Fig. 2

Methylation changes at specific transcription factor binding sites resist stochasticity. a Shannon’s entropy distributions across the Diff/Sum bins show that the cytosine methylation changes in HEK293T and GM02639 have different levels of stochasticity. The HEK293T cells show a very high and uniform stochasticity for weak as well as strong methylation changes. In GM02639 however the stochastic methylation changes were weak. The strong changes in methylation were non-stochastic specifically in GM02639. This difference in stochasticity does not exclude the possibility that some genomic bins undergo methylation change commonly in HEK293T and GM02639. b In the genomic bins sequenced (minimum sum of reads for CT and KD = 3) in CT and KD for HEK293T as well as GM02639 the JASPAR motifs occur with expected frequency showing that the MeDIP does not favour or exclude transcription factor binding sites (TFBS). c In the bins undergoing net methylation change (|Diff/Sum| > 0.2) occurrence of the same JASPAR motifs as the ones called in b show deviations from the expected frequencies. The observed CTCF motif is highlighted in orange in b and c. d A Chi² test between the TFBS occurrences (b and c) identified a panel of 72 JASPAR motifs that are enriched in genomic bins differentially methylated between CT and KD. A single-mode clustering classifies these motifs into two major groups: with opposite (orange box) or similar (green box) GoM and LoM between HEK293T and GM02639