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

真核基因组中存在入侵性转座子（transposable elements），这类元件可通过PIWI互作RNA (PIWI-interacting RNAs，piRNAs) 实现沉默，以维持动物生殖细胞的基因组完整性。然而，piRNAs是否也可调控内源基因表达程序，目前尚不明确。本研究发现，秀丽隐杆线虫（C. elegans）的piRNAs可在精子发生过程中触发数百个生精基因的转录沉默，进而促进精子分化与功能发挥。该沉默信号依赖于piRNA介导的小RNA生物发生与加载至下游核效应蛋白的过程，这一过程与生殖细胞中两种不同的核周生物分子凝聚体的动态重排密切相关。此外，piRNAs的沉默能力会在时间维度上被Argonaute蛋白CSR-1所拮抗，该蛋白可靶向并许可生精基因的转录。这两条相互拮抗的小RNA通路在时空上的重叠，有助于确立精子发生分化程序的时序。因此，本研究揭示了piRNAs在生殖系发育与配子分化过程中，作为内源转录程序直接调控因子的重要功能。整体实验设计：本研究通过全局运行测序（Global Run-On sequencing，GRO-seq）分析了17份样本，其中包含生物学重复（样本名称含'rep'标识）。