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

The human CGGBP1 is implicated in a variety of cellular functions. It regulates genomic integrity, cell cycle, gene expression and cellular response to growth signals. Evidence suggests that these functions of CGGBP1 manifest through binding to GC-rich regions in the genome and regulation of interspersed repeats. Recent works show that CGGBP1 is needed for cytosine methylation homeostasis and genome-wide occupancy patterns of the epigenome regulator protein CTCF. It has remained unknown if cytosine methylation regulation and CTCF occupancy regulation by CGGBP1 are independent or interdependent processes. By sequencing immunoprecipitated methylated DNA, we have found that some transcription factor-binding sites resist stochastic changes in cytosine methylation. Of these, we have analyzed the CTCF-binding sites thoroughly and show that cytosine methylation regulation at CTCF-binding DNA sequence motifs by CGGBP1 is deterministic. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.