title: Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. chenn@sfu.ca
authors.forename: Nansheng
authors.initials: N
authors.lastname: Chen
authors.forename: Allan
authors.initials: A
authors.lastname: Mah
authors.forename: Oliver E
authors.initials: OE
authors.lastname: Blacque
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Chu
authors.forename: Kiran
authors.initials: K
authors.lastname: Phgora
authors.forename: Mathieu W
authors.initials: MW
authors.lastname: Bakhoum
authors.forename: C Rebecca Hunt
authors.initials: CR
authors.lastname: Newbury
authors.forename: Jaswinder
authors.initials: J
authors.lastname: Khattra
authors.forename: Susanna
authors.initials: S
authors.lastname: Chan
authors.forename: Anne
authors.initials: A
authors.lastname: Go
authors.forename: Evgeni
authors.initials: E
authors.lastname: Efimenko
authors.forename: Robert
authors.initials: R
authors.lastname: Johnsen
authors.forename: Prasad
authors.initials: P
authors.lastname: Phirke
authors.forename: Peter
authors.initials: P
authors.lastname: Swoboda
authors.forename: Marco
authors.initials: M
authors.lastname: Marra
authors.forename: Donald G
authors.initials: DG
authors.lastname: Moerman
authors.forename: Michel R
authors.initials: MR
authors.lastname: Leroux
authors.forename: David L
authors.initials: DL
authors.lastname: Baillie
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D002923:Cilia / Q000378:metabolism*; D017931:DNA Primers; D020869:Gene Expression Profiling; D005816:Genetic Complementation Test; D023281:Genomics; D049452:Green Fluorescent Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic
chemical_list: D017931:DNA Primers; D049452:Green Fluorescent Proteins