Extended Data Fig. 10: H3K27me3 profile and capture Hi-C using Del(CBS1-5) stembryos.
From: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
a, H3K27me3 ChIP-seq using control (top, light brown) and Del(CBS1-5) (middle, dark brown) stembryos at 96 h (average of two replicates). The subtraction track is shown below and illustrates the decrease in H3K27me3 marks over the central and posterior part of the HoxD cluster (bracket). Genomic coordinates: chr2:74646423-74780095. b, Virtual4C contacts generated from Capture Hi-C datasets produced out of control and Del(CBS1-5) mutant stembryos at 96 h. Interactions are quantified between those Hoxd genes shown below (viewpoint) and the activated Hoxd3-Hoxd4 part of the cluster. Increased contacts are scored in mutant stembryos for all three viewpoints, illustrating the loss, in CTCF mutant stembryos, of a clear partition of the gene cluster into two separate positive and negative domains. c, Time course capture Hi-C using Del(CBS1-5) stembryos. Six time points are shown with bin size 5 kb. Libraries were mapped on a control genome (mm10). Genomic coordinates: chr2:73900037-75621560. d, Magnifications of the interactions between the Hoxd genes cluster and the CS38-40 region (dashed box) in control (left) and Del(CBS1-5) mutant specimen (right), either before (48 h, top) or after (96 h, bottom) the translocation of the anterior part of the cluster. Diagonal and vertical dashed lines indicate the position of the most prominant interactions within the Hoxd gene cluster with the CS38-40 region. While a shift toward a posterior position is observed between 48 h and 96 h in control stembryos (from CBS1 to the Hoxd8-Hoxd9 interval), interactions scored in the Del(CBS1-5) mutant condition remain diffused over the gene cluster and only a slight change in the posterior limit is observed (around Hoxd11). Genomic coordinates: chr2:74590000-74985000 e, Virtual4C contacts generated from Capture Hi-C datasets produced in control and Del(CBS1-5) mutant stembryos at 96 h. Interactions between the indicated Hoxd genes (viewpoints) and the 5′ region of sub-TAD1 are significantly higher in Del(CBS1-5) mutant. In b and e, box plots with median value and 25–75% percentiles, whiskers represent minimum and maximum. Asterisks represent significant changes determined by the Mann-Whitney nonparametric test (**** is p-value < 0.0001) (wt: sum of 3 independent replicates, Del(CBS1-5) mutant: single replicate).
