PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests that they are also present in relatively low numbers in somatic cells and actively control their gene expression.

piRNAs are named because of their association with PIWI proteins, a subfamily of the Argonaute class of proteins. This complex is called the piRNA induced silencing complex (piRISC). In Drosophila, there are three types of PIWI proteins– Piwi, Aubergine, and AGO3, and each of these proteins bind different length piRNAs. The PIWI proteins have also been observed in mammals and in mice, called Miwi, Mili, and Miwi2.

piRNAs are transcribed from piRNA clusters, specific regions of the genome. The resulting transcripts are transported to the cytoplasm, and the piRNA transcripts are cleaved into short fragments. These short transcripts are then loaded onto Piwi or Aubergine proteins and further processed at the 3' end by an unknown mechanism to generate mature primary piRNAs. Piwi-piRNA complexes are transported back to the nucleus to silence transposons. In contrast, Aubergine-piRNA complexes participate in the second phase of piRNA biogenesis, known as the ping-pong amplification pathway.

The Aubergine-piRNA complex binds and cleaves complementary transcripts, and the resulting cleaved fragments are then loaded onto another PIWI protein, AGO3. The AGO3-piRNA complex is then processed further at 3' end to generate mature secondary piRNAs. Like the Aubergine-piRNA complex, the mature AGO3-piRNA can cleave complementary transcripts. Another class of proteins, the Tudor family, also participates in the ping-pong amplification pathway where they may act as a scaffold for the binding of the components required for secondary piRNA biogenesis. In Drosophila, a dense peri-nuclear body, known as Nuage, contains proteins required for the piRNA ping-pong amplification pathway biogenesis, including Aubergine, AGO3, and Tudor. The exact steps and proteins involved in primary and secondary piRNA biogenesis pathways are still under investigation.