Detection and sequencing of ionizing radiation-induced DNA rearrangements using the inverse polymerase chain reaction

International Journal of Radiation Biology

Volumn 74, Issue 1, 1998, Pages 1-15

  Forrester, H B ^a,b   Radford, I R ^a  

^a PETER MACCALLUM CANCER CENTRE   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL DEATH; CHROMOSOME ABERRATION; CHROMOSOME REARRANGEMENT; DNA DETERMINATION; DNA FLANKING REGION; DNA SEQUENCE; DNA STRAND BREAKAGE; FIBROBLAST; GAMMA IRRADIATION; GENE DUPLICATION; GENE REARRANGEMENT; HUMAN; HUMAN CELL; IONIZING RADIATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RADIATION INJURY;

BASE SEQUENCE; CHROMOSOME BREAKAGE; CHROMOSOMES; DNA; DNA MUTATIONAL ANALYSIS; DNA REPAIR; DNA TOPOISOMERASES, TYPE I; FIBROBLASTS; GAMMA RAYS; GENES, MYC; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RADIATION, IONIZING; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS;

EID: 0031872921     PISSN: 09553002     EISSN: None     Source Type: Journal    
DOI: 10.1080/095530098141672     Document Type: Article

References (57)

1. H gene family. Oncogene, 9, 1109-1115.
2. BAE, Y.-S., KAWASAKI, I., IKEDA, H. and LIU, L. F., 1988, Illegitimate recombination mediated by calf thymus DNA topoisomerase II in vitro. Proceedings of the National Academy of Sciences, U S A, 85, 2076-2080.
3. BARONE, F., BELLI, M., PAZZAGLIA, S., SAPORA, O. and TABOCCHINI, M. A., 1989, Radiation damage and chromatin structure. Annali dell Istituto Superiore di Sanita, 25, 59-67.
4. BEEN, M. D., BURGESS, R. R. and CHAMPOUX, J. J., 1984, Nucleotide sequence preference at rat liver and wheat germ type I DNA topoisomerase breakage sites in duplex SV40 DNA. Nucleic Acids Research, 12, 3097-3114.
5. BERTELSEN, A. H., HUMAYUN, M. Z., KARFOPOULOS, S. G. and RUSH, M. G., 1982, Molecular characterization of small polydisperse circular deoxyribonucleic acid from an African green monkey cell line. Biochemistry, 21, 2076-2085.
6. BISHOP, D. T., WILLIAMSON, J. A. and SKOLNICK, M. H., 1983, A model for restriction fragment length distributions. American Journal of Human Genetics, 35, 795-815.
7. BOEHM, T. and RABBITTS, T. H., 1989, The human T cell receptor genes are targets for chromosomal abnormalities in T cell tumors. FASEB Journal, 3, 2344-2359.
8. BOOTHMAN, D. A., FUKUNAGA, N. and WANG, M., 1994, Down-regulation of topoisomerase I in mammalian cells following ionizing radiation. Cancer Research, 54, 4618-1626.
9. BREIMER, L. H., NALBANTOGLU, J. and MEUTH, M., 1986, Structure and sequence of mutations induced by ionizing radiation at selectable loci in Chinese hamster ovary cells. Journal of Molecular Biology, 192, 669-674.
10. BRYANT, P. E., 1984, Enzymatic restriction of mammalian cell DNA using Pvu II and Bam HI: evidence for double-strand break origin of chromosomal aberrations. International Journal of Radiation Biology, 46, 57-65.
11. BRYS, A. and MAIZELS, N., 1994, LR1 regulates c-myc transcription in B-cell lymphomas. Proceedings of the National Academy of Sciences, U S A, 91, 4915-4919.
12. BULLOCK, P., CHAMPOUX, J. J. and BOTCHAN, M., 1985, Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination. Science, 230, 954-958.
13. CASPERSSON, T., HAGLUND, U., LINDELL, B. and ZECH, I., 1972, Radiation-induced non-random chromosome breakage. Experimental Cell Research, 75, 541-543.
14. CATCHESIDE, D. G., 1938, The effect of x-ray dosage upon the frequency of induced structural changes in the chromosomes of Drosophila melanogaster. Genetics, 36, 307-320.
15. DEWEY, W. C., FURMAN, S. C. and MILLER, H. H., 1970, Comparison of lethality and chromosomal damage induced by x-rays in synchronized Chinese hamster cells in vitro. Radiation Research, 43, 561-581.
16. FORRESTER, H. B., RADFORD, I. R. and DEACON, N. J., 1994, Amplification of low copy number, large DNA sequences in human genomic DNA using Tub DNA polymerase. BioTechnioues, 17, 20-22.
