This project seeks to identify the herpes simplex virus proteins and mechanisms responsible for alteration of the host transcriptome, and selection of RNA polymerase II (RNAP II) complexes for elongation on viral late genes. Preliminary data using deep sequencing techniques show that herpes simplex virus (HSV) removes RNA polymerase II (RNAP II) and extends transcriptional termination zones of most cellular genes by 3 hours, leading to poor expression. Simultaneously, RNAP II complexes accumulate on all kinetic classes of HSV genes. Importantly, while progression from pausing to elongation is rapid (5 minutes) on viral early immediate genes, it is delayed on late genes which are expressed poorly at this time. This suggests the novel concept that progression to elongation is an important mechanism to regulate viral late gene expression. We have shown that one or more immediate early or early viral proteins are responsible for the effects on cellular genes, and for RNAP II loading on late genes at early times post infection. To identify the viral gene(s) responsible for these effects and release to the elongation phase on viral genes, we will determine RNAP II occupancy, processivity, RNA stability, and mRNA production on a gene- and gene feature-specific basis in cells infected with (i) wild type virus, (ii) viral mutants lacking candidate immediate early genes, or (iii) lacking the activation domains of VP16. Results will be compared with cells infected with viruses bearing restored genes. In addition, we will test two nonexclusive hypotheses to explain how transcriptional termination is effective on viral genes but ineffective on host genes: (i) whether elongation rates along viral genes are slower than on host genes, and (ii) whether the virus alters the termination endonuclease XRN2, to redirect its activities from cellular genes to viral genes. This hypothesis is supported by preliminary data. XRN2 and its binding partners such as RNA cleavage and polyadenylation factors will be examined in infected cells for proper modification, activation, interactions, localization in the cell, and association with cellular or viral sequences. Analysis in cells infected with the above mutants should indicate which viral protein(s) is responsible for any XRN2 redirection or change in elongation rates. Gene position swapping experiments will also be conducted to determine whether there is something inherent to viral DNA sequences or their context in the genome that dictates efficient transcriptional termination of viral genes.