Stefan Mundlos and colleagues report that disruption of genomic topologically associated domains (TADs) can result in new regulatory architecture, leading to disease phenotypes (Cell doi:10.1016/j.cell.2015.04.004; 7 May 2015). The authors identified patients with brachydactyly who carried heterozygous deletions effectively removing the boundaries between the TADs encompassing EPHA4, a gene expressed during limb development in mice, and PAX3. Similar alterations to this region, including an inversion and two duplications, were found in families affected by two other limb malformation syndromes. Mundlos and colleagues generated mice carrying the analogous alterations for two of the above syndromes using CRISPR/Cas9 and found that they recapitulated the human phenotypes. RNA sequencing analysis of the limbs of wild-type and mutant embryos showed specific upregulation of Pax3 in the brachydactyly model and Wnt6 in the F-syndrome model. A previously described model for polydactyly, Doublefoot, showed upregulation of Ihh. In the mutants, Pax3, Wnt6 and Ihh adopted spatial expression patterns similar to that of wild-type Epha4, which had been disrupted by the mutations. 4C-seq experiments confirmed that the Epha4 TAD interacted with Pax3, Wnt6 and Ihh in mutant but not wild-type mice. Finally, the authors showed that similar aberrant interactions were present in patient-derived cells.