Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520-8073, USA.
Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8073, USA.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkaa059.
Small noncoding RNA pathways have been implicated in diverse mechanisms of gene regulation. In Drosophila ovaries, Piwi binds to Piwi-interacting RNAs (piRNAs) of mostly 24-28 nucleotides (nt) and plays an important role in germline stem cell maintenance, transposon repression, and epigenetic regulation. To understand the mechanism underlying these functions, we report the application of the DamID-seq method to identify genome-wide binding sites of Piwi in Drosophila ovaries. Piwi localizes to at least 4535 euchromatic regions that are enriched with piRNA target sites. Surprisingly, the density of Piwi binding to euchromatin is much higher than in heterochromatin. Disrupting the piRNA binding of Piwi results in an overall change of the genomic binding profile, which indicates the role of piRNAs in directing Piwi to specific genomic sites. Most Piwi binding sites were either within or in the vicinity of protein-coding genes, particularly enriched near the transcriptional start and termination sites. The methylation signal near the transcriptional termination sites is significantly reduced when Piwi was mutated to become defective in piRNA binding. These observations indicate that Piwi might directly regulate the expression of many protein-coding genes, especially through regulating the 3' ends of targeted transcripts.
小非编码 RNA 途径参与了基因调控的多种机制。在果蝇卵巢中，Piwi 与主要为 24-28 个核苷酸 (nt) 的 Piwi 相互作用 RNA (piRNA) 结合，在生殖干细胞维持、转座子抑制和表观遗传调控中发挥重要作用。为了了解这些功能的机制，我们报告了应用 DamID-seq 方法来鉴定果蝇卵巢中 Piwi 的全基因组结合位点。Piwi 定位于至少 4535 个常染色质区域，这些区域富含 piRNA 靶位点。令人惊讶的是，Piwi 与常染色质的结合密度远高于异染色质。破坏 Piwi 与 piRNA 的结合会导致基因组结合图谱的整体变化，这表明 piRNAs 在指导 Piwi 到特定基因组位点中的作用。大多数 Piwi 结合位点位于或靠近蛋白质编码基因内，特别是在转录起始和终止位点附近富集。当 Piwi 突变导致其不能与 piRNA 结合时，转录终止位点附近的甲基化信号显著降低。这些观察结果表明，Piwi 可能直接调节许多蛋白质编码基因的表达，特别是通过调节靶向转录物的 3' 端。
