ChIP-Seq with HA-ORF34 shows multiple binding sites across the viral genome.

(A) ChIP-Seq was performed using an anti-HA antibody to immunoprecipitate DNA prepared from iSLK HA-ORF34 cells reactivated for 48 h with doxycycline and sodium butyrate. iSLK-WT cells lacking the HA tag and input DNA were used as negative controls. The alignment files were converted to the tiled data file (tdf) format and the ChIP background from the untagged cells was subtracted and visualized on the Integrated Genome Viewer (IGV) (B) ChIP-qPCR was performed using an anti-HA antibody to immunoprecipitate DNA prepared from iSLK HA-ORF24 cells reactivated for 48 h with doxycycline and sodium butyrate. The DNA was quantified by qPCR with primers specific to the promoter regions of the indicated genes. Data were normalized to the level of input DNA and are presented as percentages of the input. Data shown are from three biological replicates. (C) Consensus motif identified by MEME analysis of promoters from 19 genes whose promoters had a ChIP peak.