Institute for Plant and Microbial Biology, University of Zurich, Switzerland.
Genetic Diversity Centre, ETH Zürich, Switzerland.
Genome Biol Evol. 2020 Nov 3;12(11):1994-2001. doi: 10.1093/gbe/evaa180.
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 11 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 with 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.
转座元件 (TEs) 构成了植物基因组的很大一部分，它们主要通过抑制性的表观遗传修饰（如 DNA 甲基化）而处于转录沉默状态。TE 的沉默被认为会影响邻近基因的调控，可能是因为 DNA 甲基化从 TE 处扩散。这是一个普遍原则还是一种依赖于上下文的现象仍存在争议，因此迫切需要在其他植物物种中研究 TEs、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，并为 11 个自然品系生成了 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 TEs 对甲基化扩散的影响有限，只有少数 TE 家族与其邻近基因的低表达相关。有趣的是，我们发现一组 TE 插入多态性与品系间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 插入可能有助于 B. distachyon 中特定的基因表达模式。
