Evolutionary dynamics of collateral gene silencing by piRNA

转座元件(TE)是一种DNA序列，可以改变它们在基因组中的位置，从而产生各种有害的突变。包括果蝇在内的动物已经进化出一种防御机制来防止TE运动，在这种机制下，称为piRNAs的小RNA可以破坏TES产生的必要RNA中间产物。PiRNAs的确切作用机制尚不清楚，该项目的总体目标是研究piRNAs如何在不破坏有益RNA的情况下特定靶向TE RNAs。这项研究有可能为预防可能导致基因缺陷或死亡的有害突变提供有价值的见解。该项目将对本科生、研究生和一名博士后研究员产生更广泛的影响，他们将接受遗传学、进化论和生物信息学方面的培训。制作互联网视频将带来额外的好处，这些视频将成为关于遗传学和进化的各种主题的教育的通用工具。PiRNAs通过破坏TE RNAs在基因组防御中发挥关键作用。这项研究将确定当piRNA错误地靶向正常基因的RNA从而导致脱靶或伴随的基因沉默时，piRNA防御机制如何受到伤害的限制。以不同种类的果蝇为模型，这项工作将检验这样的假设：TE含量高的物种更容易受到这些附带效应的影响。一系列实验将确定TE含量较高的物种是否具有较小的piRNA机制表达变化，是否增加了piRNA的沉默，以及是否具有更强的母体对基因表达的影响。在其他人为增加piRNA表达的实验中，将揭示基因组防御和脱靶效应之间是否存在功能性权衡。这项工作将提供关于保护基因组的机制如何受到伴随基因沉默的有害影响的重要信息，这可以被认为是一种“基因组自身免疫”。

Transposable elements (TE) are DNA sequences that can change their position in the genome and thereby produce a variety of harmful mutations. Animals, including fruit flies, have evolved a defense mechanism to guard against TE movement whereby small RNAs, called piRNAs, can destroy essential RNA intermediates produced by the TEs. Exactly how piRNAs work is not well understood, and the overall aim of this project is to study how piRNAs specifically target TE RNAs without destroying beneficial RNAs. The research has the potential to provide valuable insights into prevention of harmful mutations that could cause genetic defects or death. The project will have broader impacts for undergraduates, graduate students and a postdoctoral researcher, who will receive training in genetics, evolution and bioinformatics. Added benefit will derive from production of internet videos that will serve as general tools for education about various topics in genetics and evolution. piRNAs play a critical role in genome defense by destroying TE RNAs. This research will determine how the piRNA defense mechanism is constrained by the harm that occurs when piRNAs mistakenly target RNAs from normal genes and thus result in off-target, or collateral, gene silencing. Using different species of Drosophila as a model, the work will test the hypothesis that species with high TE content are more affected by these collateral effects. One series of experiments will determine whether species with higher TE content have less variation in expression of the piRNA machinery, increased silencing by piRNA, and stronger maternal effects on gene expression. Other experiments, in which piRNA expression is artificially increased, will reveal whether there is a functional tradeoff between genome defense and off-target effects. This work will provide important information about how the mechanisms that protect the genome are governed by the harmful effects of collateral gene silencing, which can be considered to be a form of "genomic autoimmunity".