C. elegans male sensory ray consists of three cellular processes, one from the structural cell and two from neuronal cells, surrounded by a hypodermal sheath and the outermost cuticle. The adheren junctions between the structural cell and the hypodermis and the hemidesmosomes between the hypodermis and the cuticle act as "glue" to hold the organ in a tube shape in the cuticular fan. Thus, considerable changes of cell shape and cell association must have occurred during the ray differentiation process. A genome-wide RNAi screen identified
irx-1, an orthologs of the Iroquois homeodomain transcription factors, as a gene required for ray assembly.
irx-1(RNAi) animals display ray missing phenotype. By tracing the developmental process throughout L4 stage,
irx-1 is shown to be required for papillae formation whereby the structural cells and hypodermal cells attach to the cuticle.
irx-1 transcription reporters revealed its expression in male tail hypodermis and ray neuronal A cells, suggesting that it might control the expression of the junctional components. We aim to identify
irx-1 direct targets and to assess their functions in ray assembly. Phylogenetic footprinting was used to identify putative target genes of IRX-1. From the 500 genes predicted by CisOrtho, a combination of in silico analysis was used to pinpoint relevant genes to analyze: (1) Intersection of the potential target genes with RNAi phenome to identify
irx-1 target genes from this ray developmental gene pool; (2) paralogous pairing followed by overlay of their expression profiles to identify potential functionally redundant genes; and (3) integration of different data sets (e.g.,RNAi phenome, interactome, expression, microarray data and gene ontology terms) to identify functional gene modules among the
irx-1 direct targets and to generate hypothesis about their genetic interactions. Preliminary results have identified several potential
irx-1 target genes, the spectrum spanning transcription factors (
pop-1,
ztf-6,
unc-130, Y40B1A.4), modifying enzymes (T08G11.4,
hst-3), cytoskeleton components (
afd-1,
rap-1) and membrane proteins (
cam-1,
egl-15). The regulatory relationship of these putative targets with
irx-1 in ray assembly is being validated. The integration of computational techniques and experimental biology has allowed efficient selection of potential transcription factor target genes and has a broad application in studying transcription factors targets in ray development. Ultimately, it will provide a comprehensive description of the gene regulatory networks acting in the sensory organ assembly process. (The study is funded by Research Grants Council, Hong Kong.).