Protocol

Genomics Protocols

Volume 175 of the series Methods in Molecular Biology™ pp 201-215

Exon Trapping

Application of a Large-Insert Multiple-Exon-Trapping System
  • Martin C. WapenaarAffiliated withMGC-Department of Human and Clinical Genetics, Leiden University Medical Center
  • , Johan T. Den DunnenAffiliated withMGC-Department of Human and Clinical Genetics, Leiden University Medical Center

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Abstract

Exon trapping (Fig. 1) is a technique that has been developed to identify genes in cloned eukaryotic DNA (17). 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.
http://static-content.springer.com/image/chp%3A10.1385%2F1-59259-235-X%3A201/MediaObjects/978-1-59259-235-7_14_Fig1_HTML.jpg
Fig. 1.

Principle of exon trapping.