Fig. 3

Df and +  ^Bl6 _D DIRs along chromosome 4. a “Rainbow plot” for the 4E2 region representing the DIRs for the comparison between Df and +¹²⁹, and between +  ^Bl6 _D and + ^Bl6 computed with a 20 Kb smoothing factor for the viewpoints surrounding the deletion b. Rainbow plots were used to visualize both short and long-range interaction changes. The arcs represent increased interaction (red) or decreased interaction probabilities (blue), with the strength of signal color coded. For visual clarity we only show signals with strength >10 %, and do not include contacts inside the deletion region for +  ^Bl6 _D in b. Grey arrows annotate positions for viewpoints 1, 2 (upstream of deletion) and 11, 12 (downstream of deletion, towards telomeric end). c Positions of DIRs for all viewpoints 1, 2, 11 and 12 are compared against structural protein binding sites. First track is for Df and +¹²⁹ comparisons and second track is for +  ^Bl6 _D and + ^Bl6 comparison. DIRs with increased/decreased contact probabilities compared to WT are plotted in red/blue. Shown in the third and fourth tracks (green bars) are the running average over 20 Kb window for CTCF and Smc1 binding site footprint, respectively. The fifth track displays fold change for Df/+  ^Bl6 _D DE genes, color coded (red, over-expressed in Df/+  ^Bl6 _D MEFs; blue, over-expressed in +¹²⁹/+^Bl6 MEFs)