Computational Analysis Of HSV-1 Infected Cellular Transcriptome And Epigenome

Human Herpes Simplex Virus type â… (HSV-1) is a double-strand DNA virus, with a 152Kb genome and 80 genes, and infects over 80% of the population. HSV-1 normally enters latent infection in sensory neurons in periphery sensory ganglion. Stress signals cause the reactivation of HSV-1 from sensory neurons and lytic infection ensues in epithelial cells these neurons innervate, resulting in cold sores, Herpes keratitis and, in rare but often fatal cases, Herpes encephalitis. HSV-1 lytic infection unfolds rapidly, first with the expression of immediate early (IE) genes, including ICPO and ICP4, which quickly recruit host RNA polymerase and other transcription coregulators to make viral early genes, and prepare viral DNA synthesis and late gene expression which occurs at approximately 6 hours post infection (hpi). In this process, the virus takes advantage of many host factors, host responses and pathways to promote viral growth.The incoming virus triggers a number of host responses from activating the interferon pathway, the DNA damage response, apoptosis and other host defense mechanisms limiting viral growth. Many of the viral genes are designed to deal with these host responses to ensure viral transcription, genome synthesis and assembly. ICP34.5 is a key viral factor interfering with the interferon beta pathway. ICP27 and ICP22 are two regulators of the host apoptotic response inhibiting the host DNA damage response by inactivating the ATR kinase. ICPO inhibits host transcription silencing activity by displacing host CoREST silencing complex and degrades RNF8 and RNF168, two ubiquitin ligases in the DDR. HSV-1 also encodes ICP27 to inhibit host RNA splicing and VHS to degrade host RNAs. In spite of these advances, viral-host interaction is still not completely understood.Herpes Simplex Virus type â…  enters productive infection in Human epithelial cells and dramatically alters the host nucleus. Previous DNA array analyses in infected mouse cornea or MEF cells revealed extensive alterations of host gene expression profiles. Here we analyzed the transcriptome of HSV-1 infected human epithelial fibroblast BJ cells by High-throughput sequencing, and found differential gene expression, alternative splicing, alternative polyadenylation and gene isoform changes. The infection caused up regulation of 978 genes and down regulations of 61 genes compared to uninfected cells, while leading to changes of 217 cases of alternative splicing,161 incidences of APA and 1,827 events of isoform changes. As a result, we found gene isoform changes in over 700 genes. Interestingly, GO analyses revealed that genes involved in neurogenesis, which were up regulated by the infection, were absent from genes that underwent alternative splicing, alternative polyadenylation and isoform changes, suggesting neurogenic genes were mostly up regulated due to de-repression by the presence of ICPO. We were able to identify a number of genes important for viral host interactions including transcription regulator brd2 and cbx4. We also identified 108 genes involved in RNA metabolism including znf36, a cellular factor selectively degrades ARE element containing mRNAs. Take together, this analysis revealed a number of new identified genes involved in viral-host interactions and implicated alternative splicing and alternative polyadenylation as important mechanism generating new regulatory function in infected cells.Interestingly, infection caused dramatic reorganization of the host chromatin, exemplified by a 90% loss of CTCF binding genome wide. Highly induced genes tend to interact with CTCF, suggesting that CTCF may play important role in highly regulated genes. By comparing RNA Pol II ChIP-seq and RNA-seq data, we are able to determine that 130 number of genes are induced at transcriptional level, while 444 number of genes are regulated at RNA metabolism.To summarize, by a combination of RNA-seq, CHIP-seq, classic virology and genomics studies, we are able to reveal profound transcriptome and epigenomic changes following HSV-1 infection of human epithelial cells. These analyses shed interesting light on how the cellular genome responds to acute external stimulus such lytic viral infection and how viral-host interaction unfold at genomic scale.