Effect of CTCF shRNA on K562 cells. (A) RT–PCR analysis of globin gene transcription in K562 cells after transduction with control or CTCF shRNA. Results of three RNA preparations are shown ±SEM. (B) ChIP performed on chromatin from K562 cells after treatment with control or CTCF shRNA using an antibody against RNA pol II. Error bars represent SEM. Amplicons include ERVin and ERVdn, within and downstream (unique amplicon) of ERV9-LTR; HS5 and 3′HS1, globin locus-flanking CTCF sites; HS1–HS4, locus control region DNase I hypersensitive sites; globin gene promoters and exons as indicated; and OR51V1, odorant receptor gene in the globin locus 3′ flank. (C) ChIP was performed using K562 cell chromatin as described in B with antibodies to H3K4me2, H3K9me2, CTCF, and SMC1. H3 methylation is plotted with the highest value for each modification set to 1 in the line graphs. CTCF or cohesin ChIP enrichment is represented by superimposed bars. Diagram at the top: orange lines, globin genes; gray box, LCR; blue lines, odorant receptor genes; gray lines, other silent genes; green lines, ERV9-LTR. Note the depiction of chromosome 11 in the 5′ to 3′ direction, which is reversed compared to the Genome browser view in Figs. 1–3. Panel C is drawn to scale but the numbers below the graph are arbitrary. (D) ChIP was performed as described in B with antibodies to H3K4me2. (E) ChIP was performed as described in B using an antibody to H3K9me2.