Identification and analysis of a novel bmp4 enhancer in Fugu genome

•Tissue-specific enhancers for Bmp4 expression are difficult to identify in mammals.•Fugu has a compact genome size and is widely used in comparative genomics studies.•We used Fugu genome to evaluate the 15 kb promoter region upstream of Fugu bmp4 gene.•It is the first time a bmp4 enhancer with activity in the cells was identified.•This finding will help to decode the mechanism of tooth development in vertebrates.

Spatiotemporal expression of bone morphogenetic protein 4 (Bmp4) in epithelial and mesenchymal cells is critical for the development of many organs including teeth. Since Bmp4 has a complex and widespread regulatory area in mammals, the tissue-specific enhancers that are responsible for mesenchymal expression of Bmp4 are difficult to identify in mammals. TakiFugu rubripes (Fugu, pufferfish) has a highly compact genome size and is widely used in comparative genomics studies of gene regulatory mechanisms. In this study, we used the Fugu genome to evaluate the 15 kb promoter region upstream of the Fugu bmp4 gene. By DNA segmental cloning and luciferase assay with two dental odontoblast-like cell lines, a dental ameloblast-like cell line, and a kidney fibroblast cell line, we identified a 485 bp cis-regulatory enhancer between −4213 and −3728 bp of the Fugu bmp4 gene. This enhancer showed strong transcriptional activity in all three dental cell lines and, to a lesser extent, also in kidney fibroblast cells. Though not located in an evolutionary conserved region, the enhancer activity for the DNA segment is intense. This is the first time a bmp4 enhancer sequence with activity in both mesenchymal and epithelial cells has been identified, which will help to decode the mechanism of tooth development in vertebrates.