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PCR-Based Strategies to Clone Unknown DNA Regions from Known Foreign Integrants

An Overview
  • Eric Ka-Wai Hui
  • Po-Ching Wang
  • Szecheng J. Lo
Part of the Methods in Molecular Biology™ book series (MIMB, volume 192)

Abstract

Many foreign DNAs, such as some virus DNAs and almost all transposable elements (transposons), are capable of integrating host genomes, and the effects of integration can be pleiotropic. To investigate the mechanism and biological effect of foreign DNA insertions, characterization of the integration site, called integrant-host junction (IHJ), in the host genome becomes important. Traditional genomic library construction and screening for the cloning and analysis of IHJ are time-consuming, labor-intensive, and tedious. Therefore, a variety of efficient and reliable polymerase chain reaction (PCR)-based techniques have been developed. Application of the PCR to yield enough amounts of DNA for cloning and analysis is highly recommended especially for those specimens that are in a minute amount. Because the amplification process of PCR requires a pair of primers that can anneal to known sites at two end of the target DNA template, it seems that PCR is not applicable to IHJ searching because only one side of the fragment sequence in the integrant is known. A number of PCR-based techniques, however, have been developed to amplify the unknown cellular DNA flanking sequence from the foreign DNA. In this chapter, we introduce the PCRbased methodologies for the rapid acquisition of unknown DNA sequences. Based on the underlying principles, we classified these techniques into five categories: 1) PCR after intramolecular circularization; 2) interspersed repetitive sequence PCR (IRS-PCR); 3) ligation-anchored PCR (LA-PCR); 4) arbitrarily primed PCR (AP-PCR); and 5) reverse transcription PCR (RT-PCR).

Keywords

Polymerase Chain Reaction Long Terminal Repeat Integration Site Conventional Polymerase Chain Reaction Long Intersperse Nuclear Element 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Collins, F. S. and Weissman, S. M. (1984) Directional cloning of DNA fragments at a large distance from an initial probe: a circularization method. Proc. Natl. Acad. Sci. USA 81, 6812–6816.PubMedCrossRefGoogle Scholar
  2. 2.
    Ochman, H., Gerber, A. S., and Hartl, D. L. (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621–623.PubMedGoogle Scholar
  3. 3.
    Ochman, H., Ajioka, J. W., Garza, D., and Hartl, D. L. (1989) Amplification of flanking sequences by inverse PCR, in PCR Technology Ehrlich, H. A., ed., Stockton, New York, pp. 105–111.Google Scholar
  4. 4.
    Triglia, T., Peterson, M. G., and Kemp, D. J. (1988) A procedure for in vitro amplifica-tion of DNA segments that lie outside the boundaries of known sequence. Nucl. Acid Res. 16, 8186.CrossRefGoogle Scholar
  5. 5.
    Silver, J. and Keerikatte, V. (1989) Novel use of polymerase chain reaction to amplify cellular DNA adjacent to an integrated provirus. J. Virol. 63, 1924–1928.PubMedGoogle Scholar
  6. 6.
    Willis, T. G., Jadayel, D. M., Coignet, L. J. A., Abdul-Rauf, M., Treleaven, T. J., Catorsky, D., and Byer, M. J. S. (1997) Rapid molecular cloning of rearrangements of the IGHJ locus using long-distance inverse polymerase chain reaction. Blood 90, 2456–2462.PubMedGoogle Scholar
  7. 7.
    Garces, J. A. and Gavin, R. H. (2001) Using an inverse PCR strategy to clone large contiguous genomic DNA fragments. Meth. Mol. Biol. 161, 3–8.Google Scholar
  8. 8.
    Tsuei, D.-J., Chen, P.-J., Lai, M.-Y., Chen, D.S., Yang, C.-S., Chen, J.-Y., and Hsu, T.-Y. (1994) Inverse polymerase chain reaction for cloning cellular sequences adjacent to integrated hepatitis B virus DNA in hepatocellular carcinomas. J. Virol. Meth. 49, 269–284.CrossRefGoogle Scholar
  9. 9.
