Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
Departments of Mathematics and Biology & York Cross-disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK.
Nucleic Acids Res. 2018 Dec 14;46(22):12087-12098. doi: 10.1093/nar/gky881.
Viruses with segmented genomes, including pathogens such as influenza virus, Rotavirus and Bluetongue virus (BTV), face the collective challenge of packaging their genetic material in terms of the correct number and types of segments. Here we develop a novel network approach to predict RNA-RNA interactions between different genomic segments. Experimental data on RNA complex formation in the multi-segmented BTV genome are used to establish proof-of-concept of this technique. In particular, we show that trans interactions between segments occur at multiple specific sites, termed segment assortment signals (SASs) that are dispersed across each segment. In order to validate the putative trans acting networks, we used various biochemical and molecular techniques which confirmed predictions of the RNA network approach. A combination of mutagenesis and reverse genetics systems revealed that the RNA-RNA interacting sites identified are indeed responsible for segment assortment and complex formation, which are essential criteria for genome packaging. This paves the way for their exploitation as novel types of drug target, either to inhibit assembly, or for designing defective interfering particles containing an incomplete set of genomic segments.
具有分段基因组的病毒，包括流感病毒、轮状病毒和蓝舌病毒（BTV）等病原体，都面临着将其遗传物质正确包装成不同类型和数量的片段的共同挑战。在这里，我们开发了一种新的网络方法来预测不同基因组片段之间的 RNA-RNA 相互作用。使用多分段 BTV 基因组中 RNA 复合物形成的实验数据来验证该技术的概念验证。特别是，我们表明，片段之间的反式相互作用发生在多个特定的位点，称为片段分类信号（SAS），这些位点分散在每个片段上。为了验证假定的反式作用网络，我们使用了各种生化和分子技术，这些技术证实了 RNA 网络方法的预测。突变和反向遗传学系统的组合表明，所鉴定的 RNA-RNA 相互作用位点确实负责片段分类和复合物形成，这是基因组包装的必要条件。这为它们作为新型药物靶点的开发铺平了道路，无论是抑制组装，还是设计包含不完全基因组片段的缺陷干扰颗粒。
