UCSF

Regulatory elements provide information necessary for the spatial, temporal and dosage appropriate expression of genes. Developmental genes in particular rely on cis-regulatory enhancers to control expression in the various tissues where they are active and cause defects in development. Congenital limb malformations are the second most common class of human birth defects and can be caused both by environmental and genetic factors, and identifying the causal mutation in a patient with an isolated limb malformation is often difficult. The difficulty of identification may be due, in part, to the growing number of cases with isolated limb malformations that are shown to be the result of nucleotide changes in regulatory elements. These regulatory mutations affect gene expression in the developing limb and can cause dramatic changes to patterning, leading to congenital limb malformations. There are multiple examples of mutations in an enhancer known as the zone of polarizing activity regulatory sequence (ZRS) that cause preaxial polydactyly and other malformation phenotypes. The identification of further ZRS mutations along with changes they have to transcription factor binding and resulting phenotypes can help elucidate the mechanisms by which it controls gene expression. While the genes and pathways that determine specific limb signaling centers have been described, the identification of enhancers that determine these centers has been limited. It is possible to identify enhancers that are specific to the zone of polarizing activity (ZPA) and apical ectodermal ridge (AER) signaling centers by isolating these regions. Using H3K27ac ChIP-seq on mouse E11.5 ZPA and AER fluorescently sorted cells, I identified thousands of specific signaling center enhancers. Mouse transgenic assays confirmed that several of them function as ZPA and AER enhancers. Combined, these results provide novel ZPA and AER enhancers that may play important roles in limb development. Because the ZPA and AER have critical roles in establishing the three axes and patterning the limb, changes in enhancer function can result in malformations of limb structures.