    Wang, P.-C., Hui, E. K.-W., Chiu, J.-H., and Lo, S. J. (2001) Analysis of integrated hepatitis B virus DNA and flanking cellular sequence by inverse polymerase chain reaction. J. Virol. Meth. 92, 83–90.CrossRefGoogle Scholar
  10. 10.
    Takemoto, S., Matsuoka, M., Yamaguchi, K., and Takatsuki, K. (1994) A novel diagnostic method of adult T-cell leukemia: monoclonal integration of human T-cell lymphotropic virus type I provirus DNA detected by inverse polymerase chain reaction. Blood 84, 3080–3085.PubMedGoogle Scholar
  11. 11.
    Cavrois, M., Wain-Hobson, S., and Wattel, E. (1995) Stochastic events in the amplification of HTLV-I integration sites by linker-mediated PCR. Res. Virol. 146, 179–184PubMedCrossRefGoogle Scholar
  12. 12.
    Cavrois, M., Wain-Hobson, S., Gessain, A., Plumelle, Y., and Wattel, E. (1996) Adult T-cell leukemia/lymphoma on a background of clonally expanding HTLV-1 positive cells. Blood 88, 4646–4650.PubMedGoogle Scholar
  13. 13.
    Ohshima, K., Suzumiya, J., Kato, A., Tashiro, K., and Kikuchi, M. (1997) Clonal HTLV-I-infected CD4+T-lymphocytes and non-clonal non-HTLV-infected giant cells in incipient ATLL with Hodgkin-like histologic features. Int. J. Cancer 72, 592–598. 269PubMedCrossRefGoogle Scholar
  14. 14.
    Ohshima, K., Mukai, Y., Shiraki, H., Suzumiya, J., Tashiro, K., and Kikuchi, M. (1997) Clonal integration and expression of human T-cell lymphotropic virus type I in carriers detected by polymerase chain reaction and inverse PCR. Am. J. Hematol. 54, 306–312.PubMedCrossRefGoogle Scholar
  15. 15.
    Leclercq, I., Cavrois, M., Mortreux, F., Hermine, O., and Gessain, A. (1998) Oligoclonal proliferation of human T-cell leukemia virus type 1 bearing T cells in adult T-cell leukemia/ lymphoma without deletion of the 3′ provirus integration sites. J. Haematol. 101, 500–506.CrossRefGoogle Scholar
  16. 16.
    Carteau, S., Hoffmann, C., and Bushman, F. (1998) Chromosome structure and human immunodeficiency virus type 1 cDNA integration: centromeric alphoid repeats are a disfavored target. J. Virol. 72, 4005–4014.PubMedGoogle Scholar
  17. 17.
    Ochman, H., Ayala, F. J., and Hartl, D. L. (1993) Use of polymerase chain reaction to amplify segments outside boundaries of known sequences. Meth. Enzymol. 218, 309–321.PubMedCrossRefGoogle Scholar
  18. 18.
    Knapp, S., Larondelle, Y., Robberg, M., Furtek, D., and Theres, K. (1994) Transgenic tomato lines containing Ds elements at defined genomic positions as tools for targeted transposon tagging. Mol. Gen. Genet. 243, 666–673.PubMedGoogle Scholar
  19. 19.
    Souer, E., Quattrocchio, F., de Vetten, N., Mol, J., and Koes, R. (1995) A general method to isolate genes tagged by a high copy number transposable element. Plant J. 7, 677–685.PubMedCrossRefGoogle Scholar
  20. 20.
    Martin, V. J. and Mohn, W. W. (1999) An alternative inverse PCR (IPCR) method to amplify DNA sequence flanking Tn5 transposon insertions. J. Microbiol. Meth. 35, 163–166.CrossRefGoogle Scholar
  21. 21.
    De Lencastre, H., Wu, S. W., Pinho, M. G., Ludovice, A. M., Filipe, S., Gardete, S., et al. (1999) Antibiotic resistance as a stress response: complete sequencing of a large number of chromosomal loci in Staphylococous aureus strain COL that impact on the expression of resistance to methicillin. Microbiol. Drug Res. 5, 163–175.CrossRefGoogle Scholar
  22. 22.
