2005) 1390-1399
36. Resnick M.A., Westmoreland J., and Bloom K. Heterogeneity and maintenance of centromere plasmid copy number in Saccharomyces cerevisiae. Chromosoma 99 (1990) 281-288
37. Shimizu N., Shingaki K., Kaneko-Sasaguri Y., Hashizume T., and Kanda T. When, where and how the bridge breaks: anaphase bridge breakage plays a crucial role in gene amplification and HSR generation. Exp. Cell Res. 302 (2005) 233-243
38. Stark G.R., Debatisse M., Giulotto E., and Wahl G.M. Recent progress in understanding mechanisms of mammalian DNA amplification. Cell 57 (1989) 901-908
39. Stenger J.E., Lobachev K.S., Gordenin D., Darden T.A., Jurka J., and Resnick M.A. Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res. 11 (2001) 12-27
40. Sutherland G.R. Rare fragile sites. Cytogenet. Genome Res. 100 (2003) 77-84
41. Tanaka H., Bergstrom D.A., Yao M.C., and Tapscott S.J. Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification. Nat. Genet. 37 (2005) 320-327
42. Toledo F., Buttin G., and Debatisse M. The origin of chromosome rearrangements at early stages of AMPD2 gene amplification in Chinese hamster cells. Curr. Biol. 3 (1993) 255-264
43. Umezu K., Hiraoka M., Mori M., and Maki H. Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae: retrotransposon Ty1 plays a crucial role in chromosomal rearrangements. Genetics 160 (2002) 97-110
44. van den Berg M.A., and Steensma H.Y. Expression cassettes for formaldehyde and fluoroacetate resistance, two dominant markers in Saccharomyces cerevisiae. Yeast 13 (1997) 551-559
45. Wang P., Kim Y., Pollack J., Narasimhan B., and Tibshirani R. A method for calling gains and losses in array CGH data. Biostatistics 6 (2005) 45-58
46. Watanabe T., and Horiuchi T. A novel gene amplification system in yeast based on double rolling-circle replication. EMBO J. 24 (2005) 190-198
47. Windle B.E., and Wahl G.M. Molecular dissection of mammalian gene amplification: new mechanistic insights revealed by analyses of very early events. Mutat. Res. 276 (1992) 199-224
48. Yunis J.J., Soreng A.L., and Bowe A.E. Fragile sites are targets of diverse mutagens and carcinogens. Oncogene 1 (1987) 59-69
49. Zhou Z.H., Akgun E., and Jasin M. Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences. Proc. Natl. Acad. Sci. USA 98 (2001) 8326-8333