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. 1996 Nov 1;24(21):4234–4241. doi: 10.1093/nar/24.21.4234

Stability of an inverted repeat in a human fibrosarcoma cell.

P R Kramer 1, J R Stringer 1, R R Sinden 1
PMCID: PMC146229  PMID: 8932378

Abstract

Deletions and rearrangements of DNA sequences within the genome of human cells result in mutations associated with human disease. We have developed a selection system involving a neo gene containing a DNA sequence inserted into the NcoI site that can be used to quantitatively assay deletion of this sequence from the chromosome. The spontaneous deletion from the neo gene of a 122 bp inverted repeat occurred at a rate of 2.1 x 10(-8) to <3.1 x 10(-9) revertants/cell/generation in three different cell lines. Deletion of the 122 bp inverted repeat occurred between 6 bp flanking direct repeats. Spontaneous deletion of a 122 bp non-palindromic DNA sequence flanked by direct repeats was not observed, indicating a rate of deletion of <3.1 x 10(-9) revertants/cell/generation. This result demonstrates that a 122 bp inverted repeat can exhibit a low level of instability in some locations in the chromosome of a human cell line.

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Selected References

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  1. Albertini A. M., Hofer M., Calos M. P., Miller J. H. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell. 1982 Jun;29(2):319–328. doi: 10.1016/0092-8674(82)90148-9. [DOI] [PubMed] [Google Scholar]
  2. Balbinder E., Mac Vean C., Williams R. E. Overlapping direct repeats stimulate deletions in specially designed derivatives of plasmid pBR325 in Escherichia coli. Mutat Res. 1989 Oct;214(2):233–252. doi: 10.1016/0027-5107(89)90168-1. [DOI] [PubMed] [Google Scholar]
  3. Bissler J. J., Donaldson V. H., Davis A. E., 3rd Contiguous deletion and duplication mutations resulting in type 1 hereditary angioneurotic edema. Hum Genet. 1994 Mar;93(3):265–269. doi: 10.1007/BF00212020. [DOI] [PubMed] [Google Scholar]
  4. Bronner C. E., Baker S. M., Morrison P. T., Warren G., Smith L. G., Lescoe M. K., Kane M., Earabino C., Lipford J., Lindblom A. Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature. 1994 Mar 17;368(6468):258–261. doi: 10.1038/368258a0. [DOI] [PubMed] [Google Scholar]
  5. Campuzano V., Montermini L., Moltò M. D., Pianese L., Cossée M., Cavalcanti F., Monros E., Rodius F., Duclos F., Monticelli A. Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science. 1996 Mar 8;271(5254):1423–1427. doi: 10.1126/science.271.5254.1423. [DOI] [PubMed] [Google Scholar]
  6. Capizzi R. L., Jameson J. W. A table for the estimation of the spontaneous mutation rate of cells in culture. Mutat Res. 1973 Jan;17(1):147–148. doi: 10.1016/0027-5107(73)90265-0. [DOI] [PubMed] [Google Scholar]
  7. Chakrabarti S., Joffe S., Seidman M. M. Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells. Mol Cell Biol. 1985 Sep;5(9):2265–2271. doi: 10.1128/mcb.5.9.2265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Collick A., Drew J., Penberth J., Bois P., Luckett J., Scaerou F., Jeffreys A., Reik W. Instability of long inverted repeats within mouse transgenes. EMBO J. 1996 Mar 1;15(5):1163–1171. [PMC free article] [PubMed] [Google Scholar]
  9. Cooper D. N., Krawczak M. Mechanisms of insertional mutagenesis in human genes causing genetic disease. Hum Genet. 1991 Aug;87(4):409–415. doi: 10.1007/BF00197158. [DOI] [PubMed] [Google Scholar]
  10. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  11. Farabaugh P. J., Schmeissner U., Hofer M., Miller J. H. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J Mol Biol. 1978 Dec 25;126(4):847–857. doi: 10.1016/0022-2836(78)90023-2. [DOI] [PubMed] [Google Scholar]
