Figure 1. Relation between CTCF occupancy and methylation states in CpG poor regions.

(A) LMRs are bound by transcription factors (TF) and have intermediate average methylation levels. There are two possible scenarios how TF binding and DNA methylation at CpG poor regions could be linked. In a static situation (left), TF binding would be linked to the unmethylated state of the bound molecule, whereas unbound molecules are fully methylated as previously shown for imprinted CpG islands. In an unlinked model (right), TF binding is independent of the DNA methylation state, therefore bound molecules display the same variation of methylation levels as the entire population. (B) To distinguish these scenarios we enrich for bound molecules by ChIP and determine their methylation by bisulfite sequencing (ChIP-BisSeq). This results in a high correlation of methylation levels between ChIP-BisSeq (y-axis) and whole genome bisulfite sequencing (WG-BisSeq, x-axis). Each point represents average methylation over a 200 bp region. Shown are only regions centered at a bound CTCF motif which overlaps with an LMR and for which all considered cytosines have a minimal coverage of 10× in both, WG-BisSeq and ChIP-BisSeq. Red points represent average for 200 bp windows centered on CTCF motifs located within DMRs. Boxplots show mean deviation of methylation levels in ChIP-BisSeq from those in WG-BisSeq at LMRs and DMRs in percent methylation. (C) Examples of single cytosine methylation levels in WG-BisSeq (top bars) and ChIP-BisSeq (bottom bars). For LMRs a whole segment is shown. Each bar represents a cytosine. Methylation is shown in a color code (red: high, yellow: low). Position of CTCF motifs is indicated by black triangles. Only cytosines with at least 10× coverage in both, WG-BisSeq and ChIP-BisSeq, are shown.