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

Area of Science:

• Epigenetics
• Molecular Biology
• Genomics

Background:

• Chromatin structure is crucial for cell type-specific gene expression during embryonic stem cell differentiation.
• DNA methylation (5mC) and hydroxymethylation (5hmC) are key epigenetic modifications involved in regulating genome function.
• The transcription factor CTCF plays a significant role in genome organization and gene regulation.

Purpose of the Study:

• To investigate the interplay between DNA methylation, hydroxymethylation, nucleosome positioning, and CTCF binding during mouse embryonic stem cell differentiation.
• To understand how these factors coordinate to establish cell type-specific expression programs.
• To elucidate the genomic context-dependent mechanisms governing these epigenetic interactions.

Main Methods:

• Integration of Micrococcal Nuclease sequencing (MNase-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq) in mouse embryonic stem cells (ESC) and differentiated cells.
• Application of biophysical modeling to analyze the quantitative relationships between epigenetic marks and protein binding.
• Analysis of DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome occupancy, and CTCF binding patterns across different genomic regions.

Main Results:

• CpG islands exhibit low nucleosome occupancy and cell type-independent CTCF binding, with minimal methylation.
• Outside CpG islands, methylation density oscillates with nucleosomes, and TET1 binding correlates with labile nucleosomes.
• Cell type-specific CTCF binding sites outside CpG islands are regulated by dynamic nucleosome states influenced by TET1, 5hmC, and 5mC levels.

Conclusions:

• The interplay between DNA methylation, hydroxymethylation, nucleosome positioning, and CTCF binding is context-dependent and dynamically regulated during stem cell differentiation.
• Epigenetic modifications and chromatin architecture orchestrate cell fate decisions by modulating transcription factor accessibility.
• A biophysical model explains cell type-specific CTCF targeting based on competitive binding with histone octamers, influenced by the epigenetic landscape.