BAF chromatin remodeling complexes inhibit immediate-early and early, but not late, transcription of herpes simplex virus 1

Herpes simplex virus 1 (HSV-1) is a highly prevalent DNA virus with a major impact on human health. The HSV-1 genome is assembled into silenced stable chromatin and minimally transcribed during latency or assembled into permissive highly dynamic chromatin and highly transcribed during lytic infections. It is unclear how HSV-1 genomes transition between chromatin states, but epigenetics, including chromatin dynamics, have been proposed to play a major role. Chromatin remodeling complexes regulate cellular chromatin dynamics and contribute to DNA transcription, replication, and repair. The BAF family of chromatin remodeling complexes includes three ubiquitously expressed complexes (cBAF, PBAF, and GBAF) and several cell type-specific ones. Some common BAF subunits interact with two HSV-1 proteins, VP16 or ICP8. Three subunits shared by all BAF complexes and a unique subunit from each cBAF, PBAF, and GBAF were enriched in herpes nuclear domains (HND), the novel nuclear domains formed during lytic infection in which HSV-1 genomes are transcribed, replicated, and packaged. The shared ATPase SMARCA4 bound, directly or indirectly, to HSV-1 genomes. Bromodomains bind to acetylated histones and may thus be involved in this binding. However, none of four structurally unrelated inhibitors of BAF bromodomains drastically affected the recruitment of BAF subunits to HND, and neither of four commonly acetylated histone residues recognized by BAF bromodomains was enriched in the HND. BAF complexes are thus recruited to the HND by their interactions with VP16, which activates viral transcription, and ICP8. Surprisingly, the BAF complexes recruited by VP16 and ICP8 participate in inhibition of immediate-early, early, and early-late HSV-1 transcription, but not DNA replication or late transcription. We propose that BAF complexes are recruited to the HND by VP16 and ICP8, independently of their bromodomains, to inhibit viral transcription early in infection, thus contributing to the regulated cascade of gene expression. These findings also have implications to epigenetic anticancer drugs, in that it should be considered whether their use may reactivate latent herpes simplex viruses. Author SummaryHerpes simplex virus 1 (HSV-1) infects over two-thirds of the world population. HSV-1 establishes latency in neurons, resulting in life-long infection. Although most infections are asymptomatic, reactivation can produce a wide range of clinical manifestations, including cold sores, stromal keratitis, and encephalitis. Available treatments do not prevent reactivation or eliminate latent viral reservoirs, as no viral proteins are expressed during latency. Epigenetic regulation plays a role during the lytic and latent cycles. Lytic HSV-1 chromatin is highly dynamic whereas latent chromatin is stable. Chromatin dynamics are regulated by multiple factors, including the chromatin remodeling complexes. Here we show that the BAF chromatin remodeling complexes regulate HSV-1 transcription during lytic infection in primary fibroblast and transformed epithelial human cells. Although these complexes are recruited to the viral genomes by viral proteins, they counterintuitively downregulate viral transcription before the onset of DNA replication. We propose that BAF complexes play a major role in the regulation of the orchestrated cascade of viral gene expression and propose to consider the potential for reactivation of herpes simplex viruses when using epigenetic inhibitors in the treatment of cancer.