人类和小鼠基因组内转座元件插入的比较分析揭示了Alu在塑造人类转录组中的独特作用
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
摘要：
背景：转座元件（TE）对哺乳动物的进化有重要影响，并与许多遗传疾病有关。我们比较了TE对人类转录组和小鼠转录组的影响。结果：我们编制了人类和小鼠基因组中所有TE的数据集，分别识别了3，932，058和3，122，416个TE。我们提取了位于人类和小鼠基因内的TE，令人惊讶的是，我们发现人类和小鼠中60%的TE位于内含子序列中，尽管内含子仅占人类基因组的24%。人和小鼠的所有TE家族都可以外显子。人类和小鼠之间共有的TE家族在两个物种中表现出相同的TE外显化百分比，但Alu（灵长类特异性逆转录元件）的外显化水平显著高于人类基因组中的其他TE，导致人类中的TE外显化水平高于小鼠（分别为1，824个外显子和506个外显子）。我们发现了一种灵长类动物特有的内含子获得机制，其中Alu插入外显子会在3'非翻译区产生一个新的内含子（称为“内含子化”）。最后，TE插入到基因的第一个和最后一个外显子中在人类中比在小鼠中更频繁，导致人类的外显子更长。结论：我们的发现揭示了TE对这两个转录组的多种影响。这些作用在人类中比在小鼠中大得多，这是由于在人类中存在Alu元件。
英文摘要：
Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome. Results: We compiled a dataset of all TEs in the human and mouse genomes, identifying 3,932,058 and 3,122,416 TEs, respectively. We than extracted TEs located within human and mouse genes and, surprisingly, we found that 60% of TEs in both human and mouse are located in intronic sequences, even though introns comprise only 24% of the human genome. All TE families in both human and mouse can exonize. TE families that are shared between human and mouse exhibit the same percentage of TE exonization in the two species, but the exonization level of Alu, a primatespecific retroelement, is significantly greater than that of other TEs within the human genome, leading to a higher level of TE exonization in human than in mouse (1,824 exons compared with 506 exons, respectively). We detected a primate-specific mechanism for intron gain, in which Alu insertion into an exon creates a new intron located in the 3' untranslated region (termed 'intronization'). Finally, the insertion of TEs into the first and last exons of a gene is more frequent in human than in mouse, leading to longer exons in human. Conclusion: Our findings reveal many effects of TEs on these two transcriptomes. These effects are substantially greater in human than in mouse, which is due to the presence of Alu elements in human.
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