The pool size of SV40 minichromosomes containing RNAPII is dynamic and dependent upon replication and rate of transcription. SV40 minichromosomes were isolated from cells infected with wild-type virus at 24 and 48 hr post-infection. Infected cells were either untreated or treated from 24 to 48 hr post-infection with DRB, sodium butyrate (NaBt), or aphidicolin. Intact minichromosomes were subjected to ChIP analyses with antibody to RNAPII and the percentage of untreated and treated minichromosomes containing RNAPII was determined by real-time PCR amplification of the intact SV40 genomic DNA with primers recognizing the promoter region. The fold increase or decrease from 24 to 48 hr post-infection with or without treatment was then calculated from the percentages.