Deletions of Twist1 regulatory regions affect chromatin looping in the Hdac9-Twist1 locus. (A) A scheme of the Hdac9-Twist1 locus with Twist1 enhancers marked by black bars and CTCF-bound sites (Andrey et al. 2017) (and motif directionality) marked by blue triangles. (B) UMI-4C tracks (merged from two biological replicates) of WT E11.5 forelimb (FL), hindlimb (HL), and branchial arch (BA) demonstrate that Twist1 interaction patterns are largely conserved between limb buds and branchial arch. The Twist1 promoter serves as a viewpoint and is highlighted by the black diamond shape. Targeted eTw5-7 and CTCF regions are indicated by red and blue rectangles, respectively. (C,D) Subtraction tracks showing differential Twist1 promoter interactions in FL, HL, and BA of eTw5-7Δ/Δ and CTCF-5Δ/Δ embryos compared to WT (see also Supplemental Figs. S8, S9).
