Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Abstract

<p>The <em>Mu</em> 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 <em>Mu</em>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, <em>Mu</em> insertion sites were amplified from <em>Mu</em> stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried <em>Mu</em> TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel <em>Mu</em> TIRs were discovered, revealing additional complexity of the <em>Mu</em> transposon system. The distribution of >40,000 non-redundant<em>Mu</em> insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative <em>Mu</em> 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. <em>Mu</em> insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of <em>Mu</em>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 <em>Mu</em> insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both <em>Mu</em> insertion and meiotic recombination. The finding that <em>Mu</em> 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 <em>Mu</em> insertion and meiotic recombination.</p>