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

Additional file 3: Figure S2. Changes in methylation levels by genomic element. (A) Protein levels in knockdown lines by western blotting. As a control HCT116 colon cancer cells which are WT or have a homozygous mutation in DNMT1 (KO) are shown: the DNMT1-specific top band is indicated by the arrowhead at right. (B) Median levels of methylation are shown for each genomic element (listed at top). The positions of medians are also indicated at right (arrowheads). The differences between WT and KD medians were used to plot Fig. 1d. (C) Density distribution of methylation at the three main elements involved in gene regulation, shown by cell line. Demethylation seems most marked at gene bodies (Genes), indicated by increased density of probes at low methylation (β) values

MOESM2 of Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Additional file 2: Figure S1. Variation between shRNA clonal lines. (A) Relative similarities between cell lines based on principal component analysis (PCA) of the 450K data; three independent cultures of each line were analysed. Note the clustering of lines d8R and d10R. The fraction of total variance explained by each component is indicated in brackets. (B) The 1000 sites most variably methylated between cell lines were used for hierarchical clustering. The location of sites with respect to CpG island is indicated at left. Beta values are depicted as shades from red (low) to blue (high)

MOESM6 of Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Additional file 6: Table S3. Details of the genes showing transcriptional changes in KD cell lines from Fig. 6c