SET domain-containing proteins represent an evolutionarily conserved family of 
epigenetic regulators, which are responsible for most histone lysine 
methylation. Since some of these genes have been revealed to be essential for 
embryonic development, we propose that the zebrafish, a vertebrate model 
organism possessing many advantages for developmental studies, can be utilized 
to study the biological functions of these genes and the related epigenetic 
mechanisms during early development. To this end, we have performed a 
genome-wide survey of zebrafish SET domain genes. 58 genes total have been 
identified. Although gene duplication events give rise to several 
lineage-specific paralogs, clear reciprocal orthologous relationship reveals 
high conservation between zebrafish and human SET domain genes. These data were 
further subject to an evolutionary analysis ranging from yeast to human, leading 
to the identification of putative clusters of orthologous groups (COGs) of this 
gene family. By means of whole-mount mRNA in situ hybridization strategy, we 
have also carried out a developmental expression mapping of these genes. A group 
of maternal SET domain genes, which are implicated in the programming of histone 
modification states in early development, have been identified and predicted to 
be responsible for all known sites of SET domain-mediated histone methylation. 
Furthermore, some genes show specific expression patterns in certain tissues at 
certain stages, suggesting the involvement of epigenetic mechanisms in the 
development of these systems. These results provide a global view of zebrafish 
SET domain histone methyltransferases in evolutionary and developmental 
dimensions and pave the way for using zebrafish to systematically study the 
roles of these genes during development.