GSE110460
DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
The interplay of DNA (de)methylation and the architectural chromatin protein CTCF is an important regulator of cellular differentiation, but molecular mechanisms determining differential CTCF binding are not well understood. Mouse embryonic stem cells (ESCs) contain up to 10% of CpG residues in 5-hydroxymethylated form (5hmC) and smaller amounts in 5-formylated or 5-carboxylated forms (5fC, 5caC). Here, we studied double knock out ESCs (DKO) deficient for TET1 and TET2 enzymes which are responsible for the conversion of 5mC to 5hmC, 5fC and 5caC. For both wild type (WT) and DKO cells, we measured changes in nucleosome positions, CTCF binding, DNA methylation and gene expression. Our integrative data analysis combined with biophysical modelling suggests that both differential (de)methylation and CTCF binding are to a large degree predictable from the DNA sequence. Common CTCF sites that remained bound in DKO cells were significantly enriched at unmethylated CpG islands, while CTCF loss was associated with differential DNA methylation. 5hmCs and 5fCs had the opposite effects in terms of CTCF priming: CTCF was preferentially lost from sites that were marked in WT cells by 5hmCs but not 5fCs. Interestingly, the losses of CTCF at TAD boundaries lead to aberrant spreading of DNA methylation, as well as downregulation of neighbouring genes. Overall, our study clarifies the fundamental mechanism of differential CTCF binding and provides evidence of DNA sequence-encoded temporal chromatin changes during cell differentiation. Overall design: Two samples are analyzed without replicates. The first sample is a control sample, the other one a treated sample. Please note that the mouse embryonic stem cells used in this study were isolated from mice, that were maintained in a mixed C57BL/6 x 129 genetic background (B6;129; see also PMID: 23352810)