HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations

Alteration of Twist1 regulatory elements in mice. (A) Scheme of the aberrations within the Hdac9 sequence. In the eTw5-7^Δ/Δ model, a 23-kb sequence, containing Hdac9 exons 20–23 and Twist1 enhancers (eTw5-7), was deleted (highlighted red rectangle). In the CTCF-5^Δ/Δ model, a 1.5-kb sequence containing Hdac9 exons 6–7 was deleted (highlighted blue rectangle). In the Hdac9^INV/+ model, the whole Hdac9 sequence, 890 kb long, was inverted. The inversion breakpoints are marked by green arrows (mm9, Chr 12: 34,721,220–35,613,000). (B) Heat maps showing anatomical distributions of shape change compared to the wild type for eTw5-7^Δ/Δ, CTCF-5^Δ/Δ, and Hdac9^INV/+ mice, demonstrated by side view (right) and superior view (left) (red is larger and blue is smaller compared to the grand mean). (C) Polydactyly was found in both hindlimb (HL) (71%) and forelimb (FL) (50%) of eTw5-7^Δ/Δ mice, whereas polydactyly was found only in the HL of CTCF-5^Δ/Δ (32%) and Hdac9^INV/+ (8%) mice. The polydactyly is marked by asterisks.