Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [ATAC-Seq]

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, define each species' piRNA repertoire and therefore its capacity to recognize and silence transposons. In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells. Disruption of the flam locus or failure to process flam precursor transcripts into piRNAs results in sterility, yet it remains unknown whether this silencing mechanism is employed widely across Drosophilidae. Here, using both synteny-based analyses and de novo TE annotation, we identify candidate loci sharing both their organisation and TE targeting repertoire with flam in widely divergent Drosophila species groups. Small RNA-sequencing validated these loci as bona-fide unistrand piRNA clusters and revealed their predominant expression in somatic cells of the ovary, likely to counter TE mobilisation in this tissue. This study provides compelling evidence of co-evolution between virus-like Gypsy family transposons and a host defence mechanism in form of soma-expressed, unistrand piRNA clusters. Overall design: ATAC-seq of the whole intact ovaries across multiple fly species (Drosophilidae) to characterize the conserved chromatin accessibility landscape

PIWI相互作用RNA（PIWI-interacting RNA, piRNA）通路在抑制内源性基因组寄生虫——转座因子（transposable elements, TEs）——对动物生殖细胞遗传物质的损伤中发挥关键作用。基因组中的特定区域被称为piRNA簇（piRNA clusters），它们决定了每个物种的piRNA组成，进而决定其识别并沉默转座子的能力。在黑腹果蝇（Drosophila melanogaster）卵巢的体细胞中，flamenco（flam）单链簇是piRNA的主要来源，主要调控能够形成病毒样颗粒并感染邻近生殖细胞的Gypsy家族转座因子。破坏flam位点或无法将flam前体转录本加工为piRNA会导致果蝇不育，但目前尚不清楚这种沉默机制是否广泛存在于果蝇科（Drosophilidae）类群中。本研究通过同线性分析（synteny-based analyses）与从头转座因子注释（de novo TE annotation），在多个分化程度迥异的果蝇类群中鉴定出了与flam具有相似组织结构和转座子靶向谱的候选基因座。小RNA测序（small RNA-sequencing）验证了这些基因座为真正的单链piRNA簇，并发现它们主要在卵巢体细胞中表达，推测其功能为拮抗该组织中的转座子动员。本研究为病毒样Gypsy家族转座子与以体细胞表达的单链piRNA簇为形式的宿主防御机制之间的协同进化提供了强有力的证据。实验设计：对多个果蝇科物种的完整卵巢进行ATAC-seq测序，以解析保守的染色质可及性图谱。