Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany.
Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany.
Curr Opin Microbiol. 2018 Apr;42:7-12. doi: 10.1016/j.mib.2017.09.001. Epub 2017 Sep 26.
Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over the recent years now allow us to apply RNA sequencing to two species at the same time (dual RNA-seq), and thus to directly study the gene expression of two interacting species without the need to physically separate cells or RNA. In this review, we give an overview over the latest studies in interspecies interactions made possible by dual RNA-seq, ranging from pathogenic to symbiotic relationships. We summarize state-of-the-art experimental techniques, bioinformatic data analysis and data interpretation, while also highlighting potential problems and pitfalls starting from the selection of meaningful time points and number of reads to matters of rRNA depletion. A short outlook on new trends in the field of dual RNA-seq concludes this review, looking at sequencing of non-coding RNAs during host-pathogen interactions and the prediction of molecular interspecies interactions networks.
生物体之间并非相互孤立存在，而是不断相互作用。细胞可以通过一系列受体感知到相互作用伙伴的存在，并通过复杂的调控网络，通过改变许多基因的表达来特异性地反应。近年来，下一代测序技术的进步使得我们能够同时对两种物种进行 RNA 测序（双重 RNA-seq），从而无需物理分离细胞或 RNA 即可直接研究两种相互作用物种的基因表达。在这篇综述中，我们概述了通过双重 RNA-seq 实现的种间相互作用的最新研究，范围从致病性到共生关系。我们总结了最先进的实验技术、生物信息数据分析和解释，同时还从有意义的时间点和读段数量的选择到 rRNA 耗竭等问题，突出了潜在的问题和陷阱。本文简短展望了双重 RNA-seq 领域的新趋势，着眼于宿主-病原体相互作用过程中非编码 RNA 的测序以及分子种间相互作用网络的预测。
