Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, USA.
PLoS Genet. 2009 Nov;5(11):e1000733. doi: 10.1371/journal.pgen.1000733. Epub 2009 Nov 20.
The Mu transposon system of maize is highly active, with each of the approximately 50-100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar approximately 215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of approximately 965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.
玉米的 Mu 转座子系统非常活跃，大约 50-100 个拷贝中的每个拷贝在每一代平均转座一次。大约 12 个不同的 Mu 转座子含有高度相似的大约 215 bp 末端反向重复（TIR），并在插入时产生 9-bp 靶位重复（TSD）。利用一种新颖的基因组步行策略，该策略使用这些保守的 TIR 作为引物结合位点，从 Mu 库存中扩增 Mu 插入位点，并通过 454 技术进行测序。大约 965,000 个读取中的 94%携带 Mu TIR，证明了该策略的特异性。在这些 TIR 中，发现了 21 个新的 Mu TIR，揭示了 Mu 转座子系统的额外复杂性。>40,000 个非冗余 Mu 插入位点的分布非常不均匀，以至于速率与距离着丝粒成比例增加。识别出的假定 Mu 转座酶结合保守位点并不能解释这种非均匀性。构建并对齐到玉米参考基因组序列的包含超过 10,000 个遗传标记的综合遗传图谱。重组率（cM/Mb）也非常不均匀，与距离着丝粒成比例增加。Mu 插入位点频率与重组率密切相关。基因密度不能完全解释 Mu 插入和重组位点的染色体分布，因为即使考虑到基因密度，仍然观察到对染色体远端的明显偏好。Mu 插入和减数分裂重组位点的分布相似表明，共同的特征，如染色质结构，参与了 Mu 插入和减数分裂重组的位点选择。Mu 插入和减数分裂重组位点都集中在具有开放染色质的表观遗传标记标记的基因组区域的发现为开放染色质增强 Mu 插入和减数分裂重组的速率的假说提供了支持。
