Genome-wide analysis of RNA polymerase II occupancy during HSV-1 infection in the presence and absence of ICP4.

The goal of this study was to identify how the occupancy of RNA polymerase II (Pol II) on the host genome changes during HSV-1 infection and is impacted by the viral immediate early protein ICP4. Pol II ChIP-seq experiments after infection with the wild-type (WT) virus and mutant ICP4 (n12) virus, compared to mock infection, revealed global increases and decreases in Pol II occupancy on the host genome that depended upon ICP4. RNA polymerase II ChIP-seq in HEK 293 cells after infection with wild-type HSV-1 virus, n12 virus (lacking functional ICP4), and mock infection as the control sample. ChIP-seq under all conditions was performed in biological replicate. Input chromatin from mock and infected cells was also sequenced.