Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.

Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21–22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions. Here, we define a deterministic model that represents the propagation of active TEs, aspects of the host response and the accumulation of silenced TEs. We describe general properties of the model and also fit it to biological data in order to explore two questions. The first is why two overlapping pathways are maintained, given that both are likely energetically expensive. Under our model, RdDM silenced TEs effectively even when the initiation of silencing was weak. This relationship implies that only a small amount of RNAi is needed to initiate TE silencing, but reinforcement by RdDM is necessary to efficiently counter TE propagation. Second, we investigated the reliance of the host response on rates of TE deletion. The model predicted that low levels of deletion lead to few active TEs, suggesting that silencing is most efficient when methylated TEs are retained in the genome, thereby providing one explanation for the large size of plant genomes.

转座元件（TEs）构成了被子植物DNA的大部分。植物通过表观遗传沉默来抑制转座元件的活性。一种表观遗传沉默形式需要21 - 22核苷酸的小干扰RNA，其作用是降解转座元件的mRNA，还可能引发DNA甲基化。DNA甲基化通过第二种机制——RNA依赖的DNA甲基化（RdDM）途径得到加强。RdDM依赖24核苷酸的小干扰RNA，并最终使转座元件处于静止状态。这些宿主因子在系统层面相互作用，但尚未对它们的相互作用进行系统层面的分析。在此，我们定义了一个确定性模型，该模型代表了活性转座元件的传播、宿主反应的各个方面以及沉默转座元件的积累。我们描述了模型的一般特性，并使其与生物学数据相拟合，以探究两个问题。第一个问题是，鉴于两种重叠的途径可能都消耗大量能量，为什么要维持它们。在我们的模型中，即使沉默的起始很弱，RdDM也能有效地使转座元件沉默。这种关系意味着只需少量的RNA干扰就能启动转座元件沉默，但需要RdDM的强化才能有效对抗转座元件的传播。其次，我们研究了宿主反应对转座元件缺失率的依赖。该模型预测，低水平的缺失会导致活性转座元件很少，这表明当甲基化的转座元件保留在基因组中时，沉默效率最高，从而为植物基因组的大尺寸提供了一种解释。