Department of Zoology, Faculty of Science, Charles University in Prague, Prague 128 43, Czech Republic.
BMC Evol Biol. 2013 May 29;13:107. doi: 10.1186/1471-2148-13-107.
Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes.
Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome.
We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study.
已有人提出，反转录转座子为非等位基因同源重组（NAHR）提供了底物，从而促进了基因家族的扩张。然而，它们的确切作用仍存在争议。在这里，我们探讨了反转录转座子是否促成了独立发生在小鼠和大鼠基因组中的雄激素结合蛋白（Abp）基因家族的近期扩张。
通过点图分析，我们发现小鼠基因组 Abp 区域的最近一次复制侧翼为 L1Md_T 元件。对这些元件序列的分析揭示了导致复制的重组的断点，证实了该复制是由 L1 元件作为底物的 NAHR 引起的。L1 和 ERVII 反转录转座子在 Abp 区域比在 1 Mb 侧翼区域更为密集，而其他重复类型在 Abp 区域的丰度低于侧翼区域。L1 反转录转座子在谱系分离后优先在 Abp 基因区域积累，大致遵循 Abp 基因扩张的模式。相比之下，Abp 区域共享与谱系特异性 ERVII 重复的比例与基因组的其余部分相似。
我们通过鉴定最近发生的小鼠 Abp 基因重复的边缘处的重组 L1Md_T 元件，证实了 L1 重复在 Abp 基因重复中的作用。在 Abp 基因区域发现了 L1 和 ERVII 重复的高密度，在区域边界处存在突然的过渡，表明其高密度与 Abp 基因重复紧密相关。我们观察到，L1 元件的主要积累发生在小鼠和大鼠谱系分裂之后，并且 L1 元素的积累与小鼠基因组中 Abp 基因家族的扩张之间存在惊人的重叠。建立 L1 元素的积累与 Abp 基因家族的扩张之间的联系，并在最近的重复中鉴定出与 NAHR 相关的断点，是本研究的主要贡献。
