SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements

Britta Mersch¹ , Noa Sela² , Gil Ast² , Sándor Suhai¹ and Agnes Hotz-Wagenblatt¹

¹Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany

²Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

author email corresponding author email

BMC Genetics 2007, 8:78doi:10.1186/1471-2156-8-78


Published:	6 November 2007

Abstract

Background

Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization), or the element inserts into the exon, leading to a new transcript. Several examples in the literature show that isoforms generated by an exonization are specific to a certain tissue (for example the heart muscle) or inflict a disease. Thus, exonizations can have negative effects for the transcriptome of an organism.

Results

As we aimed at detecting other tissue- or tumor-specific isoforms in human and mouse genomes which were generated through exonization of a transposed element, we designed the automated analysis pipeline SERpredict (SER = Specific Exonized Retroelement) making use of Bayesian Statistics. With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.

Conclusion

Our results show that SERpredict produces relevant results, demonstrating the importance of transposed elements in shaping both the human and the mouse transcriptomes. The effect of transposed elements on the human transcriptome is several times higher than the effect on the mouse transcriptome, due to the contribution of the primate-specific Alu elements.