Application of Alu-splice PCR on chromosome 21: DSCR1 and Intersectin

Down syndrome (DS) is a major cause of mental retardation and congenital heart defects, with an overall incidence of one in 700 live births. DS is caused by increases in the amounts of a number of normal gene products, the exact number and identity of which are presently unknown. Elucidating the molecular basis of DS relies on the identification of the gene products whose augmentation by 50% or more causes symptoms of the disease. With the aim of contributing to the transcriptional map of human chromosome 21 and to identify new genes with potential involvement in DS, we developed a technique to isolate expressed sequences called Alu-splice PCR, which is very simple to perform and is independent of gene expression patterns. Putative exons are PCR amplified in genomic DNA by virtue of their proximity to Alu repeats using primers designed from splice-site consensus sequences in combination with specific Alu repeat primers. The Alu repeats, which are repetitive DNA elements found exclusively and at high frequency in the genomes of primates, impart the human specificity to the method. The splice-site consensus sequences were used to direct primers to exon boundaries. Using the Alu-splice technique, we have identified at least three new genes. We trapped an exon of DSCR1 (Down Syndrome Candidate Region 1) and two different exons of a gene called human Intersectin (ITSN). Presently, we are working with another novel trapped exon to identify the corresponding gene. The major advantage of Alu-splice PCR is that the technique can be readily established in any laboratory which has the basic facilities for molecular biology because no specialised materials or expertise is required.