Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.

中文翻译：

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转座元素对短枝曲霉自然种的甲基化和基因表达的影响。

转座因子（TEs）构成了植物基因组的很大一部分，并通过抑制性表观遗传修饰（例如DNA甲基化）而以转录沉默状态存在。据信TE沉默会影响相邻基因的调控，可能是因为DNA甲基化从TE扩散开来。究竟这是一般原则还是与环境有关的现象仍在争论中，迫切需要研究TEs，DNA甲基化和其他植物物种附近基因表达之间的关系。在这里，我们以草短枝曲霉为模型，为11个自然种质生成了DNA甲基化和转录组图谱。与拟南芥中观察到的相反，我们发现TEs对甲基化扩散的影响有限，只有很少的TE家族与其相邻基因的低表达有关。有趣的是，我们发现TE插入多态性的一个子集与跨越种质的差异基因表达相关。因此，尽管对基因表达没有全局影响，但不同的TE插入可能会导致B. distachyon中特定的基因表达模式。