Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome.
Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome.
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DOI：
10.1371/journal.pgen.1000733
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Schnable PS
中科院分区：
文献类型：
--
作者：
Liu S;Yeh CT;Ji T;Ying K;Wu H;Tang HM;Fu Y;Nettleton D;Schnable PS
玉米的Mu转座子系统非常活跃，每个∼的50-100个拷贝平均每代转座一次。大约12个不同的Mu转座子含有高度相似的∼215bp末端反向重复序列(TIR)，并在插入时产生9bp的靶点复制(TSD)。使用一种新的基因组行走策略，将这些保守的TIR作为引物结合位点，从Mu库中扩增出Mu插入位点，并通过454技术进行测序。∼965,000次读取中有94%携带Mu TIR，证明了此策略的特殊性。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个非冗余的Mu插入位点的分布是惊人的不均匀的，因此比率与距离着丝粒的距离成比例增加。已确定的假定的Mu转座酶结合共识位点不能解释这种不一致性。构建了一个包含10,000多个遗传标记的完整遗传图谱，并与玉米参考基因组序列进行了比对。重组率(cm/Mb)也是非常不均匀的，随着距离着丝粒的距离的增加，重组率成比例增加。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，因为即使在考虑了基因密度之后，仍然可以观察到对染色体远端部分的明显偏好。Mu插入和减数分裂重组位点分布的相似性表明，Mu插入和减数分裂重组的位点选择都涉及染色质结构等共同特征。Mu插入和减数分裂重组的发现都集中在带有开放染色质表观遗传标记的基因组区域，这支持了开放染色质提高Mu插入和减数分裂重组的速率的假说。通过下一代技术对Mu转座子的基因组插入位点进行了扩增和测序，发现了4万多个非冗余的Mu插入位点，它们非均匀地分布在玉米基因组和基因内部。在染色体上，Mu转座子插入的频率与重组率密切相关。虽然Mu和重组都优先发生在基因中，但基因密度并不能完全解释这些模式。相反，Mu插入和减数分裂重组位点的发现都集中在以开放染色质的表观遗传标记标记的基因组区域，这支持了开放染色质提高Mu插入和减数分裂重组的速率的假设。
The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ∼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 ∼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. Genomic insertion sites of Mu transposons were amplified and sequenced via next generation technology, revealing more than 40,000 non-redundant Mu insertion sites that are non-uniformly distributed across the maize genome and within genes. Along chromosomes, frequencies of Mu transposon insertions are strongly correlated with recombination rates. Although both Mu and recombination occur preferentially in genes, gene density does not fully explain these patterns. Instead, 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.
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影响因子：
46.9
作者：
Ball, Madeleine P.;Li, Jin Billy;Gao, Yuan;Lee, Je-Hyuk;LeProust, Emily M.;Park, In-Hyun;Xie, Bin;Daley, George Q.;Church, George M.
通讯作者：
Church, George M.
DOI：
10.1073/pnas.0503394102
发表时间：
2005-08-23
影响因子：
11.1
作者：
Fu, Y;Emrich, SJ;Schnable, PS
通讯作者：
Schnable, PS
影响因子：
3.3
作者：
Falque, M;Décousset, L;Murigneux, A
通讯作者：
Murigneux, A
影响因子：
7.4
作者：
Coe, E;Cone, K;Wing, R
通讯作者：
Wing, R
影响因子：
5.8
作者：
Emrich, SJ;Aluru, S;Schnable, PS
通讯作者：
Schnable, PS