Abstract
A detailed knowledge about virulence-relevant genes, as well as where and when they are expressed during the course of an infection is required to obtain a comprehensive understanding of the complex host–pathogen interactions. The development of unbiased probe-independent RNA sequencing (RNA-seq) approaches has dramatically changed transcriptomics. It allows simultaneous monitoring of genome-wide, infection-linked transcriptional alterations of the host tissue and colonizing pathogens. Here, we provide a detailed protocol for the preparation and analysis of lymphatic tissue infected with the mainly extracellularly growing pathogen Yersinia pseudotuberculosis. This method can be used as a powerful tool for the discovery of Yersinia-induced host responses, colonization and persistence strategies of the pathogen, and underlying regulatory processes. Furthermore, we describe computational methods with which we analyzed obtained datasets.
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Acknowledgments
We are grateful to M. Fenner for discussions and Robert Geffers and Michael Jarek from the Department of Genome Analytics for Illumina sequencing. This work was supported from grants of the German Research Foundation (DE616/4, DE616/6, SPP1617-young investigator startup funding for A.M. Nuss), and a stipend of the Helmholtz Center for Infection Research Graduate School for M. Kusmierek. P. Dersch is supported by the German Center for Infection Research.
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Kusmierek, M., Heroven, A.K., Beckstette, M., Nuss, A.M., Dersch, P. (2019). Discovering Yersinia–Host Interactions by Tissue Dual RNA-Seq. In: Vadyvaloo, V., Lawrenz, M. (eds) Pathogenic Yersinia. Methods in Molecular Biology, vol 2010. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9541-7_8
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DOI: https://doi.org/10.1007/978-1-4939-9541-7_8
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