MOESM4 of Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Additional file 4: Figure S3. Further analysis of enriched genes. (A)Total numbers of sites showing significant changes in methylation at different false discovery rates (FDR). Some sites showing gain were found in each KD cell line alongside the more numerous sites showing loss. (B) Differential methylation between WT and all KD lines using the 1000 best-ranking sites as identified by RnBeads (red). The majority of high-scoring sites common to all three lines lost methylation, but approx. one-third showed gain. (C) Methylation changes at neural identity genes on chromosome 5. Protocadherins in the α and γ families (PCDHA and PCDHG genes) have a clustered arrangement, while genes for the β family members are arranged individually. Tracks are as in Fig. 3. The position of the C class variable exons in the PCDHA and PCDHG clusters are also shown: gain in methylation relative to the siRNA-treated cells can be seen in the boxed regions, which includes the PCDHG constant exons, corresponding to transcriptionally active chromatin (green). (D) Median β values for gene bodies for olfactory receptors identified by DAVID: differences were significant by Mann-Whitney U (MWU). (E) Median β values for the promoters of genes in the histone modifier group identified by enrichment analysis in Table 1. No significant differences between WT and KD were found by MWU.