David Mahan Knipe

David Mahan Knipe

Program Head, PhD Program in Virology
Professor of Microbiology
David Mahan Knipe

Our laboratory studies the mechanisms of epigenetic regulation of DNA virus infection. We are interested in the mechanisms by which human cells sense foreign DNA in the cell nucleus and activate transcription of innate response genes and epigenetically silence the foreign DNA. Herpes simplex virus has a double-stranded DNA genome that has no histones associated with it in the virion. Upon entry into cells, the nucleocapsid is transported to the nuclear pore where the dsDNA genome is released into the nucleus. The host cell rapidly silences the viral lytic genes by loading of heterochromatin on the viral genome. In epithelial cells viral proteins reverse the epigenetic silencing, but in neuronal cells viral non-coding RNAs promote lytic gene silencing with facultative heterochromatin.

Relief of Epigenetic Silencing in Epithelial Cells. The HSV VP16 protein is delivered in the cytoplasm with the nucleocapsid and localizes to the nucleus where it binds to the cell Oct-1 protein, which binds to the viral immediate-early proteins and this complex recruits the cell host cell factor 1 (HCF-1) to the complex. HCF-1 recruits numerous histone modification enzymes and chromatin remodeling complexes to reduce histone occupancy, remove heterochromatin modifications and increase euchromatin modifications and activate IE gene transcription. We have shown that the VP16-Oct1-HCF-1 complex assembles on viral DNA in association with the nuclear lamina and we are currently mechanism of this novel intranuclear localization mechanism.

Epigenetic Silencing in Sensory Neurons. We have shown that transcription of the latency-associated transcript and miRNAs leads to increased heterochromatin on viral lytic genes and their epigenetic silencing, which leads to the latent infection by the virus. Binding of the CTCF insulator protein in the LAT transcriptional unit reduces heterochromatin marks on the LAT promoter, thereby assisting in the establishment of the latent infection. We are currently investigating how LAT transcription promotes heterochromatin formation on the lytic genes and the possible role of the Polycomb repressive complex in this process.

Nuclear Sensing of Foreign DNA. We have shown the cellular interferon-inducible protein 16 (IFI16) acts as a nuclear sensor of HSV DNA in infected cells and activates both an innate immune response that activates cytoplasmic IRF-3, which moves to the nucleus and activates expression of IFN-b and other genes, and an epigenetic silencing response that assembles heterochromatic marks on the histones associated with the viral DNA. We are currently investigating how the nuclear IFI16 protein and the cytoplasmic cGAS DNA sensors can both be required for interferon-b responses to HSV infection.

Replication-defective mutant viruses as a new form of viral vaccine. We have genetically engineered genital herpes strains that are mutated in essential genes for viral replication and have shown that one of these strains can serve as a genital herpes vaccine in animal models. This vaccine candidate is now in phase I safety trials at NIH. We are trying to improve the immunogenicity of the vaccine candidate by mutating viral immune evasion genes and we are studying the optimal vaccine for use in Sub-Saharan Africa, where there is an epidemic of genital herpes.

Contact Information

Harvard Medical School
New Research Building, Room 950B
77 Avenue Louis Pasteur
Boston, MA 02115
p: 617-432-1934

Community or Program Affiliation