EST-based identification of alternative splicing in disease relevant genes

M. Scharfenberger, M. Kögl  (RZPD Heidelberg)

About two third of the human genes are alternatively spliced. Recent studies showed a correlation between splicing variants and human disease, such as cancer (Roy et al. [2005] Nucleic Acids Res 33, 5026-33) and several neurodegenerative disorders (Lee and Irizarry [2003] Biol Psychiatry 54, 771-6).

The aim of this project is the cloning and following analysis of the alternative splice isoforms of disease relevant genes. Supposing that variations of the gene might contribute to tumour formation we will preferentially concentrate on genes which are involved in the cancer relevant pathways.

Furthermore, we focus on splice variants which exist in the coding region and show at least one exon difference. We aim at amplifying the complete open reading frame (ORF) of the splice variants of these genes and at cloning them into a shuttle vector system (Gateway®). This allows us to express the ORFs of the splice variants for downstream functional analysis, e.g. high throughput functional assay within SMP-Cell.

This project relies on the analytical characterisation of splice isoforms within human tissues by RT-PCR as shown in the example.

Further reading (http://www.smp-cell.org/Files/Reports/SMP-Cell_SpliceRZPD.pdf)