Subtractive hybridization identifies chick-cripto, a novel EGF–CFC ortholog expressed during gastrulation, neurulation and early cardiogenesis

EGF–CFC genes encode a novel class of extracellular, membrane-associated proteins that notably play an important role during vertebrate gastrulation. Whereas the two cysteine-rich domains that characterize these proteins, namely the extracellular EGF-like and the CFC domain, are known to be encoded by two evolutionarily conserved exons, it is generally assumed, based on weak primary sequence identity, that the remaining parts of the protein differ among vertebrates, suggesting that known members of the EGF–CFC family do not represent true orthologs. Here, by characterizing the full cDNA and genomic sequences of a new EGF–CFC gene in chick, and by comparing them with their counterparts in human ( CRIPTO), mouse ( cripto and cryptic), Xenopus ( FRL-1) and zebrafish ( one-eyed pinhead), we show that all EGF–CFC genes share an identical genomic organization over the entire coding region. Not only are the central two exons (coding for the EGF-like and CFC motifs) conserved, but also conserved are the total number of exons, their size, their intron phase and their correlation with discrete protein modules, in particular those modules that allow the EGF–CFC motif to become membrane-associated. Therefore, despite apparent divergence between their 5′ and 3′-terminal exons, all known CRIPTO-related genes are structurally orthologous. We named this novel ortholog in bird, chick-cripto. We report the mRNA distribution of chick-cripto, which begins in the epiblast of the gastrula, with a pattern similar to EGF–CFC genes of other vertebrates.