The accessibility of the HSV genome during productive infection can vary in different cell types and affect the outcome of infection

During productive herpes simplex virus type 1 (HSV-1) infection, the viral genome encounters a number of cellular and viral proteins, such as ICP4, which engage in processes that either attenuate or activate transcription. DNA replication allows the recruitment of cellular transcription factors to late gene promoters, leading to the activation of late gene transcription. We hypothesize that part of the mechanisms by which these viral processes and proteins affect transcription involves altering the accessibility of the genome to the cellular transcription machinery. Using assay for transposase accessible chromatin sequencing (ATAC-seq) to measure accessibility in diploid human lung fibroblasts (MRC5 cells), we found that ICP4 function decreased the accessibility of immediate early genes and increased the accessibility of early and late genes, consistent with the expression of these genes. We also measured accessibility before and after the onset of genome replication. Our results show that the viral genomes were most accessible just after the onset of replication. We conducted similar experiments in a human sensory neuron model (HD10.6) and found that viral genomes were most accessible immediately following infection, and accessibility was reduced as infection proceeded. This finding correlated with viral gene expression and infection outcome, which were considerably reduced compared with that seen in MRC5 cells. ATAC-seq fragment patterns were not consistent with a canonical nucleosome structure for the viral genome, in either cell type, pre- or post-replication. We conclude that accessibility is an important determinant of HSV-1 transcriptional activity and infection outcome.IMPORTANCEThe transcription of herpes simplex virus type 1 (HSV-1) genes is regulated by viral and cellular transcription factors and genome replication. One regulatory aspect is accessibility of viral genes to the host transcription machinery. In this study, we determine how the major HSV-1 transcriptional regulatory protein, ICP4, and viral DNA replication affect accessibility, and how this relates to viral gene transcription. We also assessed viral genome accessibility in a sensory neuronal model that has the potential for viral gene silencing and establishment of quiescent or latent infection. We conclude that the accessibility of the viral genome to the cellular machinery responsible for viral gene expression is an important determinant to infection outcome.