Mersch Britta, Sela Noa, Ast Gil, Suhai Sándor, Hotz-Wagenblatt Agnes
Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
BMC Genet. 2007 Nov 6;8:78. doi: 10.1186/1471-2156-8-78.
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.
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.
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.
已知转座元件（TEs）会影响转录组，原因在于要么从内含子转座元件中产生新的外显子（这被称为外显子化），要么该元件插入外显子，从而产生新的转录本。文献中的几个例子表明，由外显子化产生的异构体特定于某个组织（例如心肌）或引发疾病。因此，外显子化可能会对生物体的转录组产生负面影响。
由于我们旨在检测人类和小鼠基因组中通过转座元件外显子化产生的其他组织特异性或肿瘤特异性异构体，我们利用贝叶斯统计设计了自动化分析流程SERpredict（SER = 特异性外显子化逆转录元件）。通过这个流程，我们发现了几个基因，其中一个转座元件形成了组织特异性或肿瘤特异性异构体。
我们的结果表明，SERpredict产生了相关结果，证明了转座元件在塑造人类和小鼠转录组方面的重要性。由于灵长类特异性Alu元件的作用，转座元件对人类转录组的影响比对小鼠转录组的影响高几倍。
