Fig. 5: Contribution of CTCF binding to the insulation function of the EP boundary. | Nature Genetics

Fig. 5: Contribution of CTCF binding to the insulation function of the EP boundary.

From: In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

Fig. 5: Contribution of CTCF binding to the insulation function of the EP boundary.

a, WISH shows Pax3 expression in E11.5 forelimbs from CBS mutants. Arrowheads represent reverse- (light blue) and forward- (orange) oriented CBSs. Crosses indicate deleted CBSs and the gray rectangle represents the deleted region. Note the similarities in expression pattern between mutants. Scale bar, 250 μm. b, Pax3 qPCR analysis in E11.5 limb buds from CBS mutants. Bars represent the mean and white dots represent individual replicates. Values were normalized against DelBs mutants (ΔΔCt) (*two-sided t-test P ≤ 0.05, ΔALL versus DelB: 0.03). c, cHi-C maps from E11.5 mutant distal limbs at 10-kb resolution (top). Data mapped on custom genome containing the DelBs deletion (n = 1 with an internal control comparing 6 different experiments; Methods). Insets represent a magnification (5-kb resolution) of the centromeric (left) and telomeric (right) loops highlighted by brackets on the map. Gained or lost chromatin loops represented by full or empty dots, respectively. Subtraction maps (bottom) showing gain (red) or loss (blue) of interactions in mutants compared with DelBs (left) and DelB (right). d, Insulation score values. Lines represent mutants. Dots represent the local minima of the insulation score at the EP boundary for each mutant. e, Virtual 4C profiles for the genomic region displayed in c (viewpoint in Pax3). Light-gray rectangle highlights Epha4 enhancer region.

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