Chen Shihui, Phillips Carolyn M
Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089.
bioRxiv. 2025 Jan 17:2024.07.29.605686. doi: 10.1101/2024.07.29.605686.
RNA interference (RNAi) is a conserved gene regulation mechanism that utilizes the Argonaute protein and their associated small RNAs to exert regulatory function on complementary transcripts. While the majority of germline-expressed RNAi pathway components reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here we find that the small RNA biogenesis machinery is spatially and temporally organized during embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. We also observe that many other RNAi factors form foci in embryonic cells distinct from "SIMR granules", including the Argonaute protein CSR-1, underscoring a potential role for cytoplasmic concentrates of RNAi factors to promote gene regulation in embryos. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. Prior work has shown that NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.
RNA干扰（RNAi）是一种保守的基因调控机制，它利用AGO蛋白及其相关的小RNA对互补转录本发挥调控作用。虽然大多数生殖系表达的RNAi通路成分存在于核周生殖颗粒中，但RNAi通路在其他细胞类型中是否以及如何在空间上组织尚不清楚。在这里，我们发现小RNA生物合成机制在胚胎发育过程中在空间和时间上是有组织的。具体而言，RNAi因子SIMR-1在胚胎发育中期形成可见的聚集体，其中包含一种RNA依赖性RNA聚合酶、一种聚UG聚合酶以及空载的核AGO蛋白NRDE-3。我们还观察到许多其他RNAi因子在胚胎细胞中形成与“SIMR颗粒”不同的焦点，包括AGO蛋白CSR-1，这突出了RNAi因子的细胞质聚集体在促进胚胎基因调控方面的潜在作用。奇怪的是，与SIMR颗粒的出现同时，与NRDE-3结合的小RNA从主要的CSR类22G-RNA转变为ERGO依赖性22G-RNA。先前的研究表明，NRDE-3在幼虫和成虫的体细胞中结合ERGO依赖性22G-RNA以沉默ERGO靶向基因；在这里我们证明，与NRDE-3结合的CSR类22G-RNA在卵母细胞中抑制转录。因此，我们的研究定义了NRDE-3的两个可分离的作用，即在卵子发生过程中靶向生殖系表达的基因以促进全局转录抑制，并在胚胎发育过程中转换以抑制体细胞中最近复制的基因和逆转座子，突出了AGO蛋白的可塑性以及对AGO-小RNA相互作用进行更精确时间表征的必要性。
