Distinct labeling of host and viral genomes highlights redistribution of nuclear proteins during HSV-1 infection

Herpes simplex virus type 1 (HSV-1) coordinates viral and cellular proteins during infection. While proteins associated with HSV-1 genomes have been identified, changes in proteins associated with the host genome during infection remain poorly understood. We adapted accelerated native isolation of proteins on nascent DNA (aniPOND) to label and purify cellular and viral DNA then identify associated proteins by mass spectrometry. Using this approach, we confirm observations that cellular transcription, DNA replication, and repair proteins are enriched on viral genomes after the onset of viral DNA replication. We assessed how protein interactions with cellular DNA change during infection relative to protein abundance. Targets of the viral E3 ubiquitin ligase, ICP0, are depleted from the nucleus and cellular genome during infection. Transcription regulatory factors, Pol II, and the proteasome are depleted from the host genome, while association with DNA damage response and nuclear pore proteins increases. We also provide evidence for HSV-1 disruption of ribosome biogenesis. Results demonstrate reorganization of the nucleus during infection and validate this technique to identify changes to host genome-associated factors during infection.