PIWI-interacting RNAs (piRNA) suppress selfish genetic elements and are essential for germ cell biology in animals. They also play critical roles in regeneration in planaria, regulate gene expression in adult mammalian testes, and participate in antiviral defense in mosquitoes. Inspired by a recent workshop on PIWI proteins and piRNAs, this commentary aims to summarize fundamental aspects of piRNA biology, highlight recent advances, and discuss key outstanding questions. It is written by and for biochemists, geneticists, and evolutionary biologists, and represents our interdisciplinary perspective.

This commentary highlights, from an interdisciplinary perspective, recent advances and key outstanding questions in the field of piRNA biology. [Image: see text]

Biology of Non coding RNA Group Institute of Molecular Biology Mainz Germany

Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan

Department of Genetic Medicine and Development University of Geneva Geneva Switzerland

Department of Medical Microbiology Radboud University Medical Center Nijmegen The Netherlands

Department of Molecular Cellular and Developmental Biology Yale University New Haven CT USA

Developmental Biology Program Sloan Kettering Institute New York USA

Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

National Institutes of Diabetes and Digestive and Kidney Diseases National Institutes of Health Bethesda MD USA

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Allikka Parambil S, Li D, Zelko M, Poulet A, van Wolfswinkel JC (2024) piRNA generation is associated with the pioneer round of translation in stem cells. Nucleic Acids Res 52:2590–2608 PubMed PMC

Anzelon TA, Chowdhury S, Hughes SM, Xiao Y, Lander GC, MacRae IJ (2021) Structural basis for piRNA targeting. Nature 597:285–289 PubMed PMC

Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761–764 PubMed

Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, Zamore PD (2022) GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature 608:618–625 PubMed PMC

Chen P, Kotov AA, Godneeva BK, Bazylev SS, Olenina LV, Aravin AA (2021) piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. Genes Dev 35:914–935 PubMed PMC

Choi H, Wang Z, Dean J (2021) Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA. PLoS Genet 17:e1009485 PubMed PMC

Czech B, Munafo M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ (2018) piRNA-guided genome defense: from biogenesis to silencing. Annu Rev Genet 52:131–157 PubMed PMC

Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K, Svoboda P (2013) A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155:807–816 PubMed

Gainetdinov I, Vega-Badillo J, Cecchini K, Bagci A, Colpan C, De D, Bailey S, Arif A, Wu PH, MacRae IJ et al (2023) Relaxed targeting rules help PIWI proteins silence transposons. Nature 619:394–402 PubMed PMC

Gebert D, Neubert LK, Lloyd C, Gui J, Lehmann R, Teixeira FK (2021) Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation. Mol Cell 81:3965–3978.e3965 PubMed PMC

Genzor P, Konstantinidou P, Stoyko D, Manzourolajdad A, Marlin Andrews C, Elchert AR, Stathopoulos C, Haase AD (2021) Cellular abundance shapes function in piRNA-guided genome defense. Genome Res 31:2058–2068 PubMed PMC

Hasuwa H, Iwasaki YW, Au Yeung WK, Ishino K, Masuda H, Sasaki H, Siomi H (2021) Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters. Nat Cell Biol 23:1002–1012 PubMed

Ketting RF, Cochella L (2021) Concepts and functions of small RNA pathways in C. elegans. Curr Top Dev Biol 144:45–89 PubMed

Lai EC, Vogan AA (2023) Proliferation and dissemination of killer meiotic drive loci. Curr Opin Genet Dev 82:102100 PubMed PMC

Lewis SH, Quarles KA, Yang Y, Tanguy M, Frezal L, Smith SA, Sharma PP, Cordaux R, Gilbert C, Giraud I et al (2018) Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat Ecol Evol 2:174–181 PubMed PMC

Li D, Taylor DH, van Wolfswinkel JC (2021) PIWI-mediated control of tissue-specific transposons is essential for somatic cell differentiation. Cell Rep 37:109776 PubMed PMC

Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z et al (2013) An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell 50:67–81 PubMed PMC

Loubalova Z, Fulka H, Horvat F, Pasulka J, Malik R, Hirose M, Ogura A, Svoboda P (2021) Formation of spermatogonia and fertile oocytes in golden hamsters requires piRNAs. Nat Cell Biol 23:992–1001 PubMed PMC

