Abstract
Nucleosome repeat length (NRL) defines the average distance between adjacent nucleosomes. When calculated for specific genomic regions, NRL reflects the local nucleosome ordering and characterises its changes during developmental processes. The architectural protein CTCF provides one of the strongest nucleosome positioning signals, setting a decreased NRL for ~20 nucleosomes in its vicinity (thus affecting up to 10% of the mouse genome). We show that upon differentiation of mouse embryonic stem cells (ESCs) to neural progenitor cells and mouse embryonic fibroblasts, a subset of common CTCF sites preserved in all three cell types keeps small NRL despite genome-wide NRL increase. This suggests that differential CTCF binding not only affects 3D genome organisation but also defines genomic regions with conserved nucleosome arrangement. Our analysis revealed that NRL decrease near CTCF is correlated with CTCF affinity for DNA binding. Stronger CTCF binding is linked to increased probability to form chromatin loops and more efficient recruitment of chromatin remodellers. We show that the effect of individual remodellers on decreasing the NRL near CTCF is increasing in the order Brg1≤Chd4<Chd6<Chd1≤Chd2≤EP400≤Chd8<Snf2h.