CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation

CTCF binding sites serve as anchors for the 3D chromatin architecture in vertebrates. The functionality of these anchors is influenced by the residence time of CTCF on chromatin, which is determined by its binding affinity and its interactions with nucleosomes and other chromatin-associated factors. In this study, we demonstrate that CTCF occupancy is driven by CTCF motifs strategically positioned at the entry sites of well-positioned nucleosome, such that, upon binding, the N-terminus of CTCF is oriented towards the nucleosome. We refer to this nucleosome as the CTCF priming nucleosome (CpN). CTCF recognizes its binding sites as long as they are not methylated. It can then displace the CpN, provided the nucleosome is not marked by CpG methylation or repressive histone modifications. Under these permissive conditions, the N-terminus of CTCF recruits SMARCA5 to reposition the CpN downstream, thereby creating nucleosome-free regions that enhance CTCF occupancy and cohesin stalling. In contrast, when CpNs carry repressive epigenetic marks, CTCF binding is transient, without nucleosome displacement or chromatin opening. In such cases, cohesin is not effectively retained at CTCF binding sites. We propose that the epigenetic status of CpNs governs cell-specific CTCF binding patterns, ensuring the maintenance of chromatin architecture throughout the cell cycle.