Knudsen-Palmer Daphne R, Raman Pravrutha, Ettefa Farida, De Ravin Laura, Jose Antony M
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA.
Current address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
bioRxiv. 2024 Jun 3:2023.02.07.527351. doi: 10.1101/2023.02.07.527351.
Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode can selectively impair the silencing of some genes. Here we show that such selective requirements can be explained by an intersecting network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one somatic gene, but each is singly required for silencing another somatic gene, where only the requirement for NRDE-3 can be overcome by enhanced dsRNA processing. Quantitative models and their exploratory simulations led us to find that (1) changing -regulatory elements of the target gene can reduce the dependence on NRDE-3, (2) animals can recover from silencing in non-dividing cells and (3) cleavage and tailing of mRNAs with UG dinucleotides, which makes them templates for amplifying small RNAs, is enriched within 'pUG zones' matching the dsRNA. Similar crosstalk between pathways and restricted amplification could result in apparently selective silencing by endogenous RNAs.
由于双链RNA（dsRNA）对多种基因的沉默有效，所有基因通常被视为这种RNA干扰（RNAi）的等效靶标。然而，线虫中一些RNAi调节因子的缺失会选择性地损害某些基因的沉默。在这里，我们表明这种选择性需求可以通过作用于RNA代谢存在差异的基因的调节因子交叉网络来解释。在这个网络中，含有Maelstrom结构域的蛋白质RDE-10、内在无序的蛋白质MUT-16和Argonaute蛋白质NRDE-3共同发挥作用，使得沉默一个体细胞基因需要其中任意两个，但沉默另一个体细胞基因则各自单独需要，其中只有对NRDE-3的需求可以通过增强的dsRNA加工来克服。定量模型及其探索性模拟使我们发现：（1）改变靶基因的调控元件可以降低对NRDE-3的依赖性；（2）动物可以从非分裂细胞中的沉默中恢复；（3）具有UG二核苷酸的mRNA的切割和加尾，使其成为扩增小RNA的模板，在与dsRNA匹配的“pUG区域”内富集。途径之间类似的串扰和受限的扩增可能导致内源性RNA产生明显的选择性沉默。
