Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Jul 15;24(14):2829–2834. doi: 10.1093/nar/24.14.2829

De novo generation of simple sequence during gene amplification.

L S Kirschner 1
PMCID: PMC146008  PMID: 8759018

Abstract

Mammalian cells that have undergone gene amplification and/or gene rearrangement have been used as resources to gain insight into the questions of chromosome structure and dynamics. The multidrug resistant murine cell line J7.V2-1 has been shown previously to contain two distinct forms of the highly amplified mdr2 gene, a member of the mouse gene family responsible for the multidrug resistant (MDR) phenotype [Kirschner, L. S. (1995) DNA Cell Biol. 14, 47-59]. Characterization of both forms of the gene revealed that one form corresponded to the wild-type structure of the gene, whereas the other represented a rearrangement. Investigation of this altered gene demonstrated a deletion of 1.6 kb of the wild-type sequence, and replacement of this region with a poly(AT) tract that appears to have been generated de novo. Analysis of the native sequence in this region demonstrated the absence of repetitive elements, but was notable for the presence of two long stretches of polypurine: polypyrimidine strand asymmetry. Analysis of mdr2 transcripts in this cell line revealed that nearly all of the mRNA is transcribed from the rearranged form of the gene. This message is unable to code for a functional mdr2 gene product, owing to a deletion of the fourth exon during this event. Mechanisms of the rearrangement, as well as the significance of this curious effect on transcription, are discussed.

