PIWI proteins use PIWI-interacting RNAs (piRNAs) to identify and silence transposable elements and thereby maintain genome integrity between metazoan generations¹. The targeting of transposable elements by PIWI has been compared to mRNA target recognition by Argonaute proteins^2,3, which use microRNA (miRNA) guides, but the extent to which piRNAs resemble miRNAs is not known. Here we present cryo-electron microscopy structures of a PIWI–piRNA complex from the sponge Ephydatia fluviatilis with and without target RNAs, and a biochemical analysis of target recognition. Mirroring Argonaute, PIWI identifies targets using the piRNA seed region. However, PIWI creates a much weaker seed so that stable target association requires further piRNA–target pairing, making piRNAs less promiscuous than miRNAs. Beyond the seed, the structure of PIWI facilitates piRNA–target pairing in a manner that is tolerant of mismatches, leading to long-lived PIWI–piRNA–target interactions that may accumulate on transposable-element transcripts. PIWI ensures targeting fidelity by physically blocking the propagation of piRNA–target interactions in the absence of faithful seed pairing, and by requiring an extended piRNA–target duplex to reach an endonucleolytically active conformation. PIWI proteins thereby minimize off-targeting cellular mRNAs while defending against evolving genomic threats.

PIWI 蛋白使用 PIWI 相互作用 RNA (piRNA) 来识别和沉默转座元件，从而维持后生动物世代之间的基因组完整性¹ 。 PIWI 对转座元件的靶向与 Argonaute 蛋白^2,3的 mRNA 靶标识别进行了比较，后者使用 microRNA (miRNA) 指导，但 piRNA 与 miRNA 的相似程度尚不清楚。在这里，我们展示了来自海绵Ephydatiia Fluviatilis的 PIWI-piRNA 复合物的冷冻电子显微镜结构，有或没有目标 RNA，以及目标识别的生化分析。与 Argonaute 类似，PIWI 使用 piRNA 种子区域识别目标。然而，PIWI 产生的种子要弱得多，因此稳定的靶标关联需要进一步的 piRNA-靶标配对，从而使 piRNA 比 miRNA 更不混杂。除了种子之外，PIWI 的结构以允许错配的方式促进 piRNA-靶标配对，从而导致长寿命的 PIWI-piRNA-靶标相互作用，并可能在转座元件转录本上积累。 PIWI 通过在缺乏忠实种子配对的情况下物理阻断 piRNA-靶标相互作用的传播，并通过要求扩展的 piRNA-靶标双链体达到核酸内切活性构象来确保靶向保真度。 PIWI 蛋白从而最大限度地减少脱靶细胞 mRNA，同时防御不断变化的基因组威胁。