Locus-specific variation in piRNA production in different mouse strains.

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 individuals underlie variation in piRNA expression. We report significant differences in piRNA production at loci with endogenous retrovirus insertions. Strain-specific piRNA-producing loci include protein-coding genes. Our findings provide evidence that transposable elements contribute to inter-individual differences in expression, and potentially to the fast evolution of piRNA-producing loci in mammals. Differential expression analysis of known and predicted piRNAs in testes and spermatogonia of genetically different mouse strains (C57BL6, CAST, 129, C3H, NOD, ICR). RNA-seq profiling of testes and FACS sorted spermatogonia from five inbred mouse strains and one outbred mouse strain. NOTE: The data in this series replaces data originally included in GSE121138. The records have been updated with additional RNA-seq samples on Jul 8, 2025.PIWI互作RNA（PIWI-interacting RNAs，piRNAs）是一类小型非编码RNA，可在动物生殖系中沉默转座子。piRNA由长单链非编码转录本、蛋白编码转录本以及转座子自身转录产生。尽管部分产piRNA的基因座位于高度保守的同线区域，但总体而言，piRNA及其产生基因座的演化周转速率显著快于基因组其他功能区域。为解析驱动piRNA快速演化的序列变化机制，我们针对遗传背景各异的小鼠开展了piRNA表达差异分析。本研究报道了四种经典近交系、一种野生来源近交系及一种远交系小鼠雄性生殖系小RNA的测序与分析结果。研究发现个体间的遗传差异是piRNA表达变异的重要基础。本研究同时报道了携带内源逆转录病毒插入位点的基因座上，piRNA产生存在显著差异。品系特异性产piRNA基因座包含蛋白编码基因。本研究结果证实，转座因子促成了哺乳动物个体间的表达差异，并可能推动了产piRNA基因座的快速演化。 本数据集包含对不同遗传背景小鼠品系（C57BL6、CAST、129、C3H、NOD、ICR）睾丸及精原细胞中已知与预测piRNA的差异表达分析，以及对5种近交系小鼠和1种远交系小鼠的睾丸、经荧光激活细胞分选（Fluorescence Activated Cell Sorting，FACS）富集的精原细胞的RNA测序（RNA Sequencing，RNA-seq）谱分析。 注：本系列数据集替代了最初收录于GSE121138的原始数据。该数据集记录已于2025年7月8日更新，新增了更多RNA-seq样本。