EBNA1 is present at the promoters of induced, EBER-associated transcription factor genes but not at the promoters of pol III transcribed genes. PCR for target promoter region DNA was performed for multiple genes on cross-linked genomic DNA pulled down by HaloEBNA1 fusion protein or, as control, when pull down of HaloEBNA1 and associated cross-linked DNA was specifically blocked by a blocking ligand. Following gel elecrophoresis of PCR products, band intensities were quantitated using densitometry. Experiments were conducted in biological triplicate and the mean enrichment between target and control is indicated by the grey bars. A) The black bars at the left of the figure are the enrichments obtained using conventional ChIP in EBV-infected Ad/AH cells using an anti-EBNA1 antibody versus isotype control for the known EBNA1-binding dyad symmetry region within ori-P of EBV (EBV-DS) and for the c-jun promoter region (c-jun). Primer sets for promoter regions were within 1Kb upstream of the transcriptional start site. 5S RNA, tRNATyr and 7SL RNA refer to intragenic promoter regions for these pol III-transcribed genes whilst 7SL UR refers to the upstream regulatory region of 7SL RNA. B) Enrichments for ATF2 and EBER promoter regions obtained using HaloEBNA1 pull-down in Ad/AH-EBERs cells.