    Liao, G.-C., Rehm, E. J., and Rubin, G. M. (2000) Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 97, 3347–3351.PubMedCrossRefGoogle Scholar
  23. 23.
    Isfort, R., Jones, D., Kost, R., Witter, R., and Kung, H.-J. (1992) Retrovirus insertion into herpesvirus in vitro and in vivo. Proc. Natl. Acad. Sci. USA 89, 991–995.PubMedCrossRefGoogle Scholar
  24. 24.
    Pang, K. M. and Knecht, D. A. (1997) Partial inverse PCR: a technique for cloning flanking sequences. BioTechniques 22, 1046–1048.PubMedGoogle Scholar
  25. 25.
    Mathur, J., Szabados, L., Schaefer, S., Grunenberg, B., Lossow, A., Jonas-Straube, E., et al. (1998) Gene identification with sequenced T-DNA tags generated by transformation of Arabidopsis cell suspension. Plant J. 13, 707–716.PubMedCrossRefGoogle Scholar
  26. 26.
    Raponi, M., Dawes, I. W., and Arndt, G. M. (2000) Characterization of flanking sequences using long inverse PCR. BioTechniques 28, 839–843.Google Scholar
  27. 27.
    Smit, A. F. (1996) The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743–748.PubMedCrossRefGoogle Scholar
  28. 28.
    Mighell, A. J., Markham, A. F., and Robinson, P. A. (1997) Alu sequence. FEBSLett. 417, 1–5.CrossRefGoogle Scholar
  29. 29.
    Szmulewicz, M. N., Novick, G. E., and Herrera, R. J. (1998) Effects of Alu insertions on gene function. Electrophoresis 19, 1260–1264.PubMedCrossRefGoogle Scholar
  30. 30.
    Nelson, D. L., Ledbetters, S. A., Corbo, L., Victoria, M. F., Ramirez-Solis, R., Webster, T. D., et al. (1989) Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA 86, 6686–6690.PubMedCrossRefGoogle Scholar
  31. 31.
    Nelson, D. L., Ballabio, A., Victoria, M. F., Pieretti, M., Bies, R. D., Gibbs, R. A., et al. (1991) Alu-primer polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. Proc. Natl. Acad. Sci. USA 88, 6157–6161.PubMedCrossRefGoogle Scholar
  32. 32.
    Ledbetter, S. A., Nelson, D. L., Warren, S. T., and Ledbetter, D. H. (1990) Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequence polymerase chain reaction. Genomics 6, 475–481. 270PubMedCrossRefGoogle Scholar
  33. 33.
    Puskas, L. G., Fartmann, B., and Bottka, S. (1994) Restricted PCR: amplification of an individual sequence flanked by a highly repetive element from total human DNA. Nucl. Acids Res. 22, 3251–3252.PubMedCrossRefGoogle Scholar
  34. 34.
    Minami, M., Poussin, K., Brechot, C., and Paterlini, P. (1995) A novel PCR technique using Alu-specific primers to identify unknown flanking sequences from the human genome. Genomics 29, 403–408.PubMedCrossRefGoogle Scholar
  35. 35.
    Gyllensten, U. B. and Erlich, H. A. (1988)Generation of single-stranded DNA by the polmerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl. Acad. Sci. USA 85, 7652–7656.PubMedCrossRefGoogle Scholar
  36. 36.
    Gyllensten, U. B. and Allen, M. (1993) Sequencing of in vitro amplified DNA. Meth. Enzymol. 218, 1–16.Google Scholar
  37. 37.
    Courcoul, M., Patience, C., Rey, F., Blanc, D., Harmache, A., Sire, J., et al. (1995) Peripheral blood mononuclear cells produce normal amounts of detective Vif-human immunodeficiency virus type 1 particles which are restricted for the preretrotranscription steps. J. Virol. 69, 2068–2074.PubMedGoogle Scholar
  38. 38.
    Sonza, S., Maerz, A., Deacon, N., Meanger, J., Mills, J., and Crowe, S. (1996) Human immunodeficiency virus type 1 replication is blocked prior to reverse transcription and integration in freshly isolated peripheral blood monocytes. J. Virol. 70, 3863–3869.PubMedGoogle Scholar
  39. 39.