17. FUSCOE, J. C., ZIMMERMAN, L. J., FEKETE, A., SETZER, R. W. and ROSSITER, B. J. F., 1992, Analysis of X-ray-induced HPRT mutations in CHO cells: insertion and deletions. Mutation Research, 269, 171-183.
18. GAZIN, C., DUPONT DE DINECHIN, S., HAMPE, A., MASSON, J. M., MARTIN, P., STEHELIN, D. and GALIBERT, F., 1984, Nucleotide sequence of the human c-myc locus: provocative open reading frame within the first exon. EMBO Journal. 3, 383-387.
19. GILBERT, W. and DRESSLER, D., 1968, DNA replication: the rolling circle model, Cold Spring Harbor Symposia on Quantitative Biology, 33, 473-484.
20. GLICKMAN, B W. and RIPLEY, L. S., 1984, Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proceedings of the National Academy of Sciences, U S A, 81, 512-516.
21. GORDENIN, D. A., LOBACHEV, K. S., DEGTYAREVA, N. P., MALKOVA, A. L., PERKINS, E. and RESNICK, M. A., 1993, Inverted DNA repeats: a source of eukaryotic genomic instability. Molecular and Cellular Biology, 13, 5315-5322.
22. GREENBLATT, C. L., 1962, The evaluation of X-ray-induced chromosome aberrations in cell-cultures of the Chinese hamster. International Journal of Radiation Biology, 4, 185-210.
23. HAHN, P., NEVALDINE, B. and MORGAN, W. F., 1990, X-ray induction of methotrexate resistance due to dhfr gene amplification. Somatic Cell and Molecular Genetics, 16, 413-423.
24. HANVEY, J. C., SHIMIZU, M. and WELLS, R. D., 1988, Intramolecular DNA triplexes in supercoiled plasmids. Proceedings of the National Academy of Sciences, U S A, 85, 6292-6296.
25. HARTL, P. and LIPP, M., 1987, Generation of a variant t(2;8) translocation of Burkitt's lymphoma by site-specific recombination via the kappa light-chain joining signals. Molecular and Cellular Biology, 7, 2037-2045.
26. HIGUCHI, R. G. and OCHMAN, H., 1989, Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction. Nucleic Acids Research, 17, 5865.
27. ITO, T., SEYAMA, T., MIZUNO, K. S., HAYASHI, T., IWAMOTO, N., DOHI, K., NAKAMURA, N. and AKIYAMA, M., 1993, Induction of BCR-ABL fusion genes by in vitro X-irradiation. Japanese Journal of Cancer Research, 84, 105-109.
28. JOSHI, G. P., NELSON, W. J., REVELL, S. H. and SHAW, C. A., 1982, X-ray-induced chromosome damage in live mammalian cells, and improved measurements of its effects on their colony-forming ability. International Journal of Radiation Biology, 41, 161-181.
29. KONOPKA, A. K., 1988, Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells. Nucleic Acids Research, 16, 1739-1758.
30. KROWCZYNSKA, A. M., RUDDERS, R. A. and KRONTIRIS, T. G., 1990, The human minisatellite consensus at breakpoints of oncogene translocations. Nucleic Acids Research, 18, 1121-1127.
31. KUMAR, S. and LEFFAK, M., 1989, DNA topology of the ordered chromatin domain 5′ to the human c-myc gene. Nucleic Acids Research, 17, 2819-2833.
32. MA, C., MARTIN, S., TRASK, B. and HAMLIN, J. L., 1993, Sister chromatid fusion initiates amplification of the dihydrofolate reductase gene in Chinese hamster cells. Genes and Development, 7, 605-620.
33. MESELSON, M. S. and RADDING, C. M., 1975, A general model for genetic recombination. Proceedings of the National Academy of Sciences, U S A, 72, 358-361.
34. MEYERHANS, A., VARTANIAN, J.-P. and WAIN-HOBSON, S., 1990, DNA recombination during PCR. Nucleic Acids Research, 18, 1687-1691.
35. MILES, C., SARGENT, G., PHEAR, G. and MEUTH, M., 1990, DNA sequence analysis of gamma radiation-induced deletions and insertions at the APRT locus of hamster cells. Molecular Carcinogenesis, 3, 233-242.
36. MORRIS, T. and THACKER, J., 1993, Formation of large deletions by illegitimate recombination in the HPRT gene of primary human fibroblasts. Proceedings of the National Academy of Sciences, U S A, 90, 1392-1396.
