Paramutation-like behaviour of genic piRNA-producing loci in Drosophila virilis. Paramutation-like behaviour of genic piRNA-producing loci in Drosophila virilis

Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversion remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark H3K9me3 over genomic regions that give rise to piRNAs. Importantly, maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The subtelomeric RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. Our findings highlight that the paramutation-like behavior of piRNA clusters is influenced not only by piRNAs but also by structural features of chromosomal regions, providing new insights into epigenetic regulation in Drosophila. Overall design: The submission includes samples from chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and small RNA-seq from ovaries of female Drosophila virilis. The research focuses on two distinct Drosophila virilis strains: strain 9, collected from Batumi, Georgia, and the laboratory strain 140 (eb, va).

Piwi互作RNA（Piwi-interacting RNAs，piRNAs）在后生动物生殖细胞中可作为序列特异性向导，在转座因子（transposable elements，TEs）沉默过程中发挥关键作用。其源自被称为piRNA簇（piRNA clusters）的独特基因组位点，可通过类副突变（paramutation-like）过程，介导转座因子插入序列表观遗传转化为piRNA簇。然而，piRNA簇诱导此类转化的能力差异，目前仍未得到充分解析。本研究针对两个在RhoGEF3与Adar基因位点产生piRNA能力存在差异的维氏果蝇（Drosophila virilis）品系展开探究。研究发现，活跃的piRNA生成与产生piRNA的基因组区域上高水平的异染色质标记H3K9me3呈正相关。值得注意的是，piRNA的母系传递可驱动子代产生piRNA，即便该过程源自此前在piRNA生物发生中无活性的同源位点。亚端粒区的RhoGEF3位点一旦发生表观遗传转化，便可在后续世代中维持piRNA生成水平的提升，即便这些世代缺失携带活性piRNA簇的原始等位基因。与之相反，经转化的Adar位点所表达的piRNA，在缺失诱导等位基因的子代中会丢失。本研究结果表明，piRNA簇的类副突变行为不仅受piRNA调控，还受染色体区域结构特征的影响，为果蝇的表观遗传调控研究提供了新视角。
实验设计概述：本数据集包含维氏果蝇雌性卵巢的染色质免疫共沉淀测序（chromatin immunoprecipitation sequencing，ChIP-seq）、RNA测序（RNA-seq）以及小RNA测序（small RNA-seq）样本。本研究聚焦于两个不同的维氏果蝇品系：采自格鲁吉亚巴统的品系9，以及实验室品系140（eb, va）。