IFI16 Restricts HSV-1 Replication by Accumulating on the HSV-1 Genome, Repressing HSV-1 Gene Expression, and Directly or Indirectly Modulating Histone Modifications

Abstract

Interferon-γ inducible factor 16 (IFI16) is a multifunctional nuclear protein involved in transcriptional regulation, induction of interferon-β (IFN-β), and activation of the inflammasome response. It interacts with the sugar-phosphate backbone of dsDNA and modulates viral and cellular transcription through largely undetermined mechanisms. IFI16 is a restriction factor for human cytomegalovirus (HCMV) and herpes simplex virus (HSV-1), though the mechanisms of HSV-1 restriction are not yet understood. Here, we show that IFI16 has a profound effect on HSV-1 replication in human foreskin fibroblasts, osteosarcoma cells, and breast epithelial cancer cells. IFI16 knockdown increased HSV-1 yield 6-fold and IFI16 overexpression reduced viral yield by over 5-fold. Importantly, HSV-1 gene expression, including the immediate early proteins, ICP0 and ICP4, the early proteins, ICP8 and TK, and the late proteins gB and Us11, was reduced in the presence of IFI16. Depletion of the inflammasome adaptor protein, ASC, or the IFN-inducing transcription factor, IRF-3, did not affect viral yield. ChIP studies demonstrated the presence of IFI16 bound to HSV-1 promoters in osteosarcoma (U2OS) cells and fibroblasts. Using CRISPR gene editing technology, we generated U2OS cells with permanent deletion of IFI16 protein expression. ChIP analysis of these cells and wild-type (wt) U2OS demonstrated increased association of RNA polymerase II, TATA binding protein (TBP) and Oct1 transcription factors with viral promoters in the absence of IFI16 at different times post infection. Although IFI16 did not alter the total histone occupancy at viral or cellular promoters, its absence promoted markers of active chromatin and decreased those of repressive chromatin with viral and cellular gene promoters. Collectively, these studies for the first time demonstrate that IFI16 prevents association of important transcriptional activators with wt HSV-1 promoters and suggest potential mechanisms of IFI16 restriction of wt HSV-1 replication and a direct or indirect role for IFI16 in histone modification.

Dynamic Response of IFI16 and Promyelocytic Leukemia Nuclear Body Components to Herpes Simplex Virus 1 Infection

“…Previous publications have noted that IFI16 is also recruited efficiently to HSV-1 genomes at the early stages of infection (22)(23)(24)(25)(26)(27)(28). In order to study this in more detail, a lentiviral vector system was used to express EYFP-tagged IFI16 ( Fig.…”

“…It is possible that recruitment is related to a DNA repair response, and indeed, several DNA repair proteins respond to infection in similar manners (19), but recruitment of PML still occurs in DNA repair-deficient cells (19). More recently, cellular DNA sensor IFI16 (20,21) was also implicated in the initiation of pathways that are inhibitory to HSV-1, either through initiating events leading to an interferon response (21,22) or through more-direct effects on viral gene expression (23)(24)(25)(26). ICP0-null mutant HSV-1 has increased plaque-forming potential in cells depleted of IFI16 (23,25).…”

“…IFI16 is degraded during HSV-1 infection by a mechanism that was originally thought to be ICP0 dependent (22), although later work showed that ICP0 was neither sufficient nor necessary for this degradation (23,27). Indeed, cellular factors (and cell type) also contribute to the stability of IFI16 during HSV-1 infection (23,24,26). Nonetheless, under normal experimental conditions, IFI16 is degraded more rapidly during a wild-type (wt) infection than during an ICP0-null mutant infection, unless the latter is conducted at a very high multiplicity of infection (MOI).…”

“…Nonetheless, under normal experimental conditions, IFI16 is degraded more rapidly during a wild-type (wt) infection than during an ICP0-null mutant infection, unless the latter is conducted at a very high multiplicity of infection (MOI). Like the PML NB components, IFI16 also localizes to HSV-1 genomes during the early stages of infection (22)(23)(24)(25)(26)(27)(28), and ICP0 inhibits this process (23).…”

Promoter-Targeted Histone Acetylation of Chromatinized Parvoviral Genome Is Essential for the Progress of Infection

“…The cellular responses to the foreign DNA, such as viral DNA, include the chromatinization of the entering DNA, leading to its transcriptional silencing (9)(10)(11). How viruses resist cellular chromatinization and silencing is known for only a few viruses (9,12,13).…”