ZBTB2 reads unmethylated CpG island promoters and regulates embryonic stem cell differentiation

Proteins that bind to DNA depending on its methylation status play an important role in methylation-mediated regulation of gene expression. Using a variety of genomics and proteomics approaches, we identify zinc finger and BTB domain-containing protein 2 (ZBTB2) as a reader of unmethylated DNA in mouse embryonic stem cells. ZBTB2 preferentially binds to CpG island promoters, where it acts as a transcriptional activator. The binding of ZBTB2 to its targets is direct and independent of two other zinc finger proteins, ZBTB25 and ZNF639, which we show to interact with ZBTB2. Our data suggest an anticorrelation between ZBTB2 DNA binding and DNA methylation, indicating that ZBTB2-binding dynamics in vivo are sensitive to differential DNA methylation. ZBTB2 is intricately interwoven with DNA methylation, as we find not only that its binding to DNA is methylation sensitive, but also that ZBTB2 regulates the turnover of methylated DNA In ZBTB2 knockout cells, several pluripotency factors are upregulated, inducing a delay in differentiation. We propose that ZBTB2 is a novel DNA methylation-sensitive transcription factor that regulates cellular differentiation.