Evidence of extensive non-allelic gene conversion among LTR elements in the human genome.
Evidence of extensive non-allelic gene conversion among LTR elements in the human genome.
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DOI：
10.1038/srep28710
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发表时间：
2016-06-27
影响因子：
4.6
通讯作者：
Cruciani F
中科院分区：
文献类型：
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作者：
Trombetta B;Fantini G;D'Atanasio E;Sellitto D;Cruciani F
长末端重复序列(LTRs)是在人类内源性逆转录病毒(HERV)两端发现的几乎相同的DNA序列。不同LTRs之间存在较高的序列相似性，表明它们可能是异位基因转换事件的底物。为了了解基因转换发生的程度，并对这些元素在人类中的进化史获得新的见解，我们对不同无关Y染色体上的52个LTRs进行了种内系统发育研究。从这一分析中，我们获得了直接证据，证明了在几个LTRs中发生了异位基因转换，供体序列位于性染色体和常染色体上。我们还发现，其中一些元件具有极高的多态密度，显示出人类基因组中最高的核苷酸多样性之一，以及来自不同LTRS的复杂序列拼接。最后，我们强调了当前短读NGS研究在分析人类基因组中LTRS遗传多样性方面的局限性。总之，我们的比较测序分析表明，异位基因转换是LTR元件进化中的常见事件，表明来自不同染色体的LTRs之间存在复杂的遗传联系。
Long Terminal Repeats (LTRs) are nearly identical DNA sequences found at either end of Human Endogenous Retroviruses (HERVs). The high sequence similarity that exists among different LTRs suggests they could be substrate of ectopic gene conversion events. To understand the extent to which gene conversion occurs and to gain new insights into the evolutionary history of these elements in humans, we performed an intra-species phylogenetic study of 52 LTRs on different unrelated Y chromosomes. From this analysis, we obtained direct evidence that demonstrates the occurrence of ectopic gene conversion in several LTRs, with donor sequences located on both sex chromosomes and autosomes. We also found that some of these elements are characterized by an extremely high density of polymorphisms, showing one of the highest nucleotide diversities in the human genome, as well as a complex patchwork of sequences derived from different LTRs. Finally, we highlighted the limits of current short-read NGS studies in the analysis of genetic diversity of the LTRs in the human genome. In conclusion, our comparative re-sequencing analysis revealed that ectopic gene conversion is a common event in the evolution of LTR elements, suggesting complex genetic links among LTRs from different chromosomes.