Cohesin Mediates Chromatin Conformation Figure 2. CTCF and the cohesin binding at IGF2-H19 region in HB2 cells. (A) Enrichment of PCR products from CTCF bound regions in the HB2 cell line over the Input (IP/Input). (B) Enrichment (IP/Input) of cohesin at same regions. Strong enrichment for CTCF and cohesin is seen at the CTCF sites adjacent to DMR0 (CTCF AD1 and 2), the CCD and a CTCF downstream of H19 (CTCF DS). Error bars represent standard deviations of 3 replicate PCRs. (C) SNP analysis of CTCF and cohesin ChIP for the CTCF sites adjacent to DMR0, (CTCF AD1), the CCD, ICR, and the CTCF DS. Enriched sequences for CTCF and cohesin binding are biallelic for the CTCF site adjacent to DMR0 and to the CCD at the given SNPs. At the ICR, the G-allele at rs11564739* was preferentially enriched after CTCF and cohesin ChIP. (D) Methylation status of the DMR0 and (E) the ICR. Each horizontal group of circles represents a single sequence. Specific alleles identified by the SNPs shown in red are grouped. Each circle represents a single CpG. Gaps between circles indicate that the CpGs are not adjacent. Open circles represent unmethylated CpGs, filled circles represent methylated CpGs. The allele that binds CTCF at the ICR is the unmethylated G-allele. doi:10.1371/journal.pgen.1000739.g002 PLoS Genetics | www.plosgenetics.org 4 November 2009 | Volume 5 | Issue 11 | e1000739