pUL79 alters the rate of transcriptional elongation at various regions of the UL48 gene.

<p>(A) Schematic representation of the HCMV gene UL48. Primer-probe pairs used for analysis are indicated. (B–D) HFF cells were infected with AD<i>dd</i>UL79 at an MOI of 3 in the presence or absence of 1 µM Shld1. Cell extracts were harvested at 72 hpi and analyzed by ChIP assays as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004350#ppat-1004350-g004" target="_blank">Fig. 4</a> and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004350#ppat-1004350-g005" target="_blank">Fig. 5</a>. (B) represents the output-to-input DNA ratios of RNAP II ChIP. (C) represents the output-to-input DNA ratios of pSer5-CTD, pSer2-CTD, and non-phosphorylated CTD ChIPs. (D) represents the immunoprecipitated amount of each phosphor-isoform of RNAP II CTD relative to that of total RNAP II (immunoprecipitated with antibody N-20). Data from four independent experiments were collected with standard deviations calculated by Prism 6 software. (E–F) HFFs were infected with AD<i>dd</i>UL79 at an MOI of 3 in the presence or absence of 1 µM Shld1 (indicated by “pUL79⁺” or “pUL79⁻”, respectively). Nuclear extracts were prepared at 72 hpi and analyzed by NRO assay as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004350#ppat-1004350-g006" target="_blank">Fig. 6</a>. Relative amounts of total transcripts and run-on are presented in (E) and (F), respectively. Statistical analysis was performed using Student's <i>t</i> test (*, P<0.05; **, P<0.01; ***, P<0.005).