biostudies-literatureCasas EGovernment of Catalonia | Agència de Gestió d'Ajuts Universitaris i de RecercaFundacio Internacional Josep CarrerasCentres de Recerca de CatalunyaMinisterio de Economía y CompetitividadMinisterio de Economía y Competitividad (MEC)'la Caixa' Foundation ('la Caixa')'la Caixa' Foundation4104-4119https://www.ebi.ac.uk/biostudies/studies/S-EPMC12264111biostudies-literatureUnknown44(14)PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded noncoding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyze piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between indiviThe EMBO journalGenetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse.PMC12264111PID2019-105278RB-I00PID2019-111676GB-I00BFU2015-70581LCF/BQ/DI22/11940007Mitjavila-Ventura ACebria JVavouri TCasas ESierra PJimenez-Chillaron JCForcales SVMoreta-Moraleda CPospisilik JAPanzeri IfalseGenetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse.PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded noncoding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyze piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between indivi2025-01-01T00:00:00Z2025 Jul2026-07-15T06:30:11.157Z2026-06-30T03:22:35.582ZS-EPMC122641114047400610.1038/s44318-025-00475-4