Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

Abstract

We apply here comparative genome hybridization as a novel tool to identify the molecular lesion in two Caenorhabditis elegans mutant strains that affect a neuronal cell fate decision. The phenotype of the mutant strains resembles those of the loss-of-function alleles of the cog-1 homeobox gene, an inducer of the fate of the gustatory neuron ASER. We find that both lesions map to the cis-regulatory control region of cog-1 and affect a phylogenetically conserved binding site for the C2H2 zinc-finger transcription factor CHE-1, a previously known regulator of cog-1 expression in ASER. Identification of this CHE-1-binding site as a critical regulator of cog-1 expression in the ASER in vivo represents one of the rare demonstrations of the in vivo relevance of an experimentally determined or predicted transcription-factor-binding site. Aside from the mutationally defined CHE-1-binding site, cog-1 contains a second, functional CHE-1-binding site, which in isolation is sufficient to drive reporter gene expression in the ASER but in an in vivo context is apparently insufficient for promoting appropriate ASER expression. The cis-regulatory control regions of other ASEexpressed genes also contain ASE motifs that can promote ASE neuron expression when isolated from their genomic context, but appear to depend on multiple ASE motifs in their normal genomic context. The multiplicity of cis-regulatory elements may ensure the robustness of gene expression.

TheC. elegansTailless/TLX transcription factornhr-67controls neuronal identity and left/right asymmetric fate diversification

“…A 1.8-kb fragment including the conserved NR2E motif and ASE motifs was amplified from two constructs, cog-1promA (O'Meara et al, 2009) and cog-1promA nhr-67 del., in which the conserved sequence AAGTCA had been deleted. The resulting constructs were named cog-1promD and cog-1promD nhr-67site del.…”

“…But how does the bilateral expression of nhr-67 in both ASEL and ASER fit with its function as an ASER fate inducer, which, as we have shown, is genetically required for cog-1 function? We examined the sequence of the cog-1 promoter and found a phylogenetically conserved, consensus binding site for Tailless-type orphan nuclear receptor (NR2E motif) (DeMeo et al, 2008;Yu et al, 1994) embedded in between two binding sites for the CHE-1 transcription factor ('ASE motif') that are required to induce cog-1 expression in ASE (O'Meara et al, 2009) (Fig. 7A).…”

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

“…One such example is comparative genomic hybridization (CGH), a technique that has been extensively used in human genetics to quantify chromosomal copy number aberrations (Kallioniemi et al 1992). In C. elegans oligonucleotide CGH arrays have been used to detect deletions (Jones et al 2007;Maydan et al 2007) and to identify single-nucleotide alterations that were previously mapped (Maydan et al 2009;O'Meara et al 2009). Although WGS is by far the most efficient method for identifying singlenucleotide alteration, CGH arrays offer a useful alternative for detecting structural variations.…”

Genetic Screen Reveals Link between the Maternal Effect Sterile Gene mes-1 and Pseudomonas aeruginosa-induced Neurodegeneration in Caenorhabditis elegans

“…1A). Strain OH4168, which expresses a ceh-36::rfp transgene that allows visualization of ASE neurons (25), exhibited a num-FIGURE 1. Neurodegeneration phenotypes induced by P. aeruginosa infection.…”