  12. Fishel R., Lescoe M. K., Rao M. R., Copeland N. G., Jenkins N. A., Garber J., Kane M., Kolodner R. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell. 1993 Dec 3;75(5):1027–1038. doi: 10.1016/0092-8674(93)90546-3. [DOI] [PubMed] [Google Scholar]
  13. Glickman B. W., Ripley L. S. Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc Natl Acad Sci U S A. 1984 Jan;81(2):512–516. doi: 10.1073/pnas.81.2.512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Godwin A. R., Liskay R. M. The effects of insertions on mammalian intrachromosomal recombination. Genetics. 1994 Feb;136(2):607–617. doi: 10.1093/genetics/136.2.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gordenin D. A., Lobachev K. S., Degtyareva N. P., Malkova A. L., Perkins E., Resnick M. A. Inverted DNA repeats: a source of eukaryotic genomic instability. Mol Cell Biol. 1993 Sep;13(9):5315–5322. doi: 10.1128/mcb.13.9.5315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gordenin D. A., Malkova A. L., Peterzen A., Kulikov V. N., Pavlov Y. I., Perkins E., Resnick M. A. Transposon Tn5 excision in yeast: influence of DNA polymerases alpha, delta, and epsilon and repair genes. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3785–3789. doi: 10.1073/pnas.89.9.3785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Henderson S. T., Petes T. D. Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae. Genetics. 1993 May;134(1):57–62. doi: 10.1093/genetics/134.1.57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kazic T., Berg D. E. Context effects in the formation of deletions in Escherichia coli. Genetics. 1990 Sep;126(1):17–24. doi: 10.1093/genetics/126.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Koi M., Umar A., Chauhan D. P., Cherian S. P., Carethers J. M., Kunkel T. A., Boland C. R. Human chromosome 3 corrects mismatch repair deficiency and microsatellite instability and reduces N-methyl-N'-nitro-N-nitrosoguanidine tolerance in colon tumor cells with homozygous hMLH1 mutation. Cancer Res. 1994 Aug 15;54(16):4308–4312. [PubMed] [Google Scholar]
  20. Krawczak M., Cooper D. N. Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum Genet. 1991 Mar;86(5):425–441. doi: 10.1007/BF00194629. [DOI] [PubMed] [Google Scholar]
  21. Leach F. S., Nicolaides N. C., Papadopoulos N., Liu B., Jen J., Parsons R., Peltomäki P., Sistonen P., Aaltonen L. A., Nyström-Lahti M. Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell. 1993 Dec 17;75(6):1215–1225. doi: 10.1016/0092-8674(93)90330-s. [DOI] [PubMed] [Google Scholar]
  22. Liu H. S., Feliciano E. S., Stambrook P. J. Cytochemical observation of regulated bacterial beta-galactosidase gene expression in mammalian cells. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9951–9955. doi: 10.1073/pnas.86.24.9951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lupski J. R., de Oca-Luna R. M., Slaugenhaupt S., Pentao L., Guzzetta V., Trask B. J., Saucedo-Cardenas O., Barker D. F., Killian J. M., Garcia C. A. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell. 1991 Jul 26;66(2):219–232. doi: 10.1016/0092-8674(91)90613-4. [DOI] [PubMed] [Google Scholar]
  24. Maekawa M., Sudo K., Kanno T., Li S. S. Molecular characterization of genetic mutation in human lactate dehydrogenase-A (M) deficiency. Biochem Biophys Res Commun. 1990 Apr 30;168(2):677–682. doi: 10.1016/0006-291x(90)92374-9. [DOI] [PubMed] [Google Scholar]
  25. Ofverstedt L. G., Hammarström K., Balgobin N., Hjertén S., Pettersson U., Chattopadhyaya J. Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis). Biochim Biophys Acta. 1984 Jun 16;782(2):120–126. doi: 10.1016/0167-4781(84)90014-9. [DOI] [PubMed] [Google Scholar]
  26. Papadopoulos N., Nicolaides N. C., Wei Y. F., Ruben S. M., Carter K. C., Rosen C. A., Haseltine W. A., Fleischmann R. D., Fraser C. M., Adams M. D. Mutation of a mutL homolog in hereditary colon cancer. Science. 1994 Mar 18;263(5153):1625–1629. doi: 10.1126/science.8128251. [DOI] [PubMed] [Google Scholar]
