Dual RNA-seq of pathogen and host

The infection process is accompanied by widespread changes in gene expression in both host and pathogen. Here, Vogel and colleagues explore the feasibility of simultaneously analysing the transcriptomes of both host and pathogen using RNA deep-sequencing approaches. A comprehensive understanding of host–pathogen interactions requires a knowledge of the associated gene expression changes in both the pathogen and the host. Traditional, probe-dependent approaches using microarrays or reverse transcription PCR typically require the pathogen and host cells to be physically separated before gene expression analysis. However, the development of the probe-independent RNA sequencing (RNA-seq) approach has begun to revolutionize transcriptomics. Here, we assess the feasibility of taking transcriptomics one step further by performing 'dual RNA-seq', in which gene expression changes in both the pathogen and the host are analysed simultaneously.