Figure 6
From: CTCF regulates the local epigenetic state of ribosomal DNA repeats
CCCTC binding factor (CTCF) organizes chromatin on ribosomal (r)DNA. (A) Outline of mouse rDNA repeat. The position of the primer pairs (1 to 7) used in the second chromatin immunoprecipitation (ChIP2; panel B) is indicated by upward-pointing arrows. For comparison, the primers used in the first ChIP (ChIP1; Figure 3) are also shown. For other explanations, see Figure 3A. (B) Binding of CTCF, upstream binding factor (UBF) and RNA polymerase I to the mouse spacer promoter. ChIP analysis was performed on mouse embryonic fibroblasts (MEFs) homozygous for the conditional Ctcf knockout allele (Ctcff/(F). MEFs were either (right panels) infected or not (left panels) with a lentivirus expressing Cre recombinase. Nuclei were fixed with 1% formaldehyde, and protein-DNA complexes were immunoprecipitated with antibodies against the indicated proteins (control = rabbit IgG). The upper and lower panels show the same results, but with a different vertical axis. Numbers on the horizontal axis refer to primer pairs. (C) Binding of modified and variant histones to the mouse spacer promoter. ChIP analysis was performed as described above. Protein-DNA complexes were immunoprecipitated with antibodies against the indicated proteins (control = rabbit IgG). Numbers on the horizontal axis refer to primer pairs.