    Carmody, M. W., Jones, M., Tarraza, H., and Vary, C.P. (1996) Use of the polymerase chain reaction to specifically amplify integrated HPV-16 DNA by virtue of its linkage to interspersed repetitive DNA. Mol. Cell. Probes 10, 107–116.PubMedCrossRefGoogle Scholar
  40. 40.
    Wu, P., Phillips, M.I., Bui, J., and Terwilliger, E.F. (1998) Adeno-associated virus vectormediated transgene integration into neurons and other nondividing cell targets. J. Virol. 72, 5919–5926.PubMedGoogle Scholar
  41. 41.
    Choo, K. B., Liu, M. S., Chang, P. C., Wu, S. M., Su, M. W., Pan, C. C., and Han, S. H. (1986) Analysis of six distinct integrated hepatitis B virus sequences cloned from the cellular DNA of a human hepatocellular carcinoma. Virology 154, 405–408.PubMedCrossRefGoogle Scholar
  42. 42.
    Shaul, Y., Garcia, P. D., Schonberg, S., and Rutter, W. J. (1986) Integration of hepatitis B virus DNA in chromosome-specific satellite sequences. J. Virol. 59, 731–734.PubMedGoogle Scholar
  43. 43.
    Nagaya, T., Nakamura, T., Tokino, T., Tsurimoto, T., Imai, M., Mayumi, T., et al. (1987) The mode of hepatitis B virus DNA integration in chromosomes of human hepatomcellular carcinoma. Genes Deve. 1, 773–782.CrossRefGoogle Scholar
  44. 44.
    Matsumoto, H., Yoneyama, T., Mitamura, K., Osuga, T., Shimojo, H., and Miyamura, T. (1988) Analysis of integrated hepatitis B virus DNA and cellular flanking sequences cloned from a hepatocellular carcinoma. Int. J. Cancer 42, 1–6.PubMedCrossRefGoogle Scholar
  45. 45.
    Quada, K., Saldanha, J., Thomas, H., and Monjardino, J. (1992) Integration of hepatitis B virus DNA through a mutational hot spot within the cohesive region in a case of hepatocellular carcinoma. J. Gen. Virol. 73, 179–183.CrossRefGoogle Scholar
  46. 46.
    Chen, J. Y., Harrison, T. J., Tsuei, D. J., Hsu, T. Z., Zuckerman, A. J., Chan, T. S., and Yang, C. S. (1994) Analysis of integrated hepatitis B virus DNA and flanking cellular sequences in the hepatocellular carcinoma cell line HCC36. Intervirology 37, 41–46.PubMedGoogle Scholar
  47. 47.
    Dhruva, B. R., Shenk, T., and Subramanian, K. W. (1980) Integration in vivo into simian virus 40 DNA of a sequence that resembles a certain family of genomic interspersed repeated sequences. Proc. Natl. Acad. Sci. USA 77, 4514–4518.PubMedCrossRefGoogle Scholar
  48. 48.
    Ou, C.-Y., Boone, L. R., and Yang, W. K. (1983) A novel sequence segment and other nucleotide structural features in the long terminal repeat of a BALB/c mouse genomic leukemia virus-related DNA clone. Nucl. Acids Res. 11, 5603–5620. 271PubMedCrossRefGoogle Scholar
  49. 49.
    Taruscio, D. and Maneulidis, L. (1991) Integration site preferences of endogenous retroviruses. Chromosoma 101, 141–156.PubMedCrossRefGoogle Scholar
  50. 50.
    Stevens, S. W. and Griffith, J. D. (1994) Human immunodeficiency virus type 1 may preferentially integrate into chromatin occupied by L1Hs repetitive elements. Proc. Natl. Acad. Sci. USA 91, 5557–5561.PubMedCrossRefGoogle Scholar
  51. 51.
    Stevens, S. W. and Griffith, J. D. (1996) Sequence analysis of the human DNA flanking sites of human immunodeficiency virus type 1 integration. J. Virol. 70, 6459–6462.PubMedGoogle Scholar
  52. 52.
