Identifying muscle regulatory elements and genes in the nematode Caenorhabditis elegans

We report the identification of several putative muscle-specific regulatory elements, and genes which are expressed preferentially in the muscle of the nematode Caenorhabditis elegans. We used computational pattern finding methods to identify cis-regulatory motifs from promoter regions of a set of genes known to express preferentially in muscle; each motif describes the potential binding sites for an unknown regulatory factor. The significance and specificity of the identified motifs were evaluated using several different control sequence sets. Using the motifs, we searched the entire C. elegans genome for genes whose promoter regions have a high probability of being bound by the putative regulatory factors. Genes that met this criterion and were not included in our initial set were predicted to be good candidates for muscle expression. Some of these candidates are additional, known muscle expressed genes and several others are shown here to be preferentially expressed in muscle cells by using GFP (green fluorescent protein) constructs. The methods described here can be used to predict the spatial expression pattern of many uncharacterized genes.