CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

To study if regulation of cytosine methylation and CTCF occupancy are interdependent and governed by the levels of CGGBP1, we specifically pulled-down methylated cytosines and found that some transcription factor binding sites including that of CTCF held out against the cytosine methylation changes. The cytosine methylation at CTCF-binding repeat-free motifs show a non-stochastic depdendence on CGGBP1 and occur at sites that mark cytosine methylation transition boundaries. We also show that allelic imbalance dictates stochastic methylation changes due to CGGBP1 depletion. MeDIP-seq was performed on genomic DNA from CT (non-targeting RNAi) and KD (CGGBP1 knocked-down by RNAi) of both HEK293T and GM02639 cells.