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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转座元件对二穗短柄草天然种质甲基化和基因表达的影响。


转座元件 (TE) 构成植物基因组的很大一部分，并且大多通过 DNA 甲基化等抑制性表观遗传修饰以转录沉默状态存在。 TE 沉默被认为会影响邻近基因的调节，可能是因为 DNA 甲基化从 TE 扩散出去。这是一个一般原则还是一个与环境相关的现象仍然存在争议，迫切需要研究其他植物物种中 TE、DNA 甲基化和附近基因表达之间的关系。在这里，我们使用草Brachypodium distachyon作为模型，生成了 11 种天然材料的 DNA 甲基化和转录组图谱。与在拟南芥中观察到的情况相反，我们发现 TE 对甲基化扩散的影响有限，并且只有少数 TE 家族与其相邻基因的低表达相关。有趣的是，我们发现 TE 插入多态性的一个子集与种质间的差异基因表达相关。因此，虽然对基因表达没有全局影响，但不同的 TE 插入可能有助于二穗 B. 的特定基因表达模式。