Fig. 6. Coordination of looping and decondensation in the Hoxd region. (A) FISH using probes 5' flank (RP23-288B11, yellow), Hoxd (RP23-15M17, red) and MMU2 chromosome paint (green) on DAPI stained nuclei of undifferentiated ES cells or after 8 days of differentiation. (B) Scatter plots of the position of Hoxd (y-axes) and 5' flank (x-axes) BAC probe signals relative to the edge of the MMU2 CT during differentiation. The bottom right quadrant represents territories in which both probes are inside the CT; the top left quadrant represents situations in which both probes were located outside the CT. The other two quadrants represent discordant positions for the two BAC probe signals (one inside and one outside the CT); n>100 territories. (C) Scatter plots of the interphase separation (d) in µm between Hoxd and the 5' flank probe signals (y-axes of both graphs) and the position of each probe relative to the edge of the MMU2 CT (µm) (x-axes) (Hoxd left panels; 5' flank on right). The diagonal lines indicate the best-fit linear regression lines and their corresponding R² values; n>100 territories. (D) As in A, but with the probes Lnp (RP23-267L11, yellow) and 3' flank (RP23-7D13). At day 8 of differentiation, examples of decondensed (widely spaced probe signals) chromatin outside the CT (upper picture), of condensed chromatin outside the CT (middle picture) or of decondensed chromatin inside the CT (lower picture) are shown. (E) As in B but with BACs Lnp and 3' flank. (F) Scatter plots of the d (µm) between the Lnp (black dots) and 3' flank (red dots) signals (y-axes) and the position (µm) of each probe relative to the edge of the MMU2 CT (x-axes). Scale bars: 5 µm.