piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development [GRO-seq]

Eukaryotic genomes harbor invading transposable elements silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. This silencing signal requires the piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors, which correlates with the dynamic reorganization of two distinct perinuclear biomolecular condensates present in germ cells. In addition, the silencing capacity of piRNAs is temporally counteracted by the Argonaute CSR-1, which targets and licenses spermatogenic gene transcription. The spatial and temporal overlap between these opposing small RNA pathways contributes to setting up the timing of the spermatogenic differentiation program. Thus, our work identifies a prominent role for piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation. Overall design: 17 samples were analyzed by GRO-seq, including replicates (sample name contains 'rep').

真核基因组中存在可入侵的转座因子（transposable elements），这类元件会被PIWI互作RNA（PIWI-interacting RNAs, piRNAs）沉默，以维持动物生殖细胞的基因组完整性。然而，piRNAs是否同样调控内源基因表达程序，目前仍不明确。本研究显示，秀丽隐杆线虫（C. elegans）的piRNAs可在精子发生过程中触发数百个精子发生相关基因的转录沉默，进而促进精子分化与功能行使。该沉默信号依赖于piRNA介导的小RNA生成与加载至下游核效应因子，这一过程与生殖细胞中两种独特的核周生物分子凝聚体的动态重排相关。此外，piRNAs的沉默能力会在时间维度上被Argonaute CSR-1所拮抗，该蛋白可靶向并授权精子发生基因的转录。这两条对立小RNA通路的时空重叠，有助于精准调控精子发生分化程序的时序。综上，本研究证实piRNAs在生殖系发育与配子分化过程中，可作为内源转录程序的直接调控因子发挥关键作用。总体实验设计：本研究通过GRO-seq分析了17个样本，包含生物学重复（样本名称中包含'rep'字样）。