Influenza A virus transcribes viral mRNAs from the eight segmented viral genome when it infects. The kinetics of viral transcription, nuclear export of viral transcripts, and their potential variation between the eight segments are poorly characterised. Here, we introduce a statistical framework for estimating the nuclear export rate of each segment from a snapshot of in situ mRNA localisation. This exploits the cell-to-cell variation at a single time point observed by an imaging-based in situ transcriptome assay. Using our model, we revealed the variation in the mRNA nuclear export rate of the eight viral segments. Notably, the two influenza viral antigens hemagglutinin and neuraminidase were the slowest segments in the nuclear export, suggesting the possibility that influenza A virus uses the nuclear retention of viral transcripts to delay the expression of antigenic molecules. Our framework presented in this study can be widely used for investigating the nuclear retention of nascent transcripts produced in a transcription burst.

Bacterial pathogens employ epigenetic mechanisms, including DNA methylation, to adapt to environmental changes, and these mechanisms play important roles in various biological processes. Pseudomonas syringae is a model phytopathogenic bacterium, but its methylome is less well known than that of other species. In this study, we conducted single-molecule real-time sequencing to profile the DNA methylation landscape in three model pathovars of P. syringae. We identified one Type I restriction–modification system (HsdMSR), including the conserved sequence motif associated with N⁶-methyladenine (6mA). About 25–40% of the genes involved in DNA methylation were conserved in two or more of the strains, revealing the functional conservation of methylation in P. syringae. Subsequent transcriptomic analysis highlighted the involvement of HsdMSR in virulent and metabolic pathways, including the Type III secretion system, biofilm formation, and translational efficiency. The regulatory effect of HsdMSR on transcription was dependent on both strands being fully 6mA methylated. Overall, this work illustrated the methylation profile in P. syringae and the critical involvement of DNA methylation in regulating virulence and metabolism. Thus, this work contributes to a deeper understanding of epigenetic transcriptional control in P. syringae and related bacteria.