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


CONCLUSIONS
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.
Mersch
Britta
B
Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany. b.mersch@dkfz.de
Sela
Noa
N
Ast
Gil
G
Suhai
Sándor
S
Hotz-Wagenblatt
Agnes
A
D017398:Alternative Splicing; D020087:Alu Elements; D000818:Animals; D004251:DNA Transposable Elements; D030541:Databases, Genetic; D005091:Exons; D020224:Expressed Sequence Tags; D015723:Gene Library; D052138:Genes, Neoplasm; D006801:Humans; D051379:Mice; D009928:Organ Specificity; D020033:Protein Isoforms / Q000235:genetics*; D018626:Retroelements
D004251:DNA Transposable Elements; D020033:Protein Isoforms; D018626:Retroelements