Human cytomegalovirus (HCMV) infects over half of all Veterans and threatens the lives of those with impaired immune systems. HCMV is the leading infectious cause of birth defects. There is no HCMV vaccine, and the antiviral drugs have problems with potency, toxicity, and drug-resistance. The long-range goal of this research is to identify critical points in the viral transcription-DNA replication cycle that would serve as new targets for therapeutic intervention. This proposal is based on the premise that our gap in knowledge of how viral early transcription produces viral DNA replication and how viral DNA replication results in viral late transcription limits our ability to design new therapeutic treatments for the viral disease. By customizing advanced technologies and developing new tools, we have used integrated functional genomics (dTag system, PRO-Seq, ChIP-Seq, genetically engineered test viruses, and promoter function assays) to determine where and when Pol II initiates transcription, identify sites of viral transcription factor binding genome-wide, and quantify change in Pol II nascent transcripts from individual promoters in relation to core promoter sequences, transcription factor loss, stage of infection, and viral DNA replication. We find that there are three distinct pathways to viral late transcription. Two of these pathways involve the HCMV IE2 and late transcription factor (LTF) group members. The individual role of each of the 3 different IE2 isoforms (IE2-86, IE2-60, and IE2-40) in viral late transcription is unknown. The six-member set of LTFs bind to Pol II and a DNA sequence signature in gene promoters, forming a preinitiation complex (PIC) that drives transcription. Diversity in sequence signature pattern likely determines the amount of individual promoter output. It is unknown precisely when and how the LTF complex assembles on viral promoters and how the LTF assembly engages Pol II in transcription. Our use of a new high-resolution ChIP-Seq technique and bioinformatics pipeline to map genomic locations of nucleosomes, as well as IE2 and LTF PICs, suggests that LTF PICs occupy genome regions not occupied by nucleosomes. This new ChIP-Seq technique will strengthen our integrated functional genomics approach to further determining the mechanisms controlling viral promoter transcription in relation to chromatin structure. Our preliminary data indicate that: 1) the early-late transcription switch lags many hours behind the onset of viral DNA replication; 2) the HCMV promoter population members that are active differs by cell type and condition, and this difference may involve IE2 and LTF functions; and 3) the HCMV promoter population that is active during viral reactivation in the NT2 model differs from that in acute productive infection. We will test the hypothesis that HCMV transcription factors usurp host Pol II that navigates a modified chromatin environment suited to bring about viral late transcription (Aims 1 and 2) and to coordinate the viral transcription program in diverse cell types (Aim 2) and under cellular conditions supporting quiescent and reactivation infections in the NT2 model (Aim 3). We will apply a multifaceted approach to each of the specific aims to: 1) elucidate the regulators of the early-late transcription switch, 2) determine the mechanistic basis for cell type differences in viral transcription, and 3) determine how activation of quiescent infection changes viral transcription. Our proposal integrates the expertise of the Meier and the Price labs in virology and transcription, respectively. We will build on this productive collaboration to complete the proposed research plan. The discoveries coming from these studies will identify generalizable features of gene regulation that pertain to other members of beta- and gammaherpesvirus subfamilies, which include human herpesvirus 6 and the oncogenic herpesviruses, Epstein-Barr Virus and Kaposis sarcoma-associated herpesvirus.

Cytomegalovirus (CMV) infection takes a toll on the life and health of thousands of Veterans because the currently available antiviral drugs are woefully inadequate. The Institute of Medicine estimates an annualized healthcare cost savings of $1-4 billion if CMV infection could be prevented. A CMV vaccine that effectively prevents infection is unlikely to be realized in the next decade. Thousands of Veterans already have CMV within them that has re-activated from dormancy to produce disease. This motivates a search for alternative ways of blocking CMV infection. Our research goal is to deactivate CMV before it starts replicating. By studying how CMV activates its gene expression program for replication, we aim to identify vital targets susceptible to precision-guided pharmacologic agents that effectively neutralize the virus. We will also discover previously unknown mechanisms of gene expression control that is broadly relevant to other viruses and many human diseases.