    Awady, M. K., Kaplan, J. B., O′Brien, S. T., and Burd, R. D. (1987) Molecular analysis of integrated human HPV16 sequences in the cervical cancer cell line SiHa. Virology 159, 389–398.PubMedCrossRefGoogle Scholar
  53. 53.
    Baker, C. C., Phelps, W. C., Lindgren, V., Braun, M. J., Gonda, M. A., and Howley, P. M. (1987) Structural and transcriptional analysis of HPV16 sequences in cervical carcinoma cell lines. J. Virol. 61, 962–971.PubMedGoogle Scholar
  54. 54.
    Wagatsuma, M., Hashimoto, K., and Matsukura, T. (1990) Analysis of integrated human HPV16 DNA in cervical cancers, amplification of viral sequences together with cellular flanking sequences. J. Virol. 64, 813–821.PubMedGoogle Scholar
  55. 55.
    Bruni, R., Argentini, C., D′Ugo, E., Giuseppetti, R., and Rapicetta, M. (1997) Wood-chuck hepatitis virus DNA integration in a common chromosomal region of the wood-chuck genome in two independent hepatocellular carcinomas. Arch. Virol. 142, 499–509.PubMedCrossRefGoogle Scholar
  56. 56.
    Gong, S. S., Jensen, A. D., Chang, C. J., and Rogler, C. E. (1999) Double-stranded linear duck hepatitis virus virus (DHBV) stably integrates at higher frequency than wild-type DHBV in LMH chicken hepatoma cells. J. Virol. 73, 1492–1502.PubMedGoogle Scholar
  57. 57.
    Mueller, P. R. and Wold, B. (1989) In vivo footprinting of a muscle specific enhancer by ligated mediate PCR. Science 246, 780–786.PubMedCrossRefGoogle Scholar
  58. 58.
    Shyamala, V. and Ames, G. F.-L. (1989) Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR. Gene 84, 1–8.PubMedCrossRefGoogle Scholar
  59. 59.
    Zhang, Y. and Frohman, M. A. (1997) Using rapid amplification of cDNA ends (RACE) to obtain full-length cDNAs, in cDNA Library Protocols, Cowell, I. G. and Austin, C. A., eds., Humana, Totowa, NJ, pp.61–87.Google Scholar
  60. 60.
    Mizobuchi, M. and Frohman, L.A. (1993) Rapid amplification of genomic DNA ends. BioTechiques 15, 214–216.Google Scholar
  61. 61.
    Wattel, E., Vartanian, J. P., and Wain-Hobson, S. (1995) Clonal expansion of HTLV-I infected cells in asymptomatic and symptomatic carries without malignancy. J. Virol. 69, 2863–2868.PubMedGoogle Scholar
  62. 62.
    Cavrois, M., Gessain, A., Wain-Hobson, S., and Wattel, E. (1996) Proliferation of HTLV-1 infected circulating cells in vivo in all asymptomatic carries and patients with TSP/HAM. Oncogene 12, 2419–2423.PubMedGoogle Scholar
  63. 63.
    Riley, J., Butler, R., Ogilvie, D., Finniear, R., Jenner, D., Powell, S., et al. (1990) A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucl. Acids Res. 18, 2887–2890.PubMedCrossRefGoogle Scholar
  64. 64.
    Arnold, C. and Hodgson, I. J. (1991) Vectorette PCR: a novel approach to genomic walking. PCR Meth. Appl. 1, 39–42.Google Scholar
  65. 65.
    Rubie, C., Schulze-Bahr, E., Wedekind, H., Borggrefe, M., Haverkamp, W., and Breithardt, G. (1999) Multistep-touchdown vectorette-PC-a rapid technique for the identification of IVS in genes. BioTechniques 27, 414–418.PubMedGoogle Scholar
  66. 66.
    Proffitt, J., Fenton, J., Pratt, G., Yates, Z., and Morgan, G. (1999) Isolation and characterization of recombination events involving immunoglobulin heavy chain switch regions in 272 multiple myeloma using long distance vectorette PCR (LDV-PCR) Leukemia 13, 1100–1107.PubMedCrossRefGoogle Scholar
  67. 67.
