The introduction of H3K9me2 and H3K9me3 is inhibited by sodium butyrate stimulation of transcription during active replication. Wild-type SV40 minichromosomes were isolated at 12 hr post-infection with or without treatment from the initiation of infection with sodium butyrate and at 48 hr post-infection with or without treatment with sodium butyrate from 24 to 48 hr post-infection. Intact minichromosomes isolated at 12 hr post-infection were subjected to ChIP analyses with antibodies to methylated H3K9. Intact minichromosomes isolated at 48 h post-infection were subjected to ChIP analyses with antibodies to methylated H3K4 and methylated H3K9. The percentage of treated and untreated minichromosomes containing each form of methylated H3K4 or H3K9 was determined by real-time PCR amplification of the intact SV40 genomic DNA with primers recognizing the promoter region. The fold change resulting from treatment was then calculated from the percentages.