Shh and Gremlin1 chromosomal landscapes in development and disease.

Two regulatory signals play major roles in digit patterning during vertebrate limb development, the SHH morphogen and the BMP antagonist Gremlin1. Their dynamic expression in limb buds is controlled by distant cis-regulatory elements embedded in unrelated neighboring genes, which has confused identification of the primary cause of different types of congenital limb malformations affecting mice and humans. Comparative and functional genomics have uncovered the large and complex chromosomal landscapes that control Shh and Gremlin1 expression, identified the molecular cause of the congenital malformations and provided insights into limb evolution. While most of the transacting factors remain unknown, Hoxd proteins have been shown to bind to the far upstream Shh cis-regulatory elements and activate their expression in limb buds.