37. OCHMAN, H., GERBER, A. S. and HARTL, D. L., 1988, Genetic applications of an inverse polymerase chain reaction. Genetics, 120, 621-623.
38. PAABO, S., IRWIN, D. M. and WILSON, A. C., 1990, DNA damage promotes jumping between templates during enzymatic amplification. Journal of Biological Chemistry, 265, 4718-4721.
39. PAINTER, R. B. and KAPP, L. N., 1991, Replication intermediates as substrates for DNA rearrangements. Mutation Research, 262, 21-23.
40. RADFORD, I. R., 1988, The dose-response for low-LET radiation-induced DNA double-strand breakage: methods of measurement and implications for radiation action models. International Journal of Radiation Biology, 54, 1-11.
41. RESNICK, M. A., 1976, The repair of double-strand breaks in DNA; a model involving recombination. Journal of Theoretical Biology, 59, 97-106.
42. ROONEY, S. M. and MOORE, P. D., 1995, Antiparallel, intramolecular triplex DNA stimulates homologous recombination in human cells. Proceedings of the National Academy of Sciences, U S A, 92, 2141-2144.
43. SAGLIO, G., GRAZIA BORRELLO, M., GUERRASIO, A., et al., 1993, Preferential clustering of chromosomal breakpoints in Burkitt's lymphomas and L3 type acute lymphoblastic leukemias with a t(8;14) translocation. Genes, Chromosomes and Cancer, 8, 1-7.
44. SAIKI, R. K., GELFAND, D. H., STOFFEL, S., SCHARF, S. J., HIGUCHI, R., HORN, G. T., MULLIS, K. B. and ERLICH, H. A., 1988, Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487-491.
45. SAX, K., 1938, Chromosome aberrations induced by X-rays. Genetics, 23, 494-516.
46. SEKIGUCHI, J., SEEMAN, N. C. and SHUMAN, S., 1996, Resolution of Holliday junctions by eukaryotic DNA topoisomerase I. Proceedings of the National Academy of Sciences, U S A, 93, 785-789.
47. SHIRAMIZU, B., BARRIGA, F., NEEQUAYE, J., JAFRI, A., DALLA-FAVERA, R., NERI, A., GUTTIEREZ, M., LEVINE, P. and MAGRATH, I., 1991, Patterns of chromosomal breakpoint locations in Burkitt's lymphoma: relevance to geography and Epstein-Barr virus association. Blood, 77, 1516-1526.
48. SHUMAN, S., 1992, Two classes of DNA end-joining reactions catalyzed by vaccinia topoisomerase I. Journal of Biological Chemistry, 267, 16 755-16 758.
49. TRIGLIA, T., PETERSON, M. G. and KEMP, D. J., 1988, A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Research, 16, 8186.
50. VANIN, E. F., HENTHORN, P. S., KIOUSSIS, D., GROSVELD, F. and SMITHIES, O., 1983, Unexpected relationships between four large deletions in the human γ-globin gene cluster. Cell, 35, 701-709.
51. VON HOFF, D. D., NEEDHAM-VAN DEVANTER, D. R., YUCEL, J., WINDLE, B. E. and WAHL, G. M., 1988, Amplified human MYC oncogenes localized to replicating submicroscopic circular DNA molecules. Proceedings of the National Academy of Sciences, U S A, 85, 4804-4808.
52. WADA-KIYAMA, Y. and KIYAMA, R., 1994, Periodicity of DNA bend sites in human epsilon-globin gene region. Possibility of sequence-directed nucleosome phasing. Journal of Biological Chemistry, 269, 22 238-22 244.
53. WALTZ, S. E., TRIVEDI, A. A. and LEFFAK, M., 1996, DNA replication initiates non-randomly at multiple sites near the c-myc in HeLa cells. Nucleic Acids Research, 24, 1887-1894.
54. WARD, J. F., 1994, The complexity of DNA damage: relevance to biological consequences. International Journal of Radiation Biology, 66, 427-432.
55. WEINREB, A., COLLIER, D. A., BIRSHTEIN, B. K. and WELLS, R. D., 1990, Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange. Journal of Biological Chemistry, 265, 1352-1359.
56. ZANIER, R., DE SALVIA, R., FIORE, M. and DEGRASSI, F., 1996, Topoisomerase I activity and cellular response to radiation in Chinese hamster cells. International Journal of Radiation Biology, 70, 251-259.
57. ZHU, J. and SCHIESTL, R. H., 1996, Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae. Molecular and Cellular Biology, 16, 1805-1812.