Viral and host network analysis of the human cytomegalovirus transcriptome in latency

The human cytomegalovirus (HCMV) <i>UL135</i> and <i>UL138</i> genes play opposing roles regulating latency and reactivation in CD34⁺ human progenitor cells. We designed an RNA sequencing study to compare the transcriptional profile of HCMV infection in the presence and absence of these genes using the Tohoku Hospital Pediatrics-1 (THP-1) monocytic cell line model for latency. Relative to primary cell models, THP-1 cells offer the strength of a homogenous population that uniformly silences gene expression and will synchronously reexpress viral genes following stimulation to differentiate, which models early phases of viral reactivation. The loss of <i>UL138</i> resulted in elevated levels of viral gene expression and in spontaneous adhesion of distinct cell populations that support HCMV gene expression and genome synthesis. The loss of <i>UL135</i> resulted in diminished viral gene expression during an initial burst that occurs as latency is established and in no expression of eleven viral genes from the UL<i>b</i>' region even following differentiation and reexpression of viral genes. Transcriptional network analysis revealed host transcription factors (TFs) with potential to regulate the UL<i>b</i>' genes in coordination with pUL135. We show that the cellular TF peroxisome proliferator-activated receptor gamma binds to the viral genome and influences the expression of <i>UL133-UL138</i> locus genes. Our results define roles for <i>UL135</i> and <i>UL138</i> in regulation of patterns of viral gene expression for the establishment of latency and reexpression of viral genes for reactivation and reveal insights into differentiation-linked mechanisms of transcriptional control of the HCMV genome.