Formation of regulator/target gene relationships during evolution

The Foxn1-like forkhead/winged-helix transcription factor genes have been maintained in single copy throughout chordate evolution. Among other functions, Foxn1 (formerly known as Whn) regulates the expression of hair keratin genes in the hair follicle, which represents an evolutionarily novel organ characteristic of mammals. We show here that fish and mouse Foxn1-like genes are functionally equivalent in hair keratin gene activation, suggesting the absence of functionally relevant changes over the course of several hundred million years of vertebrate evolution. In contrast, the Foxn1-like gene from the cephalochordate Branchiostoma lanceolatum is inactive in this assay because of changes in the region located N-terminal to DNA binding and transcriptional activation domains of the protein. Our results indicate that functionally relevant changes in cis-regulatory regions are not necessarily accompanied by corresponding changes in transcription factor proteins in the formation of evolutionarily novel regulator/target gene relationships.