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

Nansheng Chen12*, Allan Mah2, Oliver E Blacque23, Jeffrey Chu2, Kiran Phgora2, Mathieu W Bakhoum2, C Rebecca Hunt Newbury4, Jaswinder Khattra4, Susanna Chan4, Anne Go4, Evgeni Efimenko5, Robert Johnsen2, Prasad Phirke5, Peter Swoboda5, Marco Marra6, Donald G Moerman4, Michel R Leroux2, David L Baillie2 and Lincoln D Stein1

Author Affiliations

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

2 Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, British Columbia, Canada V5A 1S6

3 School of Biomolecular and Biomedical Sciences, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

4 Department of Zoology, University of British Columbia, West Mall, Vancouver, British Columbia, Canada V6T 1Z4

5 Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden

6 British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia, Canada V5Z 4S6

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Genome Biology 2006, 7:R126  doi:10.1186/gb-2006-7-12-r126

Published: 22 December 2006



The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes.


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.