Fig. 6

DNA accessibility near a CTCF site. a Consensus DNA accessibility near a representative CTCF site at position 31,109,691 on chromosome 20 in the LNCaP sample. The center of the CTCF site is at position 0 of the plot. Red line: consensus based on the two chains shown in (b); blue line: consensus based on all reads. b The two dominating epi-alleles. Each point is an isolated GpC position. Black: methylated GpC position (DNA accessible), white: unmethylated GpC position (DNA inaccessible). The approximate lengths of the inaccessible intervals are computed (black lines), showing that the CTCF site appears to be flanked by nucleosomes (∼149 bp). In one epi-allele, the CTCF site appears to be inaccessible, potentially due to binding of a protein. As nucleosome positioning is dynamic and the read coverage is low for these samples, the inferred intervals are uncertain