Analysis of host and viral nascent and steady-state RNA levels in a human neuronal model of herpes simplex virus 1 infection

We used precision nuclear run-on with sequencing (PRO-seq) in conjunction with quantitative RT-qPCR to map transcription, and transcript abundance in terminally differentiated LUHMES neurons before (mock) and after infection with Herpes Simplex Virus 1 (HSV-1). Initial PRO-seq analysis of cellular transcription demonstrated that the mock-infected differentiated LUHMES neurons expressed genes associated with differentiated neurons. This gene set included transcription of genes related to dopaminergic signaling, cell adhesion, and neuronal cell differentiation. By contrast, epithelial cells transcribed genes involved in cell cycle progression and DNA damage repair. PRO-Seq analysis of HSV-1-infected LUHMES neurons indicated only modest transcription of viral genomes. Additionally, genes of LUHMES neurons maintained RNA polymerase II (Pol II) promoter proximal pausing whereas we previously showed HSV-1 infection decreases promoter-proximal pausing on genes of epithelial cells. PRO-Seq and RT-qPCRanalysis were performed during a time course of infection, spanning both acute and latent phases. The results from the acute infection demonstrated slower rates of transcription, viral mRNA accumulation, and viral genome replication compared to undifferentiated, non-neuronal cells. RT-qPCR indicated that steady-state transcripts from all viral gene kinetic classes increased in abundance from 1 h to 24 h post-infection. This accumulation correlated with an increase in transcription on the same genes as demonstrated by PRO-seq. In contrast, the latent phase of infection was distinguished by high levels of transcription on all viral genes, but very low viral transcript abundance. These results indicate that viral gene transcription initiation does not correlate with viral transcript abundance during the latent phase, and suggest that blocks to RNA polymerase processivity and other components of the RNA life cycle likely contribute to maintenance of latency in LUHMES neurons.