Summary/Abstract – Gene Expression Core The long-term objectives of this Program Project are to elucidate host and viral mechanisms that tilt the interaction of herpes simplex virus (HSV) and neurons either towards lytic infection or towards latency. HSV latency is the most fascinating biological property of the virus and its most important clinical feature, and understanding HSV latency may lead to new therapies or even a cure for this widespread pathogen. The three projects that are central to the Program Project all assess the effects of viral and host mutants or certain treatments on viral gene expression and chromatin status during establishment, maintenance, and reactivation of latency, either in mice or in vitro. The assays used for these measurements require specialized equipment, training, attention to detail, and careful analysis (including statistical analysis) to guarantee that they are sensitive and truly quantitative. Thus, to ensure standardization and quality and to allow comparisons of results across all three projects, it is highly desirable to have these assays performed by a core. A specific aim of this core then is to isolate nucleic acids and perform technically challenging yet standardized measurements of 1) viral DNA, which is normalized by measuring host DNA; 2) viral mRNAs, which are normalized by measuring a host mRNA; 3) viral miRNAs, which are normalized by measuring a host miRNA; and 4) occupancies by particular chromatin proteins on particular regions of viral DNA (chromatin immunoprecipitation, ChIP), which are normalized to occupancy on a host gene. These four assays use real-time polymerase chain reaction (PCR) based methods. A second aim is to adapt, develop, standardize, and perform new assays of gene expression and related parameters that have not been extensively applied to HSV latency. These assays include development of additional PCR-based assays of gene expression, but also ones that use deep sequencing methods to assess the transcriptome (RNA-Seq) and chromatin occupancy and accessibility (ChIP-Seq and ATAC-Seq). A third aim is to maintain real-time PCR equipment needed to conduct the assays.