Genetic and epigenetic variations contributed by Alu retrotransposition
Genetic and epigenetic variations contributed by Alu retrotransposition
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DOI：
10.1186/1471-2164-12-617
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发表时间：
2011-12-20
期刊：
影响因子：
4.4
通讯作者：
Soares, Marcelo B.
中科院分区：
文献类型：
--
作者：
de Andrade, Alexandre;Wang, Min;Soares, Marcelo B.
背景：Alu 元件的从头逆转录转座已被认为是人类插入多态性的主要驱动因素。在这项研究中，我们利用 Alu 锚定的亚硫酸氢盐 PCR 文库来识别进化上最近的 Alu 元件插入，并研究它们的遗传和表观遗传变异。结果：总共鉴定了 327 个推定的最近的 Alu 插入，总共由 1,762 个序列读数表示。几乎所有此类从头逆转录转座事件（316/327）都是新颖的。 49 个随机选择的事件中的 47 个（对应 19 个基因组位点）进行了序列验证。 Alu 元件插入在 19 个基因组位点中的 16 个中的一个或多个个体中保持半合子。研究发现，年轻的 Alu 家族的 Alu 元素富集，具有特征序列特征，例如较长的聚 (A) 尾。此外，我们还记录了紧邻侧翼序列中富含 AT 的靶位点重复的发生，这是逆转录转座的标志。此外，我们在其5'侧翼区域发现了由LINE-1编码的ORF2P蛋白识别的序列基序（TT/AAAA），这与LINE-1元件促进Alu逆转录转座的事实一致。虽然大多数 Alu 元件都高度甲基化，但我们在 TOMM5 下游 1.5 kb 处发现了一个 Alu，它表现出完全未甲基化的左臂。有趣的是，我们观察到其直接 5' 和 3' 侧翼 CpG 二核苷酸的差异甲基化，分别与其内部 5' 和 3' 序列的未甲基化和甲基化状态一致。重要的是，TOMM5 的 CpG 岛以及位于该新插入的 Alu 上游的 3 个 Alu 重复序列和 1 个 MIR 元件也被发现未甲基化。对另外两个基因组位点的甲基化分析显示，无论是否存在插入，两条同源染色体中 Alu 插入位点侧翼的 CpG 二核苷酸均没有甲基化差异。 结论：我们预计本研究中使用的方法组合（包括重复锚定亚硫酸氢盐 PCR 测序和本文报道的计算分析流程）对于生成遗传和表观遗传变异图谱将具有无价的价值。
Background: De novo retrotransposition of Alu elements has been recognized as a major driver for insertion polymorphisms in human populations. In this study, we exploited Alu-anchored bisulfite PCR libraries to identify evolutionarily recent Alu element insertions, and to investigate their genetic and epigenetic variation.Results: A total of 327 putatively recent Alu insertions were identified, altogether represented by 1,762 sequence reads. Nearly all such de novo retrotransposition events (316/327) were novel. Forty-seven out of forty-nine randomly selected events, corresponding to nineteen genomic loci, were sequence-verified. Alu element insertions remained hemizygous in one or more individuals in sixteen of the nineteen genomic loci. The Alu elements were found to be enriched for young Alu families with characteristic sequence features, such as the presence of a longer poly(A) tail. In addition, we documented the occurrence of a duplication of the AT-rich target site in their immediate flanking sequences, a hallmark of retrotransposition. Furthermore, we found the sequence motif (TT/AAAA) that is recognized by the ORF2P protein encoded by LINE-1 in their 5'-flanking regions, consistent with the fact that Alu retrotransposition is facilitated by LINE-1 elements. While most of these Alu elements were heavily methylated, we identified an Alu localized 1.5 kb downstream of TOMM5 that exhibited a completely unmethylated left arm. Interestingly, we observed differential methylation of its immediate 5' and 3' flanking CpG dinucleotides, in concordance with the unmethylated and methylated statuses of its internal 5' and 3' sequences, respectively. Importantly, TOMM5's CpG island and the 3 Alu repeats and 1 MIR element localized upstream of this newly inserted Alu were also found to be unmethylated. Methylation analyses of two additional genomic loci revealed no methylation differences in CpG dinucleotides flanking the Alu insertion sites in the two homologous chromosomes, irrespective of the presence or absence of the insertion.Conclusions: We anticipate that the combination of methodologies utilized in this study, which included repeat-anchored bisulfite PCR sequencing and the computational analysis pipeline herein reported, will prove invaluable for the generation of genetic and epigenetic variation maps.