Loubalova Z, Konstantinidou P, Haase AD (2023) Themes and variations on piRNA-guided transposon control. Mob DNA 14:10 PubMed PMC

Miesen P, Joosten J, van Rij RP (2016) PIWIs go viral: arbovirus-derived piRNAs in vector mosquitoes. PLoS Pathog 12:e1006017 PubMed PMC

Onishi R, Yamanaka S, Siomi MC (2021) piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: new insights and biodiversity. EMBO Rep 22:e53062 PubMed PMC

Ozata DM, Gainetdinov I, Zoch A, O’Carroll D, Zamore PD (2019) PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 20:89–108 PubMed

Podvalnaya N, Bronkhorst AW, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S, Ketting RF (2023) piRNA processing by a trimeric Schlafen-domain nuclease. Nature 622:402–409 PubMed PMC

Reuter M, Berninger P, Chuma S, Shah H, Hosokawa M, Funaya C, Antony C, Sachidanandam R, Pillai RS (2011) Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature 480:264–267 PubMed

Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LA, Zischler H, Butter F, Roelen BA et al (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep 10:2069–2082 PubMed

Siomi MC, Mannen T, Siomi H (2010) How does the royal family of Tudor rule the PIWI-interacting RNA pathway? Genes Dev 24:636–646 PubMed PMC

Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L et al (2019) Decoding the 5’ nucleotide bias of PIWI-interacting RNAs. Nat Commun 10:828 PubMed PMC

Suzuki Y, Baidaliuk A, Miesen P, Frangeul L, Crist AB, Merkling SH, Fontaine A, Lequime S, Moltini-Conclois I, Blanc H et al (2020) Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries. Curr Biol 30:3495–3506.e3496 PubMed PMC

van Wolfswinkel JC (2014) Piwi and potency: PIWI proteins in animal stem cells and regeneration. Integr Comp Biol 54:700–713 PubMed

van Wolfswinkel JC (2024) Insights in piRNA targeting rules. Wiley Interdiscip Rev RNA: 15:e1811 PubMed PMC

Vedanayagam J, Herbette M, Mudgett H, Lin CJ, Lai CM, McDonough-Goldstein C, Dorus S, Loppin B, Meiklejohn C, Dubruille R et al (2023) Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol 21:e3002136 PubMed PMC

Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD, Mourelatos Z (2012) Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat Struct Mol Biol 19:773–781 PubMed PMC

Wasik KA, Tam OH, Knott SR, Falciatori I, Hammell M, Vagin VV, Hannon GJ (2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev 29:1403–1415 PubMed PMC

Williams Z, Morozov P, Mihailovic A, Lin C, Puvvula PK, Juranek S, Rosenwaks Z, Tuschl T (2015) Discovery and characterization of piRNAs in the human fetal ovary. Cell Rep 13:854–863 PubMed

Wu PH, Fu Y, Cecchini K, Ozata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD (2020) The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nat Genet 52:728–739 PubMed PMC

Wu PH, Zamore PD (2021) Defining the functions of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 22:239–240 PubMed

Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Coute Y, Conn S, Kadlec J, Sachidanandam R et al (2014) RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 157:1698–1711 PubMed

Yamamoto-Matsuda H, Miyoshi K, Moritoh M, Yoshitane H, Fukada Y, Saito K, Yamanaka S, Siomi MC (2022) Lint-O cooperates with L(3)mbt in target gene suppression to maintain homeostasis in fly ovary and brain. EMBO Rep 23:e53813 PubMed PMC

Zhang H, Zhang F, Chen Q, Li M, Lv X, Xiao Y, Zhang Z, Hou L, Lai Y, Zhang Y et al (2021) The piRNA pathway is essential for generating functional oocytes in golden hamsters. Nat Cell Biol 23:1013–1022 PubMed

Zhou L, Canagarajah B, Zhao Y, Baibakov B, Tokuhiro K, Maric D, Dean J (2017) BTBD18 regulates a subset of piRNA-generating loci through transcription elongation in mice. Dev Cell 40:453–466.e455 PubMed