The human CCCTC-binding factor, CTCF, regulates transcription of the 
double-stranded DNA genomes of herpesviruses. The architectural complex cohesin 
and RNA Polymerase II also contribute to this organization. We profiled the 
occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the 
Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes 
with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences 
throughout the genome that are found not just proximal to the regulatory 
elements of latent genes, but also near lytic genes. In addition to tracking 
with known transcripts, RNA Polymerase II appears at two unannotated positions, 
one of which lies within the latent origin of replication. The widespread 
occupancy profile of each protein reveals binding near or at a myriad of 
regulatory elements and suggests context-dependent functions.