Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

Balanced chromosomalrearrangements such as inversions and translocations can cause congenital diseaseor cancer by inappropriately rewiring promoter–enhancer contacts1,2. To study the potentially pathogenic consequences of balanced chromosomalrearrangements, we generated a series of genomic inversions by placing an active limb enhancer cluster from the Epha4 regulatory domain at different positions within a neighbouring gene-dense region and investigated their effects on gene regulation in vivo in mice. Expression studies and high-throughput chromosome conformation capturefrom embryonic limb budsshowed that the enhancer cluster activated several genes downstream that are located within asymmetric regions of contact, the so-called architectural stripes3. The ectopic activation of genes led to a limb phenotype that could be rescued by deleting the CCCTC-binding factor ( CTCF) anchor of the stripe. Architectural stripes appear to be driven by enhancer activity, because they do not form in mouse embryonic stem cells. Furthermore, we show that architectural stripes are a frequent feature of developmental three-dimensional genome architecture often associated with active enhancers. Therefore, balanced chromosomalrearrangements can induce ectopic gene expression and the formation of asymmetric chromatin contact patterns that are dependent on CTCFanchors and enhancer activity.