Figure 3. ICP4 dependence of viral genome accessibility and Histone H3 binding.

MRC5 cells were infected with an ICP4 null mutant (n12) or HSV-1 (WT) and harvested prior to genome replication. (A) ChIP-Seq for ICP4, Pol II, H3 and B–D) ATAC-Seq was performed. All data was normalized for sequencing depth and viral genome number using input ChIP-Seq reads. (C) Quantitative analysis of ATAC-Seq data, measuring the relative tagmentation enrichment for the virus or host as compared to expected. (D) Histogram plot of ATAC-Seq fragment size for reads mapped to the viral (red) or cellular (black) genome. Mononucleosome protected fragments are approximately 180–250 bp.

Figure 3—figure supplement 1. Analysis of ChIP-Seq data quality.

Normalized viral aligned bigwig files were assessed using MultiBigwigSummary in 50 bp bins. The values within these bins were plotted for biological replicates and a linear regression analysis was performed.

Figure 3—figure supplement 2. Analysis of ChIP-Seq data quality.

Normalized cellular aligned bigwig files were assessed using MultiBigwigSummary in 10,000 bp bins. The values within these bins were plotted for biological replicates and a linear regression analysis was performed.

Figure 3—figure supplement 3. MRC5 cells were infected with an ICP4 null mutant (n12) or HSV-1 (WT) for 2 hr and ChIP-Seq for ICP4, Pol II, H3, H3K4me3, H3K27acetyl, H3K9me3, and H3K27me3 was performed.

All data was normalized for sequencing depth and viral genome number using input ChIP-Seq reads. Viral ORFs are indicated, color coded by gene class with IE as yellow, E as green, L1 as blue, and L2 as purple. y-axes were (A) maintained the same between IP’s or (B) maximized for each trace to aid in visualization.