Fig. 6: Deletion of the craniofacial-specific superenhancer distal to the Hoxa gene cluster mimics the Hoxa2 null phenotype.

a Schematic of deletion, mouse chr6:50673614-51196805 (mm10), spanning major predicted contacts with the Hoxa cluster. b (upper row) Three-dimensional rendered images generated from microCT scans of representative wildtype E18.5 embryos and their heterozygote and homozygote ΔGCR littermates. Ventral view of the skulls reveals multiple cranial base and palatal bony defects in homozygotes. The palatal defects include cleft palate in ~66% of homozygotes and reflected by marked separation of the palatine processes of the maxillae [ppm], separation and ventrally projecting palatine bones [pb], as well as lateral flattening of the medial pterygoid processes [mpt] of the basisphenoid. There was variability in the palatal presentation in homozygotes (see Figure S22 for all scanned embryos). The cranial base presentation, characterized by the notably abnormal appearance of the lateral pterygoids [lpt] of the basisphenoid and abnormal anterior shape of the basioccipital (denoted by the arrowhead), was fully penetrant in homozygotes. A posterior cleft (arrowhead) or small notch in the basisphenoid was also evident in ~50% of homozygotes. (lower row) Soft tissue rendering from microCT scans of E17.5 embryos confirm the cleft palate observed in some homozygotes. Note the normal formation of rugae despite the cleft. c Left lateral view of the bony (top) and soft tissue (bottom) rendering of microCT scans of littermates. Homozygotes show mirror duplications of the tympanic ring (tr; *tr), tympanic process and squamous bone (tp/sq; *tp/*sq) reminiscent of previously reported Hoxa2 null mice. The abnormal lateral pterygoid (lpt) of the basisphenoid is evident from this view of homozygotes. Although not previously described in Hoxa2 null mice, the mandibular angle was consistently hypoplastic (arrowhead) in homozygotes. On the soft tissue renderings, variable severity microtia can be clearly seen in homozygotes (arrow). Microtia ranges from grade I to grade III.