    Devon, R. S., Porteous, D.J., and Brookes, A. J. (1995) Splinkerettes-improved vectorettes for greater efficiency in PCR walking. Nucl. Acids Res. 23, 1644–1645.PubMedCrossRefGoogle Scholar
  68. 68.
    Ivics, Z., Hackett, P. B., Plasterk, R. H., and Izsvak, Z. (1997) Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition ion human cells. Cell 91, 501–510.PubMedCrossRefGoogle Scholar
  69. 69.
    Williams, J. G. K., Kubelik, A. R., Livak, K. J., and Rofalski, J. A. (1990) DNA polymorphisma amplified by arbitray primers are useful as genetic markers. Nucl. Acids Res. 18, 6531–6535.PubMedCrossRefGoogle Scholar
  70. 70.
    Parker, J. D., Rabinovitch, P. S., and Burmer, G. C. (1991) Targeted gene walking poly-merase chain reaction. Nucl. Acid Res. 19, 3055–3060.CrossRefGoogle Scholar
  71. 71.
    Hui, E. K.-W., Wang, P.-C., and Lo, S. J. (1998) Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants. Cell. Mol. Life Sci. 54, 1403–1411.PubMedCrossRefGoogle Scholar
  72. 72.
    Parks, C. L., Chang, L.-S., and Sheuk, T. (1991) A polymerase chain reaction mediated by a single primer: cloning of genomic sequences adjacent to a serotonin receptor protein coding region. Nucl. Acids Res. 19, 7155–7160.PubMedCrossRefGoogle Scholar
  73. 73.
    Liang, P. and Pardee, A. B. (1992) Differential display of eukaryotic messager RNA by means of the polymerase chain reaction. Science 257, 967–971.PubMedCrossRefGoogle Scholar
  74. 74.
    Carulli, J. P., Artinger, M., Swain, P. M., Root, C. D., Chee, L., Tulig, C., et al. (1998) High throughput analysis of differential gene expression. J. Cell. Biochem. Suppl. 30/31, 286–296.CrossRefGoogle Scholar
  75. 75.
    Matz, M. V. and Lukyanov, S. A. (1998) Different strategies of differential display: area of application. Nucl. Acids Res. 26, 5537–5543.PubMedCrossRefGoogle Scholar
  76. 76.
    Sarkar, G., Turner, R. T., and Bolander, M. E. (1993) Restriction-site PCR: a direct method of unknown sequence retrieval adjacent to a know locus by using universal primers. PCR Meth. Appl. 2, 318–322.Google Scholar
  77. 77.
    Liu, Y.-G., Mitsukawa, N., Oosumi, T., and Whittier, R. F. (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 8, 457–463.PubMedCrossRefGoogle Scholar
  78. 78.
    Campisi, L., Yang, Y., Heiling, E., Herman, B., Carsista, A. J., Allen, D. W., et al. (1999) Generation of enhancer trap lines in Arabidopsis and characterization of expression patterns in the inflorescence. Plant J. 17, 699–707.PubMedCrossRefGoogle Scholar
  79. 79.
    Smith, D., Yanai, Y., Liu, Y.-G., Ishiguro, S., Okada, K., Shibata, D., et al. (1996) Characterisation and mapping of Ds-Gus-T-DNA lines for targeted insertional mutagen-esis. Plant J. 10, 721–732.PubMedCrossRefGoogle Scholar
  80. 80.
    Parinov, S., Sevugan, M., Ye, D., Yang, W.-C., Kumaran, M., and Sundaresan, V. (2000) Analysis of flanking sequences from Dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell 11, 2263–2270.CrossRefGoogle Scholar
  81. 81.
    Okamoto, H. and Hirochika, H. (2000) Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobaao retrotransposon Tto1. Plant J. 23, 291–304.PubMedCrossRefGoogle Scholar
  82. 82.
    Casper, C., Leib-Mosch, C., Salmons, B., Gunzburg, W. H., Baumann, G., Hofler, H., et al. (1998) Mapping of mouse mammary tumor virus integration site by retroviral LTR-arbitrary polymerase chain reaction. Virus Res. 54, 207–215.PubMedCrossRefGoogle Scholar
  83. 83.
