Extended Data Fig. 5: Dynamic reallocation of intra-cluster interactions.
From: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
a, Magnifications of the capture Hi-C map shown in Fig. 3, focusing on the interactions internal to HoxD at 2 kb resolution. A CTCF ChIP track at 168 h is shown below each panel and the genes are at the bottom. The double red arrow indicates the looping out of a central part of the cluster. Full translocation of the anterior part is observed at 96 h and a weakening of the negative domain (left) is observed thereafter (48, 96 and 144 h: sum of 3 independent replicates; 72, 120 and 168 h: single replicate). Genome coordinates: chr2:74636423-74780095. b, Virtual 4C contacts generated from Capture Hi-C data at 48 h and 96 h, using the Hoxd9 gene body as a viewpoint (red vertical line). After translocation, the contacts with Hoxd4-Hoxd1 are much reduced. The region of the cluster that initially loops out is indicated with a red arrow in (same as in panel A, top) (sum of 3 independent replicates). c, H3K27me3 ChIP-seq of stembryos at various time points, showing the activation of the anterior part, followed by a step wise retraction (black arrows) up to 120 h, when it appears stabilized (see the text). A CTCF ChIP-seq profile is on top for alignment. The fragment looping out is indicated with arrowhead. The two vertical lines help to position CBS1 and CBS2. Genomic coordinates for b and c: chr2:74616423-74812095.
