Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
PLoS One. 2012;7(2):e30008. doi: 10.1371/journal.pone.0030008. Epub 2012 Feb 9.
Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.
转座元件是可移动的 DNA 序列，它们使用多种机制整合到宿主基因组中，这些机制具有不同程度的目标序列特异性。虽然一些工程化转座元件的目标位点偏好已得到很好的研究，但大多数转座元件的自然目标偏好特征描述得很差。我们利用来自 166 株黑腹果蝇的群体基因组重测序数据，在我们用来解码该物种 22 类转座元件自然目标偏好的参考基因组序列中，鉴定出了 8000 多个新的插入位点，这些插入位点不存在于参考基因组序列中。我们发现，末端反向重复转座子和长末端重复逆转录转座子家族存在特定于分支的靶位点重复和靶位点序列基序。此外，我们发现转座元件靶位点的序列基序始终是回文，其延伸超过靶位点重复。我们的研究结果表明，群体基因组学数据可用于高通量推断野生中转座元件的靶向偏好，并为真核基因组中末端反向重复转座子和长末端重复逆转录转座子靶位点选择建立一般规则。
