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

Mersch B, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A - BMC Genet. (2007)

Bottom Line: 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.With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany. b.mersch@dkfz.de

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.

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Example output of SERpredict. The output of SERpredict for [EMBL:AF466401] is presented. One of the isoforms shows a tumor-specific exon which was generated through the exonization of an Alu element.
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Figure 4: Example output of SERpredict. The output of SERpredict for [EMBL:AF466401] is presented. One of the isoforms shows a tumor-specific exon which was generated through the exonization of an Alu element.

Mentions: These results are provided as HTML for visual inspection (see Figure 4) or can be downloaded as XML for easier extraction of relevant results and for storage in private databases.


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

Mersch B, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A - BMC Genet. (2007)

Example output of SERpredict. The output of SERpredict for [EMBL:AF466401] is presented. One of the isoforms shows a tumor-specific exon which was generated through the exonization of an Alu element.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194731&req=5

Figure 4: Example output of SERpredict. The output of SERpredict for [EMBL:AF466401] is presented. One of the isoforms shows a tumor-specific exon which was generated through the exonization of an Alu element.
Mentions: These results are provided as HTML for visual inspection (see Figure 4) or can be downloaded as XML for easier extraction of relevant results and for storage in private databases.

Bottom Line: 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.With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany. b.mersch@dkfz.de

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.

Show MeSH