Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

中文翻译：

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长期的实验发展揭示了对piRNA介导的转座因子表达控制的纯化选择

转座因子（TEs）是真核基因组的几乎通用组成部分。在动物中，与Piwi相互作用的小RNA（piRNA）和抑制性染色质通常在防止TE转录从而限制TE活性方面起关键作用。然而，在真核生物中，TE的含量差异很大，人们对进化过程中TE活性和TE沉默的动力学知之甚少。在这里，我们使用线虫的实验进化种群研究了409代中TE表达的动力学。实验种群的进化规模为1、10和100个个体，以控制自然选择与遗传漂移的效率。我们证明相对于祖先人口增加的TE表达，最大的增加发生在最小的人口中。我们表明，TEs在基因组活性区域内的转录激活与piRNA介导的沉默的失败有关，而被抑制的染色质域中的沉默的TEs保留了小RNA。此外，我们发现周围区域的序列上下文会影响TEs通过小的RNA介导的沉默失败而失去沉默的倾向。我们的结果表明，秀丽隐杆线虫的自然选择负责维持低水平的TE表达，并为负责的表观基因组特征提供新见解。我们发现，周围区域的序列背景会影响TEs通过小的RNA介导的沉默失败而失去沉默的倾向。我们的结果表明，秀丽隐杆线虫的自然选择负责维持低水平的TE表达，并为负责的表观基因组特征提供新见解。我们发现，周围区域的序列背景会影响TEs通过小的RNA介导的沉默失败而失去沉默的倾向。我们的结果表明，秀丽隐杆线虫的自然选择负责维持低水平的TE表达，并为负责的表观基因组特征提供新见解。