    Borenshtein, R. and Davidson, I. (1999) Development of the hot spot-combined PCR assay for detection of retroviral insertions into Marek′s disease virus. J. Virol. Meth. 82, 119–127. 273CrossRefGoogle Scholar
  84. 84.
    Liu, Y.-G. and Whittier, R. F. (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chro-mosome walking. Genomics 25, 674–681.PubMedCrossRefGoogle Scholar
  85. 85.
    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.PubMedCrossRefGoogle Scholar
  86. 86.
    Morishita, K., Parker, D. S., Mucenski, M. L., Jenkins, N. A., Copeland, N. G., and Ihle, J. N. (1988) Retroviral activation of a novel gene encoding a zinc finger protein in IL-3-dependent myeloid leukemia cell lines. Cell 54, 831–840.PubMedCrossRefGoogle Scholar
  87. 87.
    Askew, D. S., Bartholomew, C., Buchbeg, A. M., Valentine, M. B., Jenkins, N. A., Copeland, N. G., and Ihle, J. N. (1991) His-1 and His-2: identification and chromosomal mapping of two commonly rearranged sites of viral integration in a myeloid leukemia. Oncogene 6, 2041–2047.PubMedGoogle Scholar
  88. 88.
    Loh, E. Y., Elliott, J. F., Cwirla, S., Lanier, L. L., and Davis, M. M. (1989) Polymerase chain reaction with single-sided specificity: analysis of T cell receptor d chain. Science 243, 217–220.PubMedCrossRefGoogle Scholar
  89. 89.
    Ohara, O., Dorit, R. L., and Gilbert, W. (1989) One-sided polymerase chain reaction: the amplification of cDNA. Proc. Natl. Acad. Sci. USA 86, 5673–5677.PubMedCrossRefGoogle Scholar
  90. 90.
    Valk, P. J. M., Joosten, M., Vankan, Y., Lowenberg, B., and Delwel, R. (1997) A rapid RT-PCR based method to isolate complementary DNA fragments flanking retrovirus integration sites. Nucl. Acids Res. 25, 4419–4421.PubMedCrossRefGoogle Scholar
  91. 91.
    Lagerstrom, M., Parik, J., Malmgren, H., Stewart, J., Pettersson, U., and Landegren, U. (1991) Capture PCR: efficient amplification of DNA fragments adjacent to a known sequence in human and YAC DNA. PCR Meth. Appl. 1, 111–119.Google Scholar
  92. 92.
    Sorensen, A. B., Duch, M., Jorgensen, P., and Petersen, F. S. (1993) Amplification and sequence analysis of DNA flanking integrated pproviruses by a simple two-step polymerase chain reaction method. J. Virol. 67, 7118–7124.PubMedGoogle Scholar
  93. 93.
    Frey, M., Settner, C., and Gierl, A. (1998) A general method for gene isolation in tagging approaches: Amplification of insertion mutagenised sites (AIMS) Plant J. 13, 717–721.CrossRefGoogle Scholar
  94. 94.
    Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grun, S., Winklmair, A., et al. (1997) Analysis of a chemical defense mechanism in grasses. Science 277, 696–699.PubMedCrossRefGoogle Scholar
  95. 95.
    Peters, G. (1990) Oncogenes at viral integration sites. Cell Growth Diff. 1, 503–510.PubMedGoogle Scholar
  96. 96.
    Jonkers, J. and Berns, A. (1996) Retroviral insertional mutagenesis as a strategy to identify cancer genes. Biochim. Biophys. Acta 1287, 29–57.PubMedGoogle Scholar
  97. 97.
    Huang, S.-H. (1997) Inverse PCR approach to cloning cDNA ends, in cDNA Library Protocols (Cowill, J. G. and Austin, C. A., eds., Humana, Totowa, NJ, pp.89–96.Google Scholar
  98. 98.
    Hodzic, D., Frey, B., Marechal, D., Scarcez, T., Grooteclaes, M., and Winkler, R. (1999) Cloning of breakpoints in and downstream the IGF2 gene that are associated with overexpression of IGF2 transcripts in colorectal tumours. Oncogene 18, 4710–4717.PubMedCrossRefGoogle Scholar
  99. 99.
