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) an...