Discovery and characterization of Alu repeat sequences via precise local read assembly.
Discovery and characterization of Alu repeat sequences via precise local read assembly.
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通过精确的局部读取组件发现和表征Alu重复序列。
DOI：
10.1093/nar/gkv1089
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发表时间：
2015-12-02
影响因子：
14.9
通讯作者：
Kidd JM
中科院分区：
文献类型：
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作者：
Wildschutte JH;Baron A;Diroff NM;Kidd JM
Alu插入占人类基因组的>11%，并且Alu 30-35亚家族保持活跃的移动的，但是来自短读段数据的多态性Alu插入的表征仍然是一个挑战。我们建立在现有的计算方法，结合联合收割机Alu检测和从头组装的WGS数据作为一种手段，从Illumina配对末端读取重建插入事件的全序列。与使用PacBio长读段获得的已发表调用的比较表明错误发现率低于5%，其代价是由于参考和非参考重复的共定位而降低了灵敏度。我们从人类基因组多样性项目（HGDP）的53个样本中生成了1614个完全组装的Alu变体的高度准确的调用集。我们利用重建的替代插入单倍型对1010个完全组装的插入进行基因分型，获得与通过PCR获得的基因型>99%的一致性。在我们组装的序列中，我们发现了过早插入机制的证据，并观察到16%的Ya 5和Yb 8插入的5′截短。截短位点与Alu RNA的茎环结构和SRP 9/14结合位点相吻合，表明L1 ORF 2 p在5′端截短的产生中存在停顿。此外，我们确定了可能由于非反转录转座机制而产生的可变的CNOJ和CNOS元件。
Alu insertions have contributed to >11% of the human genome and ∼30–35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5′ truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5′ truncations. Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.