Exon Trapping

Application of a Large-Insert Multiple-Exon-Trapping System
  • Martin C. Wapenaar
  • Johan T. Den Dunnen
Part of the Methods in Molecular Biology™ book series (MIMB, volume 175)


Exon trapping (Fig. 1) is a technique that has been developed to identify genes in cloned eukaryotic DNA (1, 2, 3, 4, 5, 6, 7). Compared with other techniques for gene identification, exon trapping has two main characteristic features. First, it is independent of the availability of an RNA sample in which the gene to identify is expressed. Second, the sequences isolated directly derive from the input DNA. Some 10–20% of all genes might be expressed at very low levels or only during very short stages of development, making it difficult to isolate them based on their expression using cDNA hybridization or cDNA selection protocols. Exon trapping uses an assay isolating sequences based on the presence of functional splice sites. Consequently, sequences are isolated directly from the clone under analysis without knowledge or availability of tissues expressing the gene to be identified. Furthermore, because isolation is not based on hybridization, it is not possible to isolate highly similar sequences that derive from other parts of the genome, not under analysis.
Fig. 1.

Principle of exon trapping.


  1. 1.
    Auch, D. and Reth, M. (1990) Exon trap cloning: using PCR to rapidly detect and clone exons from genomic DNA fragments. Nucleic Acids Res. 18, 6743, 6744.PubMedCrossRefGoogle Scholar
  2. 2.
    Duyk, G. M., Kim, S., Myers, R. M., and Cox, D. R. (1990) Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA. Proc. Natl. Acad. Sci. USA 87, 8995–8999.PubMedCrossRefGoogle Scholar
  3. 3.
    Church, D. M., Stotler, C. J., Rutter, J. L., Murrell, J. R., Trofatter, J. A., and Buckler, A.J. (1994) Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genet. 6, 98–105.PubMedCrossRefGoogle Scholar
  4. 4.
    Datson, N. A., Van De Vosse, E., Dauwerse, J. G., Bout, M., Van Ommen, G. J. B., and Den Dunnen, J. T. (1996) Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product. Nucleic Acids Res. 24, 1105–1111.PubMedCrossRefGoogle Scholar
  5. 5.
    Burn, T. C., Connors, T. D., Klinger, K. W., and Landes, G. M. (1995) Increased axon-trapping efficiency through modifications to the pSPL3 splicing vector. Gene 161, 83–87.CrossRefGoogle Scholar
  6. 6.
    Datson, N. A., Duyk, G. M., Van Ommen, G. J. B., and Den Dunnen, J. T. (1994) Specific isolation of 3′-terminal exons of human genes by exon trapping. Nucleic Acids Res. 22, 4148–4153.PubMedCrossRefGoogle Scholar
  7. 7.
    Krizman, D. B. and Berget, S. M. (1993) Efficient selection of 3′-terminal exons from vertebrate DNA. Nucleic Acids Res. 21, 5198–5202.PubMedCrossRefGoogle Scholar
  8. 8.
    Roest, P. A. M., Roberts, R. G., Sugino, S., Van Ommen, G. J. B., and Den Dunnen, J. T. (1993) Protein truncation test (PTT) for rapid detection of translation-terminating mutations. Hum. Mol Genet 2, 1719–1721.PubMedCrossRefGoogle Scholar
  9. 9.
    Petrij, F., Giles, R. H., Danwerse, J. G., Saris, J. J., Hennekam, R. C. M., Masuno, M., Tommerup, N., Van Ommen, G. J. B., Goodman, R. H., Peters, D. J. M., and Breuning, M. H. (1995) Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature 376, 348–351.PubMedCrossRefGoogle Scholar
  10. 10.
    Den Dunnen, J. T., Grootscholten, P. M. and Van Ommen, G. J. B. (1993) Pulsed-field gel electrophoresis in the analysis of genomic DNA and YAC clones, in Human Genetic Disease Analysis: A Practical Approach (Davies, K. E., ed.), Oxford University Press, Oxford, pp. 35–58.Google Scholar
  11. 11.
    Searle, P. F., Stuart, G. W., and Palmiter, R. D. (1985) Building a metal-responsive promoter with synthetic regulatory elements. Mol. Cell. Biol. 5, 1480–1488.PubMedGoogle Scholar
  12. 12.
    Hentze, M. W. and Kulozik, A. E. (1999) A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96, 307–310.PubMedCrossRefGoogle Scholar
  13. 13.
    Carter, M. S., Doskow, J., Morris, P., Li, S., Nhim, R. P., Sandstedt, S., and Wilkinson, M. F. (1995) A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro. J. Biol. Chem. 270, 28,995–29,003.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2001

Authors and Affiliations

  • Martin C. Wapenaar
    • 1
  • Johan T. Den Dunnen
    • 1
  1. 1.MGC-Department of Human and Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands

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