Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.
BACKGROUND
Regulatory factor X (RFX) transcription factors play a key role in ciliary assembly in nematode, Drosophila and mouse. Using the tremendous advantages of comparative genomics in closely related species, we identified novel genes regulated by dRFX in Drosophila.


RESULTS
We first demonstrate that a subset of known ciliary genes in Caenorhabditis elegans and Drosophila are regulated by dRFX and have a conserved RFX binding site (X-box) in their promoters in two highly divergent Drosophila species. We then designed an X-box consensus sequence and carried out a genome wide computer screen to identify novel genes under RFX control. We found 412 genes that share a conserved X-box upstream of the ATG in both species, with 83 genes presenting a more restricted consensus. We analyzed 25 of these 83 genes, 16 of which are indeed RFX target genes. Two of them have never been described as involved in ciliogenesis. In addition, reporter construct expression analysis revealed that three of the identified genes encode proteins specifically localized in ciliated endings of Drosophila sensory neurons.


CONCLUSIONS
Our X-box search strategy led to the identification of novel RFX target genes in Drosophila that are involved in sensory ciliogenesis. We also established a highly valuable Drosophila cilia and basal body dataset. These results demonstrate the accuracy of the X-box screen and will be useful for the identification of candidate genes for human ciliopathies, as several human homologs of RFX target genes are known to be involved in diseases, such as Bardet-Biedl syndrome.
Laurençon
Anne
A
Université de Lyon, Lyon, F-69003, France. laurencon@cgmc.univ-lyon1.fr.
Dubruille
Raphaëlle
R
Efimenko
Evgeni
E
Grenier
Guillaume
G
Bissett
Ryan
R
Cortier
Elisabeth
E
Rolland
Vivien
V
Swoboda
Peter
P
Durand
Bénédicte
B
D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D023281:Genomics / Q000379:methods; D006801:Humans; D011401:Promoter Regions, Genetic; D000071701:Regulatory Factor X Transcription Factors; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics*
D004268:DNA-Binding Proteins; D000071701:Regulatory Factor X Transcription Factors; D014157:Transcription Factors