Identification of hoxb1b downstream genes: hoxb1b as a regulatory factor controlling transcriptional networks and cell movement during zebrafish gastrulation

Hox proteins are homeobox containing transcription factors that play important roles in patterning the presumptive central nervous system and the axial mesoderm in the early vertebrate embryo. Hox genes are first expressed during gastrula stages and recent studies suggest that their function goes beyond their role as patterning determinants. To improve our understanding of the role of Hox proteins during early vertebrate development, we designed a strategy to identify target genes of the zebrafish hoxb1b using overexpression and whole-genome microarray analysis. We directly compared the hoxb1b microarray data with those resulting from heterologous over-expression of the Xenopus XhoxD1 gene in zebrafish embryos. Both genes are the first expressed hox genes in their respective native embryos and display similar spatial expression patterns. The zebrafish transcriptome was analysed prior to the start of the expression of the endogenous hoxb1b gene and we observed extensive overlap between the hoxb1b and XhoxD1 putative downstream genes suggesting evolutionary functional conservation between these hox genes. Furthermore, genes encoding transcription factors and proteins that are known to be involved in cell adhesion and movement were over-represented among the candidate downstream genes, indicating the involvement of the developmentally earliest expressed hox genes in transcriptional networks and cell movement processes.