Immediate early proteins of herpes simplex virus transiently repress viral transcription before subsequent activation.

This study was undertaken to further clarify the roles of HSV-1 immediately early (IE) genes ICP4, ICP0, and ICP22 in early viral transcription. Precision nuclear Run On followed by deep Sequencing (PRO-Seq) was used to identify sites of Pol activity to high resolution on the genomes of HSV-1 viruses bearing mutations in a0, a4 or a22/US1, and corresponding viruses in which these loci were genetically restored. The results indicated that prior to initiating activation of transcription, IE genes first mediate transcriptional repression. PRO-Seq was performed on nuclei extracted at either 1.5, 3 or 6 hpi from HEp-2 or HFF cells infected with HSV-1 mutant viruses: n12 (ICP4-null), n212, (ICP0-null), DICP22 and their genetically restored repairs at an MOI of 5. Infection experiments with n12 and repair were also performed in the presence of cycloheximide (CHX). Drosophila melanogaster nuclei were spiked-in before the run-on to normalise for sequencing depth across samples.