Transcriptional consequences of herpes simplex virus 1 ICP4 inducible expression in uninfected cells

Abstract

Successful viral infections reflect the balanced outcome of a tightly regulated program of viral gene expression and manipulation of the host cell environment to favor production of new infectious particles. The productive (lytic) replication cycle of herpes simplex virus 1 (HSV-1) is dependent on the essential transcription factor ICP4 encoded by one of five immediate-early genes. At different steps in the HSV-1 temporal cascade, ICP4 either positively or negatively regulates transcription of immediate-early, early, and late HSV-1 genes, largely through sequence-specific binding to cis-acting regulatory elements. In contrast, the direct regulation of host transcription by ICP4 is less well understood. In this study we exogenously expressed doxycycline-inducible wild-type and mutant ICP4 proteins in uninfected primary human fibroblasts and performed RNA-Seq to identify ICP4-driven changes to the host transcriptome. Cross-referencing our findings to a published dataset of ICP4-dependent changes to the host transcriptome in HSV-1 infected cells provided validation for a subset of differentially-expressed genes regulated by ICP4. Furthermore, disrupting the ICP4 DNA-binding domain was sufficient to alter the cellular gene transcriptional program responsive to ICP4. This indicates that the DNA-binding domain of ICP4, which is required for site-specific DNA binding to the virus genome, may also regulate binding to the host genome. Together, these data provide a comprehensive transcriptomic analysis of how wild-type and mutant ICP4 expression impact cellular gene expression in uninfected cells. IMPORTANCEHerpes simplex virus 1 (HSV-1) is a widespread human pathogen responsible for a variety of mild to severe disease states. The viral lifecycle is driven by the essential viral transcription factor ICP4, which ensures the coordinated expression of most viral genes. Expression of ICP4-regulated genes and viral lifecycle progression impacts host gene expression; therefore, determining the specific impact of ICP4 on host gene expression has been challenging. Here, we provide a more direct analysis, examining changes in the transcriptome of primary fibroblasts when ICP4 is expressed alone. Differentially expressed genes were identified and cross-referenced to published data from infections with wild-type and ICP4-null viruses. We show that mutations in ICP4 that disrupt interactions with the host transcriptional machinery or interfere with site-specific DNA binding further modified this ICP4-driven remodeling of the host transcription. These data provide a comprehensive transcriptomic analysis of ICP4-driven dysregulation of host gene expression in uninfected cells.