Figure 6. Estimation of Dnmt efficiencies using a Hidden Markov Model.

A: Dnmt efficiencies. In this diagram the methylation efficiencies for all three Dnmts are given. For all three Dnmts, we discriminate between the activity to methylate unmethylated CpG positions (unmeth.) and to methylate hemimethylated CpGs (hemim.). For Dnmt1, we find element specific methyltransferase activity at unmethylated CpG positions. At L1 and Igf2 sequences, Dnmt1 shows reduced activity at hemimethylated CpG sites. For Dnmt3a/3b, we find for some elements higher activity at hemimethylated positions. For some elements, the efficiencies are not given, since standard deviations were too high (marked with a cross) (for values see Table S3). B: Prediction of WT methylation. Taking the efficiencies, estimated in the HMM with the KO data, we predicted the methylation of the WT ESC line. This prediction (pred.) fits to the real (experimentally observed) methylation data (data).