Characterization of the Octamer, A Cis-Regulatory Element that Modulates Excretory Cell Gene-Expression in Caenorhabditis Elegans

Background: We have previously demonstrated that the POU transcription factor CEH-6 is required for drivingaqp-8 expression in the C. elegans excretory (canal) cell, an osmotic regulatory organ that is functionally analogousto the kidney. This transcriptional regulation occurs through a CEH-6 binding to a cis-regulatory element called theoctamer (ATTTGCAT), which is located in the aqp-8 promoter.Results: Here, we further characterize octamer driven transcription in C. elegans. First, we analyzed the positionalrequirements of the octamer. To do so, we assayed the effects on excretory cell expression by placing the octamerwithin the well-characterized promoter of vit-2. Second, using phylogenetic footprinting between threeCaenorhabditis species, we identified a set of 165 genes that contain conserved upstream octamers in theirpromoters. Third, we used promoter::GFP fusions to examine the expression patterns of 107 of the 165 genes. Thisanalysis demonstrated that conservation of octamers in promoters increases the likelihood that the gene isexpressed in the excretory cell. Furthermore, we found that the sequences flanking the octamers may havefunctional importance. Finally, we altered the octamer using site-directed mutagenesis. Thus, we demonstrated thatsome nucleotide substitutions within the octamer do not affect the expression pattern of nearby genes, butchange their overall expression was changed. Therefore, we have expanded the core octamer to include flankingregions and variants of the motif.Conclusions: Taken together, we have demonstrated that octamer-containing regions are associated withexcretory cell expression of several genes that have putative roles in osmoregulation. Moreover, our analysis of theoctamer sequence and its sequence variants could aid in the identification of additional genes that are expressedin the excretory cell and that may also be regulated by CEH-6.