MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK.
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3TF, UK.
Dev Cell. 2019 Mar 25;48(6):793-810.e6. doi: 10.1016/j.devcel.2018.12.026. Epub 2019 Jan 31.
Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an ∼28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription.
Piwi 相互作用 RNA（piRNA）在后生动物的基因组调控中非常重要，但它们的生物发生迅速进化。在秀丽隐杆线虫中，piRNA 基因座簇集在染色体 IV 上的两个 3-Mb 区域内。每个 piRNA 基因座都有一个上游基序，该基序招募 RNA 聚合酶 II 产生约 28 nt 的初级转录本。我们使用线虫的比较表观基因组学来深入了解线虫 piRNA 生物发生的起源、进化和机制。我们表明，piRNA 上游基序源自控制 snRNA 转录的核心启动子元件。我们描述了线虫中两种替代的 piRNA 组织方式：在秀丽隐杆线虫和密切相关的线虫中，piRNAs 簇集在抑制性 H3K27me3 染色质内，而在其他物种中，以太平洋真涡虫为代表，piRNAs 位于活性基因的内含子中。此外，我们发现 piRNA 的产生依赖于与 RNA 聚合酶 II 暂停相关的序列信号。我们表明，暂停信号与染色质协同控制 piRNA 转录。
