PIWI-piRNA pathway mediated transposon repression in Hydra somatic stem cells

Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations, all of which express PIWI proteins; endodermal and ectodermal epithelial stem cells are somatic, whereas the interstitial stem cells have germline competence. To study somatic function of the pathway we isolated piRNAs from Hydra that lack the interstitial lineage and found that these somatic piRNAs map predominantly to TE transcripts and display the conserved sequence signatures typical of germline piRNAs. Three lines of evidence suggest that the PIWI-piRNA pathway represses TEs in Hydra epithelial stem cells. First, epithelial knockdown of the Hydra piwi gene hywi resulted in upregulation of TE expression. Second, degradome sequencing revealed evidence of PIWI-mediated cleavage of TE RNAs in epithelial cells using the ping-pong mechanism. Finally, we demonstrated a direct association between Hywi protein and TE transcripts in epithelial cells using RNA immunoprecipitation. Altogether, our data reveal that the PIWI-piRNA pathway represses TE expression in the somatic cell lineages of Hydra, which we propose contributes to the extreme longevity of the organism. Furthermore, our results, in combination with others, suggest that somatic TE repression is an ancestral function of the PIWI-piRNA pathway.转座因子（Transposable elements, TEs）可对基因组造成损伤，故而生物体演化出多种机制以抑制TE的表达。PIWI-piRNA通路是一类小型RNA介导的通路，在动物生殖系中发挥抑制TE表达的功能。本研究聚焦于该通路在长寿淡水刺胞动物水螅的体细胞干细胞中的功能。 水螅拥有三类干细胞群体，所有群体均表达PIWI蛋白：其中内胚层上皮干细胞与外胚层上皮干细胞属于体细胞干细胞，而间质干细胞则具备生殖系分化潜能。为探究该通路的体细胞功能，我们从缺失间质谱系的水螅样本中分离piRNAs，结果显示此类体细胞piRNAs主要靶向TE转录本，并呈现出生殖系piRNA典型的保守序列特征。 共有三项实验证据表明，PIWI-piRNA通路可在水螅上皮干细胞中抑制TE的表达：其一，敲低水螅piwi基因hywi的上皮细胞中，TE的转录水平显著上调；其二，降解组测序结果证实，上皮细胞内PIWI通过乒乓机制介导切割TE RNA；其三，我们通过RNA免疫沉淀实验，直接证明了上皮细胞内Hywi蛋白与TE转录本存在特异性结合。 综合上述实验结果，我们证实PIWI-piRNA通路可在水螅的体细胞谱系中抑制TE的表达，我们推测该功能是水螅具备极端长寿特性的重要原因之一。此外，结合已有研究成果，我们的结果提示体细胞TE抑制是PIWI-piRNA通路的祖先性功能。