Full Text

The Full Text of this article is available as a PDF (91.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ardeshir F., Giulotto E., Zieg J., Brison O., Liao W. S., Stark G. R. Structure of amplified DNA in different Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate. Mol Cell Biol. 1983 Nov;3(11):2076–2088. doi: 10.1128/mcb.3.11.2076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brereton H. M., Firgaira F. A., Turner D. R. Origins of polymorphism at a polypurine hypervariable locus. Nucleic Acids Res. 1993 Jun 11;21(11):2563–2569. doi: 10.1093/nar/21.11.2563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Caskey C. T., Pizzuti A., Fu Y. H., Fenwick R. G., Jr, Nelson D. L. Triplet repeat mutations in human disease. Science. 1992 May 8;256(5058):784–789. doi: 10.1126/science.1589758. [DOI] [PubMed] [Google Scholar]
  4. Cohen D., Higman S. M., Hsu S. I., Horwitz S. B. The involvement of a LINE-1 element in a DNA rearrangement upstream of the mdr1a gene in a taxol multidrug-resistant murine cell line. J Biol Chem. 1992 Oct 5;267(28):20248–20254. [PubMed] [Google Scholar]
  5. Cohen D., Piekarz R. L., Hsu S. I., DePinho R. A., Carrasco N., Horwitz S. B. Structural and functional analysis of the mouse mdr1b gene promoter. J Biol Chem. 1991 Feb 5;266(4):2239–2244. [PubMed] [Google Scholar]
  6. Cohen M. M., Rosenblum-Vos L. S., Prabhakar G. Human cytogenetics. A current overview. Am J Dis Child. 1993 Nov;147(11):1159–1166. doi: 10.1001/archpedi.1993.02160350033005. [DOI] [PubMed] [Google Scholar]
  7. Collier D. A., Griffin J. A., Wells R. D. Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. J Biol Chem. 1988 May 25;263(15):7397–7405. [PubMed] [Google Scholar]
  8. Daniels G. R., Deininger P. L. Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res. 1985 Dec 20;13(24):8939–8954. doi: 10.1093/nar/13.24.8939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Debatisse M., Saito I., Buttin G., Stark G. R. Preferential amplification of rearranged sequences near amplified adenylate deaminase genes. Mol Cell Biol. 1988 Jan;8(1):17–24. doi: 10.1128/mcb.8.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Devine S. E., Hussain A., Davide J. P., Melera P. W. Full length and alternatively spliced pgp1 transcripts in multidrug-resistant Chinese hamster lung cells. J Biol Chem. 1991 Mar 5;266(7):4545–4555. [PubMed] [Google Scholar]
  11. Federspiel N. A., Beverley S. M., Schilling J. W., Schimke R. T. Novel DNA rearrangements are associated with dihydrofolate reductase gene amplification. J Biol Chem. 1984 Jul 25;259(14):9127–9140. [PubMed] [Google Scholar]
  12. Furano A. V., Somerville C. C., Tsichlis P. N., D'Ambrosio E. Target sites for the transposition of rat long interspersed repeated DNA elements (LINEs) are not random. Nucleic Acids Res. 1986 May 12;14(9):3717–3727. doi: 10.1093/nar/14.9.3717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Grabczyk E., Fishman M. C. A long purine-pyrimidine homopolymer acts as a transcriptional diode. J Biol Chem. 1995 Jan 27;270(4):1791–1797. doi: 10.1074/jbc.270.4.1791. [DOI] [PubMed] [Google Scholar]
  14. Gros P., Raymond M., Bell J., Housman D. Cloning and characterization of a second member of the mouse mdr gene family. Mol Cell Biol. 1988 Jul;8(7):2770–2778. doi: 10.1128/mcb.8.7.2770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hamlin J. L., Leu T. H., Vaughn J. P., Ma C., Dijkwel P. A. Amplification of DNA sequences in mammalian cells. Prog Nucleic Acid Res Mol Biol. 1991;41:203–239. doi: 10.1016/s0079-6603(08)60010-0. [DOI] [PubMed] [Google Scholar]
  17. Hsu S. I., Lothstein L., Horwitz S. B. Differential overexpression of three mdr gene family members in multidrug-resistant J774.2 mouse cells. Evidence that distinct P-glycoprotein precursors are encoded by unique mdr genes. J Biol Chem. 1989 Jul 15;264(20):12053–12062. [PubMed] [Google Scholar]
  18. Kirschner L. S. Amplification of the murine mdr2 gene and a reconsideration of the structure of the murine mdr gene locus. DNA Cell Biol. 1995 Jan;14(1):47–59. doi: 10.1089/dna.1995.14.47. [DOI] [PubMed] [Google Scholar]
  19. Kirschner L. S., Greenberger L. M., Hsu S. I., Yang C. P., Cohen D., Piekarz R. L., Castillo G., Han E. K., Yu L. J., Horwitz S. B. Biochemical and genetic characterization of the multidrug resistance phenotype in murine macrophage-like J774.2 cells. Biochem Pharmacol. 1992 Jan 9;43(1):77–87. doi: 10.1016/0006-2952(92)90664-5. [DOI] [PubMed] [Google Scholar]
  20. Kohwi Y., Panchenko Y. Transcription-dependent recombination induced by triple-helix formation. Genes Dev. 1993 Sep;7(9):1766–1778. doi: 10.1101/gad.7.9.1766. [DOI] [PubMed] [Google Scholar]
  21. Looney J. E., Hamlin J. L. Isolation of the amplified dihydrofolate reductase domain from methotrexate-resistant Chinese hamster ovary cells. Mol Cell Biol. 1987 Feb;7(2):569–577. doi: 10.1128/mcb.7.2.569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. McCarthy J. G., Heywood S. M. A long polypyrimidine/polypurine tract induces an altered DNA conformation on the 3' coding region of the adjacent myosin heavy chain gene. Nucleic Acids Res. 1987 Oct 12;15(19):8069–8085. doi: 10.1093/nar/15.19.8069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. McClellan J. A., Palecek E., Lilley D. M. (A-T)n tracts embedded in random sequence DNA--formation of a structure which is chemically reactive and torsionally deformable. Nucleic Acids Res. 1986 Dec 9;14(23):9291–9309. doi: 10.1093/nar/14.23.9291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Meese E. U., Horwitz S. B., Trent J. M. Evidence for linear extrachromosomal elements mediating gene amplification in the multidrug-resistant J774.2 murine cell line. Cancer Genet Cytogenet. 1992 Mar;59(1):20–25. doi: 10.1016/0165-4608(92)90151-w. [DOI] [PubMed] [Google Scholar]
  25. Michel D., Chatelain G., Herault Y., Brun G. The long repetitive polypurine/polypyrimidine sequence (TTCCC)48 forms DNA triplex with PU-PU-PY base triplets in vivo. Nucleic Acids Res. 1992 Feb 11;20(3):439–443. doi: 10.1093/nar/20.3.439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nalbantoglu J., Miles C., Meuth M. Insertion of unique and repetitive DNA fragments into the aprt locus of hamster cells. J Mol Biol. 1988 Apr 5;200(3):449–459. doi: 10.1016/0022-2836(88)90535-9. [DOI] [PubMed] [Google Scholar]
  27. Nicholls R. D., Fischel-Ghodsian N., Higgs D. R. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. doi: 10.1016/0092-8674(87)90289-3. [DOI] [PubMed] [Google Scholar]
  28. Noonan K. E., Roninson I. B. mRNA phenotyping by enzymatic amplification of randomly primed cDNA. Nucleic Acids Res. 1988 Nov 11;16(21):10366–10366. doi: 10.1093/nar/16.21.10366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Panyutin I., Lyamichev V., Mirkin S. A structural transition in d(AT)n.d(AT)n inserts within superhelical DNA. J Biomol Struct Dyn. 1985 Jun;2(6):1221–1234. doi: 10.1080/07391102.1985.10507634. [DOI] [PubMed] [Google Scholar]
  30. Schlötterer C., Tautz D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 1992 Jan 25;20(2):211–215. doi: 10.1093/nar/20.2.211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Schoenlein P. V., Shen D. W., Barrett J. T., Pastan I., Gottesman M. M. Double minute chromosomes carrying the human multidrug resistance 1 and 2 genes are generated from the dimerization of submicroscopic circular DNAs in colchicine-selected KB carcinoma cells. Mol Biol Cell. 1992 May;3(5):507–520. doi: 10.1091/mbc.3.5.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schroth G. P., Chou P. J., Ho P. S. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J Biol Chem. 1992 Jun 15;267(17):11846–11855. [PubMed] [Google Scholar]
  33. Slovak M. L., Lothstein L., Horwitz S. B., Trent J. M. Molecular/cytogenetic alterations accompanying the development of multidrug resistance in the J774.2 murine cell line. Leukemia. 1988 Jul;2(7):453–458. [PubMed] [Google Scholar]
  34. Stark G. R., Debatisse M., Giulotto E., Wahl G. M. Recent progress in understanding mechanisms of mammalian DNA amplification. Cell. 1989 Jun 16;57(6):901–908. doi: 10.1016/0092-8674(89)90328-0. [DOI] [PubMed] [Google Scholar]
  35. Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989 Aug 25;17(16):6463–6471. doi: 10.1093/nar/17.16.6463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tautz D., Schlötterer Simple sequences. Curr Opin Genet Dev. 1994 Dec;4(6):832–837. doi: 10.1016/0959-437x(94)90067-1. [DOI] [PubMed] [Google Scholar]
  37. Usdin K., Furano A. V. Insertion of L1 elements into sites that can form non-B DNA. Interactions of non-B DNA-forming sequences. J Biol Chem. 1989 Dec 5;264(34):20736–20743. [PubMed] [Google Scholar]
  38. Usdin K., Furano A. V. The structure of the guanine-rich polypurine:polypyrimidine sequence at the right end of the rat L1 (LINE) element. J Biol Chem. 1989 Sep 15;264(26):15681–15687. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES