Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics

By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of different tissue types and of daf-19(+) and daf-19(-) animals. Finally, we demonstrate that the dye-filling defect of dyf-5(mn400) animals, which is indicative of compromised exposure of cilia to the environment, is caused by a nonsense mutation in the serine/threonine protein kinase gene M04C9.5.Our comparative genomics-based predictions may be useful for identifying genes involved in human ciliopathies, including Bardet-Biedl Syndrome (BBS), since the C. elegans orthologs of known human BBS genes contain X-box motifs and are required for normal dye filling in C. elegans ciliated neurons.The cilium is an evolutionarily conserved subcellular organelle that projects from the surface of many eukaryotic cells in vertebrates, including kidney and endothelial cells, myocardial cells, odontoblasts, retinal photoreceptor cells and cortical and hypothalamic neurons [1]. The biogenesis and maintenance of cilia is dependent on intraflagellar transport (IFT), which is a bidirectional motility process driven by anterograde and retrograde motors that operate along the microtubule-based ciliary axoneme [2]. Consistent with the ubiquitous distribution of cilia, many physiological processes are critically dependent on their function, which can be broadly classified into two categories, namely cell (and fluid) motility and sensory perception [3]. Defects in the molecular components of cilia and IFT are associated with a variety of h