Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

ABSTRACT: During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we find that the interplay between these factors depends on their large-scale genomic context. The mostly unmethylated CpG islands have a reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast,

ORGANISM(S): Mus musculus

SUBMITTER: Vladimir Teif 

PROVIDER: E-GEOD-56938 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress