BACKGROUND Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. RESULTS We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection. CONCLUSIONS Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage.

中文翻译：

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非 LTR 反转录转座子对解剖学现代人分化和进化的影响。

背景转座因子是真核生物基因组的生物学重要组成部分。特别是，非 LTR 反转录转座子 (N-LTRrs) 在整个进化过程中在塑造人类基因组方面发挥了关键作用。在这项研究中，我们比较了在解剖学上现代人类、尼安德特人、丹尼索瓦人和黑猩猩基因组中存在差异的反转录转座子插入，以评估反转录转座对人类谱系分化的可能影响。结果 我们首先确定了物种特异性的 N-LTRrs 并确定了它们在当今人群中的分布。这些分析入围了一组仅在解剖学现代人类中发现的 N-LTRr 插入。这些插入与它们插入的那些基因的转录/剪接变体数量的增加有关。对含有人类特异性 N-LTRr 插入的基因功能的分析反映了人类进化过程中发生的变化。特别是，含有最近 N-LTRr 插入的基因在大脑中的表达丰富，特别是在未分化的神经元中，并且这些基因与与神经元成熟和迁移相关的网络相关联。此外，我们确定了候选 N-LTRr 插入，这些插入可能产生了现代人类独有的新功能变体，其基因组基因座显示出正选择的痕迹。结论 我们的结果强烈表明 N-LTRr 影响了我们作为一个物种的分化，很可能导致神经复杂性的增加，并且在整个人类谱系的进化过程中一直是基因组变异的恒定来源。