CTCF-binding sites demarcate chromatin domains enriched with H3K9me2 or H3K9me3 and restrict the spreading of these histone modifications in human cells

However, the role of CTCF-binding sites in chromatin domains marked by H3K9me2 or H3K9me3 remains poorly understood. In this study, we analyzed CTCF-binding sites and the distribution of H3K9me2 and H3K9me3 around these sites in human K562 cells, and investigated the spreading of these modifications following CTCF depletion.

Genome-wide analysis revealed that certain CTCF-binding sites are located at the boundaries of chromatin domains enriched with H3K9me2 or H3K9me3. Upon loss of CTCF binding, both modifications spread to neighboring chromatin at over half of boundaries delimiting highly and distinctly enriched domains. Boundaries where such spreading did not occur (non-spreading boundaries) were flanked by regions with a more active chromatin state compared to those where spreading occurred (spreading boundaries).