  27. Parsons R., Li G. M., Longley M., Modrich P., Liu B., Berk T., Hamilton S. R., Kinzler K. W., Vogelstein B. Mismatch repair deficiency in phenotypically normal human cells. Science. 1995 May 5;268(5211):738–740. doi: 10.1126/science.7632227. [DOI] [PubMed] [Google Scholar]
  28. Pearson C. E., Sinden R. R. Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci. Biochemistry. 1996 Apr 16;35(15):5041–5053. doi: 10.1021/bi9601013. [DOI] [PubMed] [Google Scholar]
  29. Pierce J. C., Kong D., Masker W. The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7. Nucleic Acids Res. 1991 Jul 25;19(14):3901–3905. doi: 10.1093/nar/19.14.3901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ripley L. S. Frameshift mutation: determinants of specificity. Annu Rev Genet. 1990;24:189–213. doi: 10.1146/annurev.ge.24.120190.001201. [DOI] [PubMed] [Google Scholar]
  31. Ruskin B., Fink G. R. Mutations in POL1 increase the mitotic instability of tandem inverted repeats in Saccharomyces cerevisiae. Genetics. 1993 May;134(1):43–56. doi: 10.1093/genetics/134.1.43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Scearce L. M., Pierce J. C., McInroy B., Masker W. Deletion mutagenesis independent of recombination in bacteriophage T7. J Bacteriol. 1991 Jan;173(2):869–878. doi: 10.1128/jb.173.2.869-878.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Sinden R. R., Carlson J. O., Pettijohn D. E. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell. 1980 Oct;21(3):773–783. doi: 10.1016/0092-8674(80)90440-7. [DOI] [PubMed] [Google Scholar]
  34. Sinden R. R., Wells R. D. DNA structure, mutations, and human genetic disease. Curr Opin Biotechnol. 1992 Dec;3(6):612–622. doi: 10.1016/0958-1669(92)90005-4. [DOI] [PubMed] [Google Scholar]
  35. Sinden R. R., Zheng G. X., Brankamp R. G., Allen K. N. On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo. Genetics. 1991 Dec;129(4):991–1005. doi: 10.1093/genetics/129.4.991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Singer B. S., Westlye J. Deletion formation in bacteriophage T4. J Mol Biol. 1988 Jul 20;202(2):233–243. doi: 10.1016/0022-2836(88)90454-8. [DOI] [PubMed] [Google Scholar]
  37. Sutherland G. R., Richards R. I. Simple tandem DNA repeats and human genetic disease. Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3636–3641. doi: 10.1073/pnas.92.9.3636. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Trinh T. Q., Sinden R. R. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature. 1991 Aug 8;352(6335):544–547. doi: 10.1038/352544a0. [DOI] [PubMed] [Google Scholar]
  39. Trinh T. Q., Sinden R. R. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli. Genetics. 1993 Jun;134(2):409–422. doi: 10.1093/genetics/134.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Weston-Hafer K., Berg D. E. Limits to the role of palindromy in deletion formation. J Bacteriol. 1991 Jan;173(1):315–318. doi: 10.1128/jb.173.1.315-318.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Weston-Hafer K., Berg D. E. Palindromy and the location of deletion endpoints in Escherichia coli. Genetics. 1989 Apr;121(4):651–658. doi: 10.1093/genetics/121.4.651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Zheng G. X., Kochel T., Hoepfner R. W., Timmons S. E., Sinden R. R. Torsionally tuned cruciform and Z-DNA probes for measuring unrestrained supercoiling at specific sites in DNA of living cells. J Mol Biol. 1991 Sep 5;221(1):107–122. doi: 10.1016/0022-2836(91)80208-c. [DOI] [PubMed] [Google Scholar]
  43. Zheng G. X., Sinden R. R. Effect of base composition at the center of inverted repeated DNA sequences on cruciform transitions in DNA. J Biol Chem. 1988 Apr 15;263(11):5356–5361. [PubMed] [Google Scholar]

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