NRL

The study investigates the role of CTCF in organizing chromatin boundaries in mouse embryonic stem cells. The key findings are:

1. Chromatin boundaries are defined by regions with decreased Nucleosome Repeat Length (NRL) near CTCF sites, affecting up to 10% of the genome.

2. The nucleosome-depleted region (NDR) is asymmetrically located upstream of the CTCF motif center.

3. CTCF binding strength and cohesin presence correlate with the NRL decrease and anti-correlate with nucleosome array asymmetry.

4. Chromatin remodelers, particularly Snf2h and Chd4, contribute to the NRL decrease and symmetry breaking, respectively.

5. Upon differentiation, common CTCF sites maintain asymmetric nucleosome patterns and small NRL, while sites that lose CTCF show nucleosome rearrangement downstream of the motif.

6. Topologically associated chromatin domain boundaries often contain multiple inward-oriented CTCF motifs, whose effects synergistically contribute to the observed chromatin organization.