    Moynihan, T. P., Markham, A. F., and Robinson, P. A. (1996) Genomic analysis of human multigene families using chromosome-specific vectorette PCR. Nucl. Acids Res. 24, 4094–4095.PubMedCrossRefGoogle Scholar
  100. 100.
    Triglia, T. (2000) Inverse PCR (IPCR) for obtaining promoter sequence. Meth. Mol. Biol. 130, 79–83.Google Scholar
  101. 101.
    Terauchi, R. and Kahl, G. (2000) Rapid isolation of promoter sequences by TAIL-PCR: the 5′-flanking regions of Pal and Pgi genes from yams (Dioscorea) Mol. Gen. Genet. 263, 554–560. 274PubMedCrossRefGoogle Scholar
  102. 102.
    Witthuhn, R. C., Harrington, T. C., Wingfield, B. D., Steimel, J. P., and Wingfield, M. J. (2000) Deletion of the MAT-2 mating-type gene during uni-directional mating-type switching in Ceratocystis. Curr. Genet. 38, 48–52.PubMedCrossRefGoogle Scholar
  103. 103.
    Akiyama, K., Watanabe, H., Tsukada, S., and Sasai, H. (2000) A novel method for con-structing gene-targeting vectors. Nucl. Acids Res. 28, E77.PubMedCrossRefGoogle Scholar
  104. 104.
    Cormack, R. S. and Somssich, I. E. (1997) Rapid amplification of genomic ends (RAGE) as a simple method to clone flanking genomic DNA. Gene 194, 273–276.PubMedCrossRefGoogle Scholar
  105. 105.
    Jones, D. H. and Winistorfer, S. C. (1992) Sequence specific generation of a DNA panhandle permits PCR amplification of unknown flanking DNA. Nucl. Acids Res. 20, 595–600PubMedCrossRefGoogle Scholar
  106. 106.
    Jones, D. H. and Winistorfer, S. C. (1993) Genome walking with 2-to 4-kb steps using panhandle PCR. PCR Meth. Appl. 2, 197–203.Google Scholar
  107. 107.
    Jones, D. H. (1995) Panhandle PCR, in PCR Primer: A Laboratory Manual, Dieffenbach, C. W. and Dveksler, G. S., eds., Cold Spring Harbor Laboratory Press, NY, pp.411–419.Google Scholar
  108. 108.
    Weber, K. L., Bolander, M. E., and Sarkab, G. (1998) Rapid acquisition of unknown DNA sequence adjacent to a known segment by multiplex restriction site PCR. BioTechniques 25, 415–419.PubMedGoogle Scholar
  109. 109.
    Baury, B., Masson, D., Lustenberge, P., and Denis, M. G. (1999) Gene walking by PCR amplification of short fragments from Taq DNA polymerase-modified P1 plasmid DNA and TA cloning. BioTechniques 27, 1118–1122.PubMedGoogle Scholar
  110. 110.
    Rudi, K., Fossheim, T., and Jakobsen, K. S. (1999) Restriction cutting independent method for cloning genomic DNA segments outside the boundaries of known sequences. BioTechniques 27, 1170–1177.PubMedGoogle Scholar
  111. 111.
    Zhang, Z. and Gurr, S. J. (2000) Walking into the unknown: a “step down” PCR-based technique leading to the direct sequence analysis of flanking genomic DNA. Gene 253, 145–150.PubMedCrossRefGoogle Scholar
  112. 112.
    Tamme, R., Camp, E., Kortschak, R. D., and Lardelli, M. (2000) Nonspecific, nested suppression PCR method for isolation of unknown flanking DNA. BioTechniques 28, 895–902.PubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2002

Authors and Affiliations

  • Eric Ka-Wai Hui
    • 1
  • Po-Ching Wang
    • 2
  • Szecheng J. Lo
    • 3
  1. 1.Department of Microbiology, Immunology and Molecular GeneticsUniversity of California Los AngelesLos Angeles
  2. 2.Department of MedicineNational Yang-Ming UniversityTaipeiTaiwan
  3. 3.Institute of Microbiology and ImmunologyNational Yang-Ming UniversityTaipeiTaiwan, ROC

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