Target RNA recognition drives PIWI* complex assembly for transposon silencing

PIWI clade Argonaute proteins and their associated piRNAs are essential guardians of genome integrity, silencing transposable elements through distinct nuclear and cytoplasmic pathways. Nuclear PIWI proteins direct heterochromatin formation to repress transposon transcription, while cytoplasmic PIWIs cleave transposon transcripts to initiate piRNA amplification. Both processes rely on target RNA recognition by PIWI–piRNA complexes, yet how this recognition leads to pathway-specific effector recruitment has remained unclear. Here, we show that target engagement triggers the formation of conserved PIWI* complexes—comprising a PIWI protein, a piRNA–target RNA duplex, a GTSF-family protein, and Maelstrom—that serve as molecular platforms to recruit downstream effectors. In Drosophila, nuclear Piwi* engages the SFiNX complex to induce transcriptional silencing, while cytoplasmic Aubergine* complexes recruit the helicase Spindle-E to promote piRNA biogenesis. Evolutionary analysis reveals that PIWI* complex formation is deeply conserved across metazoans, uncovering an ancient mechanism that couples small RNA-guided target recognition to effector function. These findings define a unifying molecular principle for piRNA-mediated silencing across cellular compartments.