It is over 20 years since the publication of experiments that showed that influenza A virus RNA synthesis takes place in the cell nucleus and that here, the virus subverts the cellular transcription machinery to express and replicate its own single-strand RNA genome. In the years since, our understanding of the organisation of the nucleus has increased enormously, particularly with regards to the functional integration of the RNA polymerase II transcriptosome. This review summarises recent progress in defining the intimate association between the viral and cellular transcriptional machinery.