diversity of Pcdh genes among teleosts

• In mammals, the protocadherins are encoded by three closely-linked clusters (α, β and γ) of tandem genes and are hypothesized to provide a molecular code for specifying the remarkably-diverse neural connections in the central nervous system.
• Like mammals, the coelacanth, a lobe-finned fish, contains a single protocadherin locus, also arranged into α, β and γ clusters.
• Zebrafish, however, possesses two protocadherin loci that contain more than twice the number of genes as the coelacanth, but arranged only into α and γ clusters.
• Fugu contains two unlinked protocadherin loci, Pcdh1 and Pcdh2, that collectively consist of at least 77 genes. The fugu Pcdh1 locus has been subject to extensive degeneration, resulting in the complete loss of Pcdh1γ cluster.The fugu Pcdh genes have undergone lineage-specific regional gene conversion processes that have resulted in a remarkable regional sequence homogenization among paralogs in the same subcluster.
• Besides the 'fish-specific' whole genome duplication, the evolution of protocadherin genes in teleost fishes is influenced by lineage-specific gene losses, tandem gene duplications and regional sequence homogenization.

Comparison of the fugu (FrPcdh1 and FrPcdh2), zebrafish (DrPcdh1 and DrPcdh2)and coelacanth (LmPcdh) protocadherin clusters. Variable exons in each paralog group are shown in different colors. Orthologs between fugu and zebrafish as well as the inter-locus paralogs between the two Pcdh loci in fugu or zebrafish are shown in the same colors. 'Teleost Pcdh1' and 'Teleost Pcdh2' are the Pcdh clusters predicted in the common ancestor of fugu and zebrafish, and 'Fish Pcdh ancestor' is the single Pcdh cluster predicted in the ray-finned fish prior to the 'fish-specific' whole genome duplication. The corresponding exons in the 'Fish Pcdh ancestor' and the inter-locus paralogs between 'Teleost Pcdh1' and 'Teleost Pcdh2' are shown in the same color except the 'αIV', which represents a common ancestor for fugu FrPcdh2α8–25 and zebrafish DrPcdh2α8–25. Among the exons predicted in the 'Fish Pcdh ancestor', those present in the Pcdh loci of both fugu and zebrafish are labeled with an asterisk.

300bp intronic regulatory element in hand gene

"Herein we describe the identification of a regulatory region in the hand gene essential and sufficient for the expression in the visceral mesoderm during embryogenesis. We found that hand expression in the circular visceral mesoderm is abolished in embryos mutant for the FoxF domain containing transcription factor Biniou. Furthermore we demonstrate that Biniou regulates hand expression by direct binding to a 300 bp sequence element, located within the 3rd intron of the hand gene. This regulatory element is highly conserved in different Drosophila species. In addition, we provide evidence that Hand is dispensable for the initial differentiation of the embryonic visceral mesoderm." (Hand is a direct target of the forkhead transcription factor Biniou during Drosophila visceral mesoderm differentiation.)