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.
Researchers at the University of Würzburg, Germany have assessed 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.
They found that dual RNA-Seq will require high sequencing depth in order to provide accurate representations of the host and pathogen genomes and propose that this is highly likely to be attainable in the future given the potential for near-infinite sequencing power. However, current dual RNA-Seq on the population level appears to be costly but feasible. The latest sequencing platforms can generate an output of up to several hundred gigabases per experimental run, suggesting that the ~200–2,000 million reads required for dual RNA-Seq can be achieved.
- Westermann AJ, Gorski SA, Vogel J. (2012) Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10(9), 618-30. [article]