During organogenesis, multiple cell types are established at precise times and locations to build a cohesive, functioning organ. In worms, one of the most complex organs is the pharynx, which is composed of seven cell types and which undergoes a complex pattern of morphogenesis. We have taken a genomics approach to identify genes that guide pharyngeal development. First, we used microarray to identify genes likely to be expressed in the pharynx [1]. Second we are examining the loss of function phenotypes associated with 295 of these genes, using a sensitized RNAi screen. From 135 genes surveyed so far, 45 (33%) are associated with a phenotype and 24 (18%) have an obvious pharyngeal phenotype. Of the 45 genes with phenotypes, only thirteen were identified by the recent genome-wide RNAi screen [2], suggesting that our approach increased sensitivity at least four-fold compared to published procedures. We are classifying phenotypes into those that affect function, morphogenesis, and patterning. Troponins and myosins are examples of dsRNAs that appear to affect pharyngeal function (e.g. lack of pumping, slower pump rate, or arrhythmic pumping). Other dsRNAs are associated with phenotypes that likely reflect morphological defects. These dsRNAs include those with homology to galectins or a CC domain (cysteine repeat domain). Finally, we have observed phenotypes from alterations in cell fate patterning, including the T box transcription factor homologue
tbx-2. Our goal is to complete the RNAi survey and initiate an in-depth analysis of those genes that encode likely regulators of pharyngeal development. 1. Gaudet, J.Mango, S.E., Regulation of Organogenesis by the Caenorhabditis elegans FoxA Protein PHA-4. Science, 2002. 295(5556): p. 821-5; 2. Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D.P., Zipperlen, P.Ahringer, J., Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 2003. 